diff --git a/moose-examples/.travis.yml b/moose-examples/.travis.yml
index 8799d5a775fd4da7347f8d539d697b64f00a0b2a..9dd0e12f56f0581926f81b81d1a92905da260ef8 100644
--- a/moose-examples/.travis.yml
+++ b/moose-examples/.travis.yml
@@ -3,7 +3,7 @@ notifications:
recipients:
- dilawar.s.rajput@gmail.com
- upi.bhalla@gmail.com
- - ray.shubhasis@gmail.com
+ - malavs@ncbs.res.in
- hrani@ncbs.res.in
@@ -12,8 +12,9 @@ install:
- sudo apt-key add - < Release.key
- sudo sh -c "echo 'deb http://download.opensuse.org/repositories/home:/moose/xUbuntu_12.04/ /' >> /etc/apt/sources.list.d/moose.list"
- sudo apt-get -y update
- - sudo apt-get -y install python-qt4
- - sudo apt-get -y install moose
+ - sudo apt-get -y --force-yes install python-qt4 python-pip
+ - sudo apt-get -y --force-yes install moose
+ - sudo pip install python-libsbml
script:
- # Making sure no python3 incompatible file.
diff --git a/moose-examples/docs/Makefile b/moose-examples/docs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..a8997d1c346f7c346662c40921a5ac724e994366
--- /dev/null
+++ b/moose-examples/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+SPHINXPROJ = MOOSE
+SOURCEDIR = source
+BUILDDIR = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
diff --git a/moose-examples/docs/make.bat b/moose-examples/docs/make.bat
new file mode 100644
index 0000000000000000000000000000000000000000..a6f889c4bcb8fbf45278fe061954d3d191649c41
--- /dev/null
+++ b/moose-examples/docs/make.bat
@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=MOOSE
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.http://sphinx-doc.org/
+ exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd
diff --git a/moose-examples/docs/source/conf.py b/moose-examples/docs/source/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..90f32dddf02f48cca52bbeedbbae1e2f091fb5b8
--- /dev/null
+++ b/moose-examples/docs/source/conf.py
@@ -0,0 +1,173 @@
+# -*- coding: utf-8 -*-
+#
+# MOOSE documentation build configuration file, created by
+# sphinx-quickstart on Tue Jan 31 14:57:39 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+# sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('../python'))
+sys.path.append(os.path.abspath('../../../moose-examples/snippets'))
+sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ChemicalOscillators'))
+sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ChemicalBistables'))
+sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ExcInhNet'))
+sys.path.append(os.path.abspath('../../../moose-examples/neuroml/lobster_pyloric'))
+sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ExcInhNetCaPlasticity'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
+#extensions = ['numpydoc']
+#extensions = ['sphinx.ext.autodoc', 'numpydoc']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['ntemplates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'MOOSE'
+copyright = '(c) 2017, Malav Shah <malavs@ncbs.res.in>'
+author = 'Malav Shah <malavs@ncbs.res.in>'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '3.1.1'
+# The full version, including alpha/beta/rc tags.
+release = 'Chamcham'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['nstatic']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'MOOSEdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+ # The paper size ('letterpaper' or 'a4paper').
+ #
+ # 'papersize': 'letterpaper',
+
+ # The font size ('10pt', '11pt' or '12pt').
+ #
+ # 'pointsize': '10pt',
+
+ # Additional stuff for the LaTeX preamble.
+ #
+ # 'preamble': '',
+
+ # Latex figure (float) alignment
+ #
+ # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+ (master_doc, 'MOOSE.tex', 'MOOSE Documentation',
+ 'Malav Shah', 'manual'),
+]
+
+# -----NumpyDoc----------------
+numpydoc_show_class_members = False
+#numpydoc_use_plots: True
+#numpydoc_show_class_members: True
+#numpydoc_show_inherited_class_members: True
+#numpydoc_class_members_toctree: True
+#numpydoc_edit_link: True
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ (master_doc, 'moose', 'MOOSE Documentation',
+ [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ (master_doc, 'MOOSE', 'MOOSE Documentation',
+ author, 'MOOSE', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+
+
diff --git a/moose-examples/docs/source/docs/source/modules.rst b/moose-examples/docs/source/docs/source/modules.rst
new file mode 100644
index 0000000000000000000000000000000000000000..733da1c55c012340a920a07efc1c464af5967b99
--- /dev/null
+++ b/moose-examples/docs/source/docs/source/modules.rst
@@ -0,0 +1,6 @@
+projectdir
+==========
+
+.. toctree::
+ :maxdepth: 4
+
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diff --git a/moose-examples/docs/source/images/neuroncompartment.fig b/moose-examples/docs/source/images/neuroncompartment.fig
new file mode 100644
index 0000000000000000000000000000000000000000..fa7e32a22b4b31d5fb4ec33059c75d12f8a282a5
--- /dev/null
+++ b/moose-examples/docs/source/images/neuroncompartment.fig
@@ -0,0 +1,369 @@
+#FIG 3.2 Produced by xfig version 3.2.5b
+Portrait
+Center
+Metric
+A4
+200.00
+Single
+-2
+1200 2
+6 3465 3285 7155 5085
+6 3465 3285 7155 5085
+6 5805 3645 6165 4770
+6 5805 3671 6165 4770
+6 5805 4320 6165 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 5805 4500 6165 4500
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 5895 4590 6075 4590
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 5985 4500 5985 4320
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 5985 4590 5985 4770
+-6
+# Resistor
+6 5880 3671 6060 4346
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 5985 3686 5985 3824 5914 3847 6057 3893 5914 3939 6057 3984
+ 5914 4030 6057 4076 5914 4122 6057 4167 5985 4190 5985 4329
+-6
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
+ 0 0 1.00 60.00 120.00
+ 5850 4230 6120 3735
+-6
+6 5040 3645 5400 4770
+# Resistor
+6 5115 3671 5295 4346
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 5220 3686 5220 3824 5149 3847 5292 3893 5149 3939 5292 3984
+ 5149 4030 5292 4076 5149 4122 5292 4167 5220 4190 5220 4329
+-6
+6 5040 4320 5400 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 5400 4590 5040 4590
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 5310 4500 5130 4500
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 5220 4590 5220 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 5220 4500 5220 4320
+-6
+-6
+# Resistor
+6 3493 3585 4168 3765
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 4153 3690 4015 3690 3992 3619 3946 3762 3900 3619 3855 3762
+ 3809 3619 3763 3762 3717 3619 3672 3762 3649 3690 3510 3690
+-6
+# Resistor
+6 6464 3585 7139 3765
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 7124 3690 6986 3690 6963 3619 6917 3762 6871 3619 6826 3762
+ 6780 3619 6734 3762 6688 3619 6643 3762 6620 3690 6481 3690
+-6
+# Non-polar capacitor
+6 4237 3782 4745 4652
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 4269 4146 4730 4146
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 4500 3800 4500 4146
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 4500 4261 4500 4605
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 4269 4261 4730 4261
+-6
+# Ground
+6 5265 4725 5580 5085
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 5409 4761 5409 4903
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 5266 4903 5551 4903
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 5337 4975 5480 4975
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 5380 5046 5451 5046
+-6
+6 4435 3642 4570 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 4498 3689 28 28 4498 3689 4526 3689
+-6
+6 5156 3642 5291 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5219 3689 28 28 5219 3689 5247 3689
+-6
+6 5921 3642 6056 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5984 3689 28 28 5984 3689 6012 3689
+-6
+6 5344 4723 5479 4813
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5407 4770 28 28 5407 4770 5435 4770
+-6
+6 4798 3374 4933 3509
+1 3 0 1 0 7 1 0 20 0.000 1 0.0000 4858 3461 47 47 4858 3461 4906 3461
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 4140 3690 6480 3690
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 4500 3825 4500 3690
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 4500 4590 4500 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 4500 4770 5985 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 4860 3510 4860 3690
+4 0 0 50 -1 0 12 0.0000 4 150 300 5355 4500 Em\001
+4 0 0 50 -1 0 12 0.0000 4 150 300 5355 4050 Rm\001
+4 0 0 50 -1 0 12 0.0000 4 150 270 6165 4050 Gk\001
+4 0 0 50 -1 0 12 0.0000 4 150 240 6165 4590 Ek\001
+4 0 0 50 -1 0 12 0.0000 4 150 315 4635 4500 Cm\001
+4 0 0 50 -1 0 12 0.0000 4 150 300 4955 3452 Vm\001
+4 0 0 50 -1 0 12 0.0000 4 180 405 3664 3978 Ra/2\001
+4 0 0 50 -1 0 12 0.0000 4 180 405 6637 3987 Ra/2\001
+-6
+6 5158 4724 5293 4814
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5221 4771 28 28 5221 4771 5249 4771
+-6
+6 4798 3641 4933 3731
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 4861 3688 28 28 4861 3688 4889 3688
+-6
+-6
+6 -360 3285 3330 5085
+6 -360 3285 3330 5085
+6 1980 3645 2340 4770
+6 1980 3671 2340 4770
+6 1980 4320 2340 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 1980 4500 2340 4500
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 2070 4590 2250 4590
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 2160 4500 2160 4320
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 2160 4590 2160 4770
+-6
+# Resistor
+6 2055 3671 2235 4346
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 2160 3686 2160 3824 2089 3847 2232 3893 2089 3939 2232 3984
+ 2089 4030 2232 4076 2089 4122 2232 4167 2160 4190 2160 4329
+-6
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
+ 0 0 1.00 60.00 120.00
+ 2025 4230 2295 3735
+-6
+6 1215 3645 1575 4770
+# Resistor
+6 1290 3671 1470 4346
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 1395 3686 1395 3824 1324 3847 1467 3893 1324 3939 1467 3984
+ 1324 4030 1467 4076 1324 4122 1467 4167 1395 4190 1395 4329
+-6
+6 1215 4320 1575 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 1575 4590 1215 4590
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 1485 4500 1305 4500
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 1395 4590 1395 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 1395 4500 1395 4320
+-6
+-6
+# Resistor
+6 -332 3585 343 3765
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 328 3690 190 3690 167 3619 121 3762 75 3619 30 3762
+ -16 3619 -62 3762 -108 3619 -153 3762 -176 3690 -315 3690
+-6
+# Resistor
+6 2639 3585 3314 3765
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 3299 3690 3161 3690 3138 3619 3092 3762 3046 3619 3001 3762
+ 2955 3619 2909 3762 2863 3619 2818 3762 2795 3690 2656 3690
+-6
+# Non-polar capacitor
+6 412 3782 920 4652
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 444 4146 905 4146
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 675 3800 675 4146
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 675 4261 675 4605
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 444 4261 905 4261
+-6
+# Ground
+6 1440 4725 1755 5085
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 1584 4761 1584 4903
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 1441 4903 1726 4903
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 1512 4975 1655 4975
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 1555 5046 1626 5046
+-6
+6 610 3642 745 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 673 3689 28 28 673 3689 701 3689
+-6
+6 1331 3642 1466 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1394 3689 28 28 1394 3689 1422 3689
+-6
+6 2096 3642 2231 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 2159 3689 28 28 2159 3689 2187 3689
+-6
+6 1519 4723 1654 4813
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1582 4770 28 28 1582 4770 1610 4770
+-6
+6 973 3374 1108 3509
+1 3 0 1 0 7 1 0 20 0.000 1 0.0000 1033 3461 47 47 1033 3461 1081 3461
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 315 3690 2655 3690
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 675 3825 675 3690
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 675 4590 675 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 675 4770 2160 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 1035 3510 1035 3690
+4 0 0 50 -1 0 12 0.0000 4 150 300 1530 4500 Em\001
+4 0 0 50 -1 0 12 0.0000 4 150 300 1530 4050 Rm\001
+4 0 0 50 -1 0 12 0.0000 4 150 270 2340 4050 Gk\001
+4 0 0 50 -1 0 12 0.0000 4 150 240 2340 4590 Ek\001
+4 0 0 50 -1 0 12 0.0000 4 150 315 810 4500 Cm\001
+4 0 0 50 -1 0 12 0.0000 4 150 300 1130 3452 Vm\001
+4 0 0 50 -1 0 12 0.0000 4 180 405 -161 3978 Ra/2\001
+4 0 0 50 -1 0 12 0.0000 4 180 405 2812 3987 Ra/2\001
+-6
+6 1333 4724 1468 4814
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1396 4771 28 28 1396 4771 1424 4771
+-6
+6 973 3641 1108 3731
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1036 3688 28 28 1036 3688 1064 3688
+-6
+-6
+6 7290 3285 10980 5085
+6 7290 3285 10980 5085
+6 9630 3645 9990 4770
+6 9630 3671 9990 4770
+6 9630 4320 9990 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 9630 4500 9990 4500
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 9720 4590 9900 4590
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 9810 4500 9810 4320
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 9810 4590 9810 4770
+-6
+# Resistor
+6 9705 3671 9885 4346
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 9810 3686 9810 3824 9739 3847 9882 3893 9739 3939 9882 3984
+ 9739 4030 9882 4076 9739 4122 9882 4167 9810 4190 9810 4329
+-6
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
+ 0 0 1.00 60.00 120.00
+ 9675 4230 9945 3735
+-6
+6 8865 3645 9225 4770
+# Resistor
+6 8940 3671 9120 4346
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 9045 3686 9045 3824 8974 3847 9117 3893 8974 3939 9117 3984
+ 8974 4030 9117 4076 8974 4122 9117 4167 9045 4190 9045 4329
+-6
+6 8865 4320 9225 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 9225 4590 8865 4590
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 9135 4500 8955 4500
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 9045 4590 9045 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 9045 4500 9045 4320
+-6
+-6
+# Resistor
+6 7318 3585 7993 3765
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 7978 3690 7840 3690 7817 3619 7771 3762 7725 3619 7680 3762
+ 7634 3619 7588 3762 7542 3619 7497 3762 7474 3690 7335 3690
+-6
+# Resistor
+6 10289 3585 10964 3765
+2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
+ 10949 3690 10811 3690 10788 3619 10742 3762 10696 3619 10651 3762
+ 10605 3619 10559 3762 10513 3619 10468 3762 10445 3690 10306 3690
+-6
+# Non-polar capacitor
+6 8062 3782 8570 4652
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 8094 4146 8555 4146
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 8325 3800 8325 4146
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 8325 4261 8325 4605
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 8094 4261 8555 4261
+-6
+# Ground
+6 9090 4725 9405 5085
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 9234 4761 9234 4903
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 9091 4903 9376 4903
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 9162 4975 9305 4975
+2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 9205 5046 9276 5046
+-6
+6 8260 3642 8395 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 8323 3689 28 28 8323 3689 8351 3689
+-6
+6 8981 3642 9116 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9044 3689 28 28 9044 3689 9072 3689
+-6
+6 9746 3642 9881 3732
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9809 3689 28 28 9809 3689 9837 3689
+-6
+6 9169 4723 9304 4813
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9232 4770 28 28 9232 4770 9260 4770
+-6
+6 8623 3374 8758 3509
+1 3 0 1 0 7 1 0 20 0.000 1 0.0000 8683 3461 47 47 8683 3461 8731 3461
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 7965 3690 10305 3690
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 8325 3825 8325 3690
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 8325 4590 8325 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 8325 4770 9810 4770
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 8685 3510 8685 3690
+4 0 0 50 -1 0 12 0.0000 4 150 300 9180 4500 Em\001
+4 0 0 50 -1 0 12 0.0000 4 150 300 9180 4050 Rm\001
+4 0 0 50 -1 0 12 0.0000 4 150 270 9990 4050 Gk\001
+4 0 0 50 -1 0 12 0.0000 4 150 240 9990 4590 Ek\001
+4 0 0 50 -1 0 12 0.0000 4 150 315 8460 4500 Cm\001
+4 0 0 50 -1 0 12 0.0000 4 150 300 8780 3452 Vm\001
+4 0 0 50 -1 0 12 0.0000 4 180 405 7489 3978 Ra/2\001
+4 0 0 50 -1 0 12 0.0000 4 180 405 10462 3987 Ra/2\001
+-6
+6 8983 4724 9118 4814
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9046 4771 28 28 9046 4771 9074 4771
+-6
+6 8623 3641 8758 3731
+1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 8686 3688 28 28 8686 3688 8714 3688
+-6
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 3285 3690 3510 3690
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+ 7110 3690 7335 3690
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+ 3420 3240 7245 3240 7245 5130 3420 5130 3420 3240
diff --git a/moose-examples/docs/source/images/neuroncompartment.png b/moose-examples/docs/source/images/neuroncompartment.png
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diff --git a/moose-examples/docs/source/index.rst b/moose-examples/docs/source/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e6b924a2570dce52cabc101ab9fdc81ed6dc3653
--- /dev/null
+++ b/moose-examples/docs/source/index.rst
@@ -0,0 +1,23 @@
+.. MOOSE documentation master file, created by
+ sphinx-quickstart on Tue Jan 31 14:57:39 2017.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+MOOSE
+=====
+
+.. toctree::
+
+ introduction/index_intro
+ install/index_install
+ user/py/quickstart/index_qs
+ user/py/cookbook/index_ckbk
+ user/py/graphics/index_graphics
+ user/py/references/index_ref
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/moose-examples/docs/source/install/index_install.rst b/moose-examples/docs/source/install/index_install.rst
new file mode 100644
index 0000000000000000000000000000000000000000..75b466ccc640a9d6c60481e86dfb79c106b1aa2d
--- /dev/null
+++ b/moose-examples/docs/source/install/index_install.rst
@@ -0,0 +1,208 @@
+Installation
+=============
+
+Use pre-built packages
+-----------------------
+
+Linux
+^^^^^^
+
+We recommend that you use our repositories hosted at `Open Build Service
+<http://build.opensuse.org>`_. We have packages for the following distributions
+
+- Debian 7.0, 8.0
+- Ubuntu 12.04, 14.04, 15.04, 15.10, 16.04
+- CentOS 6, 7
+- Fedora 20, 21, 22, 23
+- OpenSUSE 13.1, 13.2, Factory ARM, Leap 42.1, Tumbleweed
+- SLE 12, 12 SP1
+- RHEL 7
+- Scientific Linux 7
+
+Visit `this page
+<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
+to pick your distribution and follow instructions.
+
+.. note::
+ ``moogli`` (tool to visualize network activity) is not available for CentOS-6.
+
+.. raw:: html
+ <iframe
+ src="http://software.opensuse.org/download/package.iframe?project=moose&package=moose"></iframe>
+
+.. todo:: Packages for gentoo, Arch Linux
+
+Mac OSX
+^^^^^^^
+
+Download the ``dmg`` file from `here <https://github.com/BhallaLab/moose/releases/download/ghevar_3.0.2/Moose_3.0.2_OSX.dmg>`_.
+
+Alternatively, you can use ``homebrew`` to install ``moose``
+::
+ $ brew install homebrew/science/moose
+
+
+Windows/Cygwin
+^^^^^^^^^^^^^^
+
+Building MOOSE
+--------------
+
+In case your distribution is not listed on `our repository page
+<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
+, or if you want to build the lastest development code, read on.
+
+First, you need to get the source code. You can use ``git`` (clone the
+repository) or download snapshot of github repo by clicking on `this link
+<https://github.com/BhallaLab/moose/archive/master.zip>`_.::
+ $ git clone https://github.com/BhallaLab/moose
+
+Or,
+::
+ $ wget https://github.com/BhallaLab/moose/archive/master.zip
+ $ unzip master.zip
+
+If you don't want lasest snapshot of ``MOOSE``, you can download other released
+versions from here `https://github.com/BhallaLab/moose/releases`.
+
+Install dependencies
+^^^^^^^^^^^^^^^^^^^^
+
+Next, you need to install required dependencies. Depending on your OS, names of
+following packages may vary.
+
+- cmake (version 2.8 or higher)
+- gsl-1.16 or higher `download <ftp://ftp.gnu.org/gnu/gsl/>`_.
+- libhdf5 development package e.g. `libhdf5-serial-dev` or `libhdf5-devel`
+- python development package e.g. `python-dev` or `python-devel`
+- numpy e.g. `python-numpy` or `numpy`
+
+Most of the dependencies can be installed using package manager.
+
+On ``Debian/Ubuntu``
+::
+ $ sudo apt-get install libhdf5-dev cmake libgsl0-dev libpython-dev python-numpy
+
+.. note::
+ Ubuntu 12.04 does not have required version of ``gsl`` (required 1.16 or
+ higher, available 1.15). On Ubuntu 16.04, package name is ``libgsl-dev``.
+
+On ``CentOS/Fedora/RHEL/Scientific Linux``
+::
+ $ sudo yum install hdf5-devel cmake libgsl-dev python-devel python-numpy
+
+On ``OpenSUSE``
+::
+ $ sudo zypper install hdf5-devel cmake libgsl-dev python-devel python-numpy
+
+Now use `cmake` to build moose
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+ $ cd /to/moose/source/code
+ $ mkdir _build
+ $ cd _build
+ $ cmake ..
+ $ make
+ $ ctest --output-on-failure # optional
+
+This will build pyMOOSE (MOOSE's python extention), `ctest` will run few tests to
+check if build process was successful.
+
+.. note::
+ To install MOOSE into non-standard directory, pass additional argument
+ `-DCMAKE_INSTALL_PREFIX=path/to/install/dir` to cmake
+ ::
+ $ cmake -DCMAKE_INSTALL_PREFIC=$HOME/.local ..
+
+ To use different version of python
+ ::
+ $ cmake -DPYTHON_EXECUTABLE=/opt/python3/bin/python3 ..
+
+After that installation is pretty easy
+::
+ $ sudo make install
+
+If everything went fine, you should be able to import moose in python shell.
+
+.. code-block:: python
+
+ import moose
+
+
+Graphical User Interface (GUI)
+------------------------------
+
+You can get the source of ``moose-gui`` from `here
+<https://github.com/BhallaLab/moose-gui>`_. You can download it either by
+clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`_
+or by using ``git`` ::
+ $ git clone https://github.com/BhallaLab/moose-gui
+
+To be able to launch ``moose-gui``, you need to install some more packages
+
+- matplotlib
+- python-qt4
+
+On ``Ubuntu/Debian``, these can be installed with
+::
+ $ sudo apt-get install python-matplotlib python-qt4
+
+On ``CentOS/Fedora/RHEL``
+::
+ $ sudo yum install python-matplotlib python-qt4
+
+Now you can fire up the GUI
+::
+ $ cd /to/moose-gui
+ $ python mgui.py
+
+.. note::
+ If you have installed ``moose`` package, then GUI is launched by
+ running following commnad::
+ $ moose
+
+Building moogli
+---------------
+
+``moogli`` is subproject of ``MOOSE`` for visualizing models. More details can
+be found `here <http://moose.ncbs.res.in/moogli>`_.
+
+`Moogli` is part of `moose` package. Building moogli can be tricky because of
+multiple depednecies it has.
+
+
+To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`_.
+
+Moogli depends on ``OpenSceneGraph`` (version 3.2.0 or higher) which may not
+be easily available for your operating system.
+For this reason, we distribute required ``OpenSceneGraph`` with ``moogli``
+source code.
+
+Depending on distribution of your operating system, you would need following
+packages to be installed.
+
+On ``Ubuntu/Debian``
+::
+ $ sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev
+
+On ``Fedora/CentOS/RHEL``
+::
+ $ sudo yum install sip-devel PyQt4-devel qt4-devel libjpeg-devel PyQt4
+
+On ``openSUSE``
+::
+ $ sudo zypper install python-sip python-qt4-devel libqt4-devel python-qt4
+
+After this, building and installing ``moogli`` should be as simple as
+::
+ $ cd /path/to/moogli
+ $ mkdir _build
+ $ cd _build
+ $ cmake ..
+ $ make
+ $ sudo make install
+
+If you run into troubles, please report it on our `github repository
+<https://github.com/BhallaLab/moose/issues>`_.
diff --git a/moose-examples/docs/source/introduction/changes/index.rst b/moose-examples/docs/source/introduction/changes/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9a167f14daf7633c581babd2cd82e2b452ad0900
--- /dev/null
+++ b/moose-examples/docs/source/introduction/changes/index.rst
@@ -0,0 +1,4 @@
+Changes
+=======
+
+.. todo:: collect changes from OBS.
diff --git a/moose-examples/docs/source/introduction/index_intro.rst b/moose-examples/docs/source/introduction/index_intro.rst
new file mode 100644
index 0000000000000000000000000000000000000000..424ca9a2f0a5d738871656b9710d3d8800e0a4e2
--- /dev/null
+++ b/moose-examples/docs/source/introduction/index_intro.rst
@@ -0,0 +1,24 @@
+Introduction
+============
+
+What is MOOSE and what is it good for?
+--------------------------------------
+MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed to simulate neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, circuits, and large networks. MOOSE can operate at many levels of detail, from stochastic chemical computations, to multicompartment single-neuron models, to spiking neuron network models.
+
+.. figure:: ../../images/Gallery_Moose_Multiscale.png
+ :alt: **multiple scales in moose**
+ :scale: 50%
+
+ *Multiple scales can be modelled and simulated in MOOSE*
+
+MOOSE is multiscale: It can do all these calculations together. One of its major uses is to make biologically detailed models that combine electrical and chemical signaling.
+
+MOOSE is object-oriented. Biological concepts are mapped into classes, and a model is built by creating instances of these classes and connecting them by messages. MOOSE also has numerical classes whose job is to take over difficult computations in a certain domain, and do them fast. There are such solver classes for stochastic and deterministic chemistry, for diffusion, and for multicompartment neuronal models.
+
+MOOSE is a simulation environment, not just a numerical engine: It provides data representations and solvers (of course!), but also a scripting interface with Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for many model formats. These include SBML, NeuroML, GENESIS kkit and cell.p formats, HDF5 and NSDF for data writing.
+
+.. toctree::
+
+ release_notes/index
+ changes/index
+ known_issues/index
diff --git a/moose-examples/docs/source/introduction/known_issues/index.rst b/moose-examples/docs/source/introduction/known_issues/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0ad5cdd653f187c374b75e0d605f748d2e3c8ea9
--- /dev/null
+++ b/moose-examples/docs/source/introduction/known_issues/index.rst
@@ -0,0 +1,9 @@
+Known issues
+============
+
+Full report can be found at the following places
+
+- Related to build, packages and documentation `https://github.com/BhallaLab/moose/issues`
+- Related to python interface of MOOSE `https://github.com/BhallaLab/moose-core/issues`
+- Related to MOOSE GUI `https://github.com/BhallaLab/moose-gui/issues`
+- Related to ``moogli`` `https://github.com/BhallaLab/moogli/issues`
diff --git a/moose-examples/docs/source/introduction/release_notes/index.rst b/moose-examples/docs/source/introduction/release_notes/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..862216e95c1d42e9c53d4f176e75ffdfe2987165
--- /dev/null
+++ b/moose-examples/docs/source/introduction/release_notes/index.rst
@@ -0,0 +1,4 @@
+Release Notes
+============
+
+.. todo:: Collect release notes from github.
diff --git a/moose-examples/docs/source/user/py/cookbook/chem.rst b/moose-examples/docs/source/user/py/cookbook/chem.rst
new file mode 100644
index 0000000000000000000000000000000000000000..fa4c9cf098b2c818e3401703e3376c26eed48b5b
--- /dev/null
+++ b/moose-examples/docs/source/user/py/cookbook/chem.rst
@@ -0,0 +1,249 @@
+****************
+Chemical Aspects
+****************
+
+.. _ckbk-chem-load-run:
+
+Load - Run - Save models
+========================
+
+Load a Kinetic Model
+--------------------
+
+.. automodule:: loadKineticModel
+ :members:
+
+Load an SBML Model
+-------------------
+
+.. automodule:: loadSbmlmodel
+ :members:
+
+Load a CSpace Model
+-------------------
+
+.. automodule:: loadCspaceModel
+ :members:
+
+Save a model into SBML format
+-----------------------------
+
+.. automodule:: convert_Genesis2Sbml
+ :members:
+
+Save a model
+------------
+
+.. automodule:: savemodel
+ :members:
+
+.. _ckbk-chem-snippets:
+
+Simple Examples
+===============================
+
+Set-up a kinetic solver and model
+---------------------------------
+
+with Scripting
+^^^^^^^^^^^^^^
+
+.. automodule:: scriptGssaSolver
+ :members:
+
+With something else
+^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: changeFuncExpression
+ :members:
+
+Building a chemical Model from Parts
+------------------------------------
+
+.. automodule:: scriptKineticSolver
+ :members:
+
+Cross-Compartment Reaction Systems
+----------------------------------
+
+.. automodule:: crossComptSimpleReac
+ :members:
+
+.. automodule:: crossComptOscillator
+ :members:
+
+.. automodule:: crossComptNeuroMesh
+ :members:
+
+.. automodule:: crossComptSimpleReacGSSA
+ :members:
+
+Tweaking Parameters
+-------------------
+
+.. automodule:: tweakingParameters
+ :members:
+
+Models' Demonstration
+---------------------
+
+Oscillation Model
+^^^^^^^^^^^^^^^^^
+
+.. automodule:: slowFbOsc
+ :members:
+
+Bistability Models
+^^^^^^^^^^^^^^^^^^
+
+MAPK feedback loop model
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: mapkFB
+ :members:
+
+Simple minimal bistable model
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: scaleVolumes
+ :members:
+
+Strongly bistable Model
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: strongBis
+ :members:
+
+Model of bidirectional synaptic plasticity
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+[showing bistable chemical switch]
+
+.. automodule:: bidirectionalPlasticity
+ :members:
+
+Reaction Diffusion Models
+-------------------------
+[Reaction-diffusion + transport in a tapering cylinder]
+
+.. automodule:: cylinderDiffusion
+ :members:
+
+.. automodule:: cylinderMotor
+ :members:
+
+.. automodule:: gssaCylinderDiffusion
+ :members:
+
+Neuronal Diffusion Reaction
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: rxdFuncDiffusion
+ :members:
+
+.. automodule:: rxdReacDiffusion
+ :members:
+
+.. automodule:: rxdFuncDiffusionStoch
+ :members:
+
+A Turing Model
+--------------
+
+.. automodule:: TuringOneDim
+ :members:
+
+A Spatial Bistable Model
+------------------------
+
+.. automodule::
+ :members:
+
+Reaction Diffusion in Neurons
+-----------------------------
+
+.. automodule:: reacDiffConcGradient
+ :members:
+
+.. automodule:: reacDiffBranchingNeuron
+ :members:
+
+.. automodule:: reacDiffSpinyNeuron
+ :members:
+
+.. automodule:: diffSpinyNeuron
+ :members:
+
+Manipulating Chemical Models
+----------------------------
+
+Running with different numerical methods
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: switchKineticSolvers
+ :members:
+
+Changing volumes
+^^^^^^^^^^^^^^^^
+
+.. automodule:: scaleVolumes
+ :members:
+
+Feeding tabulated input to a model
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: analogStimTable
+ :members:
+
+Finding steady states
+^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: findChemSteadyState
+ :members:
+
+Making a dose-response curve
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: chemDoseResponse
+ :members:
+
+Transport in branching dendritic tree
+-------------------------------------
+
+.. automodule:: transportBranchingNeuron
+ :members:
+
+.. _ckbk-chem-rde:
+
+RDesigneur
+==========
+
+.. _ckbk-chem-tut:
+
+Tutorials
+=========
+
+Deterministic Simulation
+------------------------
+
+Stochastic Simulation
+---------------------
+
+Finding Steady State (CSpace)
+-----------------------------
+
+.. automodule:: cspaceSteadyState
+ :members:
+
+Building Simple Reaction Model
+------------------------------
+
+Define a kinetic model using the scripting
+---------------------
+
+.. automodule:: scriptKineticModel
+ :members:
+
+.. _ckbk-chem-adv:
+
+Advanced Examples
+=================
diff --git a/moose-examples/docs/source/user/py/cookbook/elec.rst b/moose-examples/docs/source/user/py/cookbook/elec.rst
new file mode 100644
index 0000000000000000000000000000000000000000..60c3974e699e4aca04200b9f12e621d5c009fbf6
--- /dev/null
+++ b/moose-examples/docs/source/user/py/cookbook/elec.rst
@@ -0,0 +1,119 @@
+*********************************************
+Single Neuron Electrical Aspects (BioPhysics)
+*********************************************
+
+.. _ckbk-elec-load-run:
+
+Load and Run simple models
+==========================
+
+Single Cubicle Compartmental Neuron
+-----------------------------------
+
+.. automodule:: cubeMeshSigNeur
+ :members:
+
+Single Neuron Model
+-------------------
+
+.. automodule:: testSigNeur
+ :members:
+
+Load neuron model from GENESIS
+------------------------------
+
+.. automodule:: neuronFromDotp
+ :members:
+
+Integrate-and-fire models
+-------------------------
+
+.. automodule:: IntegrateFireZoo
+ :members:
+
+.. _ckbk-elec-snippets:
+
+Simple Examples
+===============================
+
+Gap Junction
+------------
+
+.. automodule:: gapjunction
+ :members:
+
+Voltage Clamping
+----------------
+
+.. automodule:: vclamp
+ :members:
+
+Synapse
+-------
+
+.. automodule:: synapse
+ :members:
+
+Generate Pulse
+----------------
+
+.. automodule:: pulsegen
+ :members:
+
+.. automodule:: pulsegen2
+ :members:
+
+Create a Leaky Neuron
+---------------------
+
+.. automodule:: lif
+ :members:
+
+Create a Leaky Compartment
+--------------------------
+
+.. automodule:: lifcomp
+ :members:
+
+Message transmission via synapse
+--------------------------------
+
+.. automodule:: intfire
+ :members:
+
+Insert Spine heads
+------------------
+
+.. automodule:: insertSpinesWithoutRdesigneur
+ :members:
+
+Multi compartmental Neuron model
+--------------------------------
+
+.. automodule:: testHsolve
+ :members:
+
+.. _ckbk-elec-gui:
+
+GUI
+===
+
+.. _ckbk-elec-snippets:
+
+Simple Examples
+===============================
+
+.. _ckbk-elec-rde:
+
+RDesigneur
+==========
+
+.. _ckbk-elec-tut:
+
+Tutorials
+=========
+
+.. _ckbk-elec-adv:
+
+Advanced Examples
+=================
diff --git a/moose-examples/docs/source/user/py/cookbook/index_ckbk.rst b/moose-examples/docs/source/user/py/cookbook/index_ckbk.rst
new file mode 100644
index 0000000000000000000000000000000000000000..af47c0892c4fb126bf14751d40c8e63bfa69ae0c
--- /dev/null
+++ b/moose-examples/docs/source/user/py/cookbook/index_ckbk.rst
@@ -0,0 +1,14 @@
+.. MOOSE documentation master file, created by
+ sphinx-quickstart on Tue Jul 1 19:05:47 2014.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Cook Book
+===========
+
+.. toctree::
+
+ elec
+ chem
+ network
+ multiscale
diff --git a/moose-examples/docs/source/user/py/cookbook/multiscale.rst b/moose-examples/docs/source/user/py/cookbook/multiscale.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a406742280af7856067c41a85a8c8b4b2021a6f3
--- /dev/null
+++ b/moose-examples/docs/source/user/py/cookbook/multiscale.rst
@@ -0,0 +1,78 @@
+*******************
+MultiScale Modeling
+*******************
+
+.. _ckbk-multi-load-run:
+
+Load and Run simple models
+==========================
+
+.. _ckbk-multi-snippets:
+
+Simple Examples
+===============
+
+Single-compartment multiscale model
+-----------------------------------
+
+.. automodule:: multiscaleOneCompt
+ :members:
+
+Multi compartment Single Neuron Model
+-------------------------------------
+
+.. automodule:: multiComptSigNeur
+ :members:
+
+Multi-compartment multiscale model
+----------------------------------
+
+Modeling chemical reactions in neurons
+--------------------------------------
+
+.. automodule:: gssaRDspiny
+ :members:
+
+.. automodule:: rxdSpineSize
+ :members:
+
+.. _ckbk-multi-gui:
+
+GUI
+===
+
+.. _ckbk-multi-rdes:
+
+RDesigneur
+==========
+
+Building Chemical-Electrical Signalling Models using Rdesigneur
+---------------------------------------------------------------
+
+Building a compartment
+^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: testRdesigneur
+ :members:
+
+Inserting Spines and viewing
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: insertSpines
+ :members:
+
+Proceeding with Spines
+^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: testWigglySpines
+ :members:
+
+.. _ckbk-multi-tut:
+
+Tutorials
+=========
+
+.. _ckbk-multi-adv:
+
+Advanced Examples
+=================
diff --git a/moose-examples/docs/source/user/py/cookbook/network.rst b/moose-examples/docs/source/user/py/cookbook/network.rst
new file mode 100644
index 0000000000000000000000000000000000000000..94631ed52160bba03946297de7207f9a7bc67024
--- /dev/null
+++ b/moose-examples/docs/source/user/py/cookbook/network.rst
@@ -0,0 +1,94 @@
+**********
+Networking
+**********
+
+.. _ckbk-net-load-run:
+
+Load and Run simple models
+==========================
+
+.. _ckbk-net-snippets:
+
+Simple Examples
+===============================
+
+Connecting two cells via a synapse
+----------------------------------
+
+.. automodule:: twocells
+ :members:
+
+Multi Compartmental Leaky Neurons
+---------------------------------
+
+.. automodule:: multicomp_lif
+ :members:
+
+Providing random input to a cell
+--------------------------------
+
+.. automodule:: randomspike
+ :members:
+
+Plastic synapse
+---------------
+
+.. automodule:: STDP
+ :members:
+
+Synapse Handler for Spikes
+--------------------------
+
+.. automodule:: RandSpikeStats
+ :members:
+
+Recurrent integrate-and-fire network
+------------------------------------
+
+.. automodule:: recurrentIntFire
+ :members:
+
+Recurrent integrate-and-fire network with plasticity
+----------------------------------------------------
+
+.. automodule:: recurrentLIF
+ :members:
+
+Demonstration Models
+--------------------
+
+.. automodule:: compartment_net
+ :members:
+
+.. automodule:: compartment_net_no_array
+ :members:
+
+Building Models
+---------------
+
+.. automodule:: synapse_tutorial
+ :members:
+
+.. _ckbk-net-gui:
+
+GUI
+===
+
+.. _ckbk-net-tut:
+
+Tutorials
+=========
+
+Network with Ca-based plasticity
+--------------------------------
+
+.. automodule:: GraupnerBrunel2012_STDPfromCaPlasticity
+ :members:
+
+.. automodule:: HigginsGraupnerBrunel2014_LifetimeCaPlasticity
+ :members:
+
+.. _ckbk-net-adv:
+
+Advanced Examples
+=================
diff --git a/moose-examples/docs/source/user/py/graphics/index_graphics.rst b/moose-examples/docs/source/user/py/graphics/index_graphics.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/moose-examples/docs/source/user/py/quickstart/demos.rst b/moose-examples/docs/source/user/py/quickstart/demos.rst
new file mode 100644
index 0000000000000000000000000000000000000000..7451bd68adc78e9a9df2a50f7c7101c5eedb9059
--- /dev/null
+++ b/moose-examples/docs/source/user/py/quickstart/demos.rst
@@ -0,0 +1,187 @@
+**************************************
+Demonstration of basic functionalities
+**************************************
+
+.. _quickstart-load-run:
+
+Load and Run a Model
+====================
+
+.. automodule:: helloMoose
+ :members:
+
+.. _quickstart-timing:
+
+Start, Stop, and setting clocks
+===============================
+
+.. automodule:: startstop
+ :members:
+
+.. automodule:: stimtable
+ :members:
+
+.. _quickstart-python_from_moose:
+
+Run Python from MOOSE
+=====================
+
+.. automodule:: pyrun
+ :members:
+
+.. automodule:: pyrun1
+ :members:
+
+.. _quickstart-classes:
+
+MOOSE Classes
+=====================
+
+Messages
+--------
+
+One-to-one message
+^^^^^^^^^^^^^^^^^^
+
+.. automodule:: onetoonemsg
+ :members:
+
+Show the message
+^^^^^^^^^^^^^^^^
+
+.. automodule:: showmsg
+ :members:
+
+Single Message Cross
+^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: singlemsgcross
+ :members:
+
+Time
+----
+
+Clocks
+^^^^^^
+
+.. automodule:: showclocks
+ :members:
+
+Generating Time Data Table
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: timetable
+ :members:
+
+Vectors
+-------
+
+.. automodule:: vectors
+ :members:
+
+Data Entries
+------------
+
+.. automodule:: wildcard
+ :members:
+
+Interpolation
+-------------
+
+1-dimentional Interpolation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: interpol
+ :members:
+
+2-dimentional interpolation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: interpol2d
+ :members:
+
+Function
+--------
+
+.. automodule:: func
+ :members:
+
+SymCompartment
+--------------
+
+.. automodule:: symcompartment
+ :members:
+
+Tables
+------
+
+.. automodule:: tabledemo
+ :members:
+
+Data Types
+----------
+
+HDF DataType
+^^^^^^^^^^^^
+
+.. automodule:: hdfdemo
+ :members:
+
+NSDF DataType
+^^^^^^^^^^^^^
+
+.. automodule:: nsdf
+ :members:
+
+.. automodule:: nsdf_vec
+ :members:
+
+Threading
+---------
+
+.. automodule:: threading_demo
+ :members:
+
+PyMoose
+-------
+
+.. automodule:: traub_naf
+ :members:
+
+.. _quickstart-maths:
+
+Mathematics with MOOSE
+======================
+
+Computing an arbitrary function
+-------------------------------
+
+.. automodule:: function
+ :members:
+
+Differential Equation Solving
+-----------------------------
+
+.. automodule:: diffEqSolution
+ :members:
+
+Harmonic Oscillatory Function
+-----------------------------
+
+.. automodule:: funcRateHarmonicOsc
+ :members:
+
+Lotka-Voltera Model
+-------------------
+
+.. automodule:: funcReacLotkaVolterra
+ :members:
+
+.. automodule:: stochasticLotkaVolterra
+ :members:
+
+Vary Concentration with mathematical function
+---------------------------------------------
+
+.. automodule:: funcInputToPools
+ :members:
diff --git a/moose-examples/docs/source/user/py/quickstart/index_qs.rst b/moose-examples/docs/source/user/py/quickstart/index_qs.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d6d0c42b0785d972871b1dbb1ee561d1875e0ee7
--- /dev/null
+++ b/moose-examples/docs/source/user/py/quickstart/index_qs.rst
@@ -0,0 +1,13 @@
+.. MOOSE documentation master file, created by
+ sphinx-quickstart on Tue Jul 1 19:05:47 2014.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Quick Start
+===========
+
+.. toctree::
+ :maxdepth: 2
+
+ moose_quickstart
+ demos
diff --git a/moose-examples/docs/source/user/py/quickstart/moose_quickstart.rst b/moose-examples/docs/source/user/py/quickstart/moose_quickstart.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f552fb900164f43ea2913a63241f3d552f6c89d9
--- /dev/null
+++ b/moose-examples/docs/source/user/py/quickstart/moose_quickstart.rst
@@ -0,0 +1,683 @@
+***********************************************
+Getting started with python scripting for MOOSE
+***********************************************
+
+.. :Author: Subhasis Ray
+.. :Date: December 12, 2012,
+.. :Last-Updated: Jan 21, 2016
+.. :By: Harsha Rani
+
+.. _quickstart-intro:
+
+Introduction
+============
+
+This document describes how to use the ``moose`` module in Python
+scripts or in an interactive Python shell. It aims to give you enough
+overview to help you start scripting using MOOSE and extract farther
+information that may be required for advanced work. Knowledge of
+Python or programming in general will be helpful. If you just want to
+simulate existing models in one of the supported formats, you can fire
+the MOOSE GUI and locate the model file using the ``File`` menu and
+load it. The GUI is described in separate document. If you
+are looking for recipes for specific tasks, take a look at
+:doc:`moose_cookbook`. The example code in the boxes can be entered in
+a Python shell.
+
+.. _quickstart-importing:
+
+Importing MOOSE and accessing built-in documentation
+====================================================
+
+In a python script you import modules to access the functionalities they
+provide. ::
+
+ >>> import moose
+
+This makes the ``moose`` module available for use in Python. You can use
+Python's built-in ``help`` function to read the top-level documentation
+for the moose module ::
+
+ >>> help(moose)
+
+This will give you an overview of the module. Press ``q`` to exit the
+pager and get back to the interpreter. You can also access the
+documentation for individual classes and functions this way. ::
+
+ >>> help(moose.connect)
+
+To list the available functions and classes you can use ``dir``
+function [1]_. ::
+
+ >>> dir(moose)
+
+MOOSE has built-in documentation in the C++-source-code independent of
+Python. The ``moose`` module has a separate ``doc`` function to extract
+this documentation. ::
+
+ >>> moose.doc(moose.Compartment)
+
+The class level documentation will show whatever the author/maintainer
+of the class wrote for documentation followed by a list of various kinds
+of fields and their data types. This can be very useful in an
+interactive session.
+
+Each field can have its own detailed documentation, too. ::
+
+ >>> moose.doc('Compartment.Rm')
+
+Note that you need to put the class-name followed by dot followed by
+field-name within quotes. Otherwise, ``moose.doc`` will receive the
+field value as parameter and get confused.
+
+.. _quickstart-creating:
+
+Creating objects and traversing the object hierarchy
+----------------------------------------------------
+
+Different types of biological entities like neurons, enzymes, etc are
+represented by classes and individual instances of those types are
+objects of those classes. Objects are the building-blocks of models in
+MOOSE. We call MOOSE objects ``element`` and use object and element
+interchangeably in the context of MOOSE. Elements are conceptually laid
+out in a tree-like hierarchical structure. If you are familiar with file
+system hierarchies in common operating systems, this should be simple.
+
+At the top of the object hierarchy sits the ``Shell``, equivalent to the
+root directory in UNIX-based systems and represented by the path ``/``.
+You can list the existing objects under ``/`` using the ``le`` function. ::
+
+ >>> moose.le()
+ Elements under /
+ /Msgs
+ /clock
+ /classes
+ /postmaster
+
+``Msgs``, ``clock`` and ``classes`` are predefined objects in MOOSE. And
+each object can contain other objects inside them. You can see them by
+passing the path of the parent object to ``le`` ::
+
+ >>> moose.le('/Msgs')
+ Elements under /Msgs[0]
+ /Msgs[0]/singleMsg
+ /Msgs[0]/oneToOneMsg
+ /Msgs[0]/oneToAllMsg
+ /Msgs[0]/diagonalMsg
+ /Msgs[0]/sparseMsg
+
+Now let us create some objects of our own. This can be done by invoking
+MOOSE class constructors (just like regular Python classes). ::
+
+ >>> model = moose.Neutral('/model')
+
+The above creates a ``Neutral`` object named ``model``. ``Neutral`` is
+the most basic class in MOOSE. A ``Neutral`` element can act as a
+container for other elements. We can create something under ``model`` ::
+
+ >>> soma = moose.Compartment('/model/soma')
+
+Every element has a unique path. This is a concatenation of the names of
+all the objects one has to traverse starting with the root to reach that
+element. ::
+
+ >>> print soma.path
+ /model/soma
+
+The name of the element can be printed, too. ::
+
+ >>> print soma.name
+ soma
+
+The ``Compartment`` elements model small sections of a neuron. Some
+basic experiments can be carried out using a single compartment. Let us
+create another object to act on the ``soma``. This will be a step
+current generator to inject a current pulse into the soma. ::
+
+ >>> pulse = moose.PulseGen('/model/pulse')
+
+You can use ``le`` at any point to see what is there ::
+
+ >>> moose.le('/model')
+ Elements under /model
+ /model/soma
+ /model/pulse
+
+And finally, we can create a ``Table`` to record the time series of the
+soma's membrane potential. It is good practice to organize the data
+separately from the model. So we do it as below ::
+
+ >>> data = moose.Neutral('/data')
+ >>> vmtab = moose.Table('/data/soma_Vm')
+
+Now that we have the essential elements for a small model, we can go on
+to set the properties of this model and the experimental protocol.
+
+.. _quickstart-properties:
+
+Setting the properties of elements: accessing fields
+====================================================
+
+Elements have several kinds of fields. The simplest ones are the
+``value fields``. These can be accessed like ordinary Python members.
+You can list the available value fields using ``getFieldNames``
+function ::
+
+ >>> soma.getFieldNames('valueFinfo')
+
+Here ``valueFinfo`` is the type name for value fields. ``Finfo`` is
+short form of *field information*. For each type of field there is a
+name ending with ``-Finfo``. The above will display the following
+list ::
+
+ ('this',
+ 'name',
+ 'me',
+ 'parent',
+ 'children',
+ 'path',
+ 'class',
+ 'linearSize',
+ 'objectDimensions',
+ 'lastDimension',
+ 'localNumField',
+ 'pathIndices',
+ 'msgOut',
+ 'msgIn',
+ 'Vm',
+ 'Cm',
+ 'Em',
+ 'Im',
+ 'inject',
+ 'initVm',
+ 'Rm',
+ 'Ra',
+ 'diameter',
+ 'length',
+ 'x0',
+ 'y0',
+ 'z0',
+ 'x',
+ 'y',
+ 'z')
+
+Some of these fields are for internal or advanced use, some give access
+to the physical properties of the biological entity we are trying to
+model. Now we are interested in ``Cm``, ``Rm``, ``Em`` and ``initVm``.
+In the most basic form, a neuronal compartment acts like a parallel
+``RC`` circuit with a battery attached. Here ``R`` and ``C`` are
+resistor and capacitor connected in parallel, and the battery with
+voltage ``Em`` is in series with the resistor, as shown below:
+
+
+
+.. figure:: ../../../images/neuronalcompartment.jpg
+ :alt: **Passive neuronal compartment**
+
+ **Passive neuronal compartment**
+
+
+
+The fields are populated with some defaults. ::
+
+ >>> print soma.Cm, soma.Rm, soma.Vm, soma.Em, soma.initVm
+ 1.0 1.0 -0.06 -0.06 -0.06
+
+
+You can set the ``Cm`` and ``Rm`` fields to something realistic using
+simple assignment (we follow SI unit) [2]_. ::
+
+ >>> soma.Cm = 1e-9
+ >>> soma.Rm = 1e7
+ >>> soma.initVm = -0.07
+
+Instead of writing print statements for each field, you could use the
+utility function showfield to see that the changes took effect ::
+
+ >>> moose.showfield(soma)
+ [ /soma[0] ]
+ diameter = 0.0
+ Ra = 1.0
+ y0 = 0.0
+ Rm = 10000000.0
+ numData = 1
+ inject = 0.0
+ initVm = -0.07
+ Em = -0.06
+ y = 0.0
+ numField = 1
+ path = /soma[0]
+ dt = 5e-05
+ tick = 4
+ z0 = 0.0
+ name = soma
+ Cm = 1e-09
+ x0 = 0.0
+ Vm = -0.06
+ className = Compartment
+ length = 0.0
+ Im = 0.0
+ x = 0.0
+ z = 0.0
+
+Now we can setup the current pulse to be delivered to the soma ::
+
+ >>> pulse.delay[0] = 50e-3
+ >>> pulse.width[0] = 100e-3
+ >>> pulse.level[0] = 1e-9
+ >>> pulse.delay[1] = 1e9
+
+This tells the pulse generator to create a 100 ms long pulse 50 ms after
+the start of the simulation. The amplitude of the pulse is set to 1 nA.
+We set the delay for the next pulse to a very large value (larger than
+the total simulation time) so that the stimulation stops after the first
+pulse. Had we set ``pulse.delay = 0`` , it would have generated a pulse
+train at 50 ms intervals.
+
+.. _quickstart-connections:
+
+Putting them together: setting up connections
+=============================================
+
+In order for the elements to interact during simulation, we need to
+connect them via messages. Elements are connected to each other using
+special source and destination fields. These types are named
+``srcFinfo`` and ``destFinfo``. You can query the available source and
+destination fields on an element using ``getFieldNames`` as before. This
+time, let us do it another way: by the class name ::
+
+ >>> moose.getFieldNames('PulseGen', 'srcFinfo')
+ ('childMsg', 'output')
+
+This form has the advantage that you can get information about a class
+without creating elements of that class.
+
+Here ``childMsg`` is a source field that is used by the MOOSE internals
+to connect child elements to parent elements. The second one is of our
+interest. Check out the built-in documentation here ::
+
+ >>> moose.doc('PulseGen.output')
+ PulseGen.output: double - source field
+ Current output level.
+
+so this is the output of the pulse generator and this must be injected
+into the ``soma`` to stimulate it. But where in the ``soma`` can we send
+it? Again, MOOSE has some introspection built in. ::
+
+ >>> soma.getFieldNames('destFinfo')
+ ('parentMsg',
+ 'setThis',
+ 'getThis',
+ ...
+ 'setZ',
+ 'getZ',
+ 'injectMsg',
+ 'randInject',
+ 'cable',
+ 'process',
+ 'reinit',
+ 'initProc',
+ 'initReinit',
+ 'handleChannel',
+ 'handleRaxial',
+ 'handleAxial')
+
+Now that is a long list. But much of it are fields for internal or
+special use. Anything that starts with ``get`` or ``set`` are internal
+``destFinfo`` used for accessing value fields (we shall use one of those
+when setting up data recording). Among the rest ``injectMsg`` seems to
+be the most likely candidate. Use the ``connect`` function to connect
+the pulse generator output to the soma input ::
+
+ >>> m = moose.connect(pulse, 'output', soma, 'injectMsg')
+
+``connect(source, source_field, dest, dest_field)`` creates a
+``message`` from ``source`` element's ``source_field`` field to ``dest``
+elements ``dest_field`` field and returns that message. Messages are
+also elements. You can print them to see their identity ::
+
+ >>> print m
+ <moose.SingleMsg: id=5, dataId=733, path=/Msgs/singleMsg[733]>
+
+You can print any element as above and the string representation will
+show you the class, two numbers(\ ``id`` and ``dataId``) uniquely
+identifying it among all elements, and its path. You can get some more
+information about a message ::
+
+ >>> print m.e1.path, m.e2.path, m.srcFieldsOnE1, m.destFieldsOnE2
+ /model/pulse /model/soma ('output',) ('injectMsg',)
+
+
+will confirm what you already know.
+
+
+A message element has fields ``e1`` and ``e2`` referring to the elements
+it connects. For single one-directional messages these are source and
+destination elements, which are ``pulse`` and ``soma`` respectively. The
+next two items are lists of the field names which are connected by this
+message.
+
+You could also check which elements are connected to a particular field ::
+
+ >>> print soma.neighbors['injectMsg']
+ [<moose.vec: class=PulseGen, id=729,path=/model/pulse>]
+
+Notice that the list contains something called vec. We discuss this
+`later <#some-more-details>`__. Also ``neighbors`` is a new kind of
+field: ``lookupFinfo`` which behaves like a dictionary. Next we connect
+the table to the soma to retrieve its membrane potential ``Vm``. This is
+where all those ``destFinfo`` starting with ``get`` or ``set`` come in
+use. For each value field ``X``, there is a ``destFinfo`` ``get{X}`` to
+retrieve the value at simulation time. This is used by the table to
+record the values ``Vm`` takes. ::
+
+ >>> moose.connect(vmtab, 'requestOut', soma, 'getVm')
+ <moose.SingleMsg: id=5, dataIndex=0, path=/Msgs[0]/singleMsg[0]>
+
+This finishes our model and recording setup. You might be wondering
+about the source-destination relationship above. It is natural to think
+that ``soma`` is the source of ``Vm`` values which should be sent to
+``vmtab``. But here ``requestOut`` is a ``srcFinfo`` acting like a
+reply card. This mode of obtaining data is called *pull* mode. [3]_
+
+You can skip the next section on fine control of the timing of updates
+and read :ref:`quickstart-running`.
+
+.. _quickstart-scheduling:
+
+Scheduling
+==========
+
+With the model all set up, we have to schedule the
+simulation. Different components in a model may have different rates
+of update. For example, the dynamics of electrical components require
+the update intervals to be of the order 0.01 ms whereas chemical
+components can be as slow as 1 s. Also, the results may depend on the
+sequence of the updates of different components. These issues are
+addressed in MOOSE using a clock-based update scheme. Each model
+component is scheduled on a clock tick (think of multiple hands of a
+clock ticking at different intervals and the object being updated at
+each tick of the corresponding hand). The scheduling also guarantees
+the correct sequencing of operations. For example, your Table objects
+should always be scheduled *after* the computations that they are
+recording, otherwise they will miss the outcome of the latest calculation.
+
+MOOSE has a central clock element (``/clock``) to manage
+time. Clock has a set of ``Tick`` elements under it that take care of
+advancing the state of each element with time as the simulation
+progresses. Every element to be included in a simulation must be
+assigned a tick. Each tick can have a different ticking interval
+(``dt``) that allows different elements to be updated at different
+rates.
+
+By default, every object is assigned a clock tick with reasonable default
+timesteps as soon it is created::
+
+ Class type tick dt
+ Electrical computations: 0-7 50 microseconds
+ electrical compartments,
+ V and ligand-gated ion channels,
+ Calcium conc and Nernst,
+ stimulus generators and tables,
+ HSolve.
+
+ Table (to plot elec. signals) 8 100 microseconds
+
+ Diffusion solver 10 0.01 seconds
+ Chemical computations: 11-17 0.1 seconds
+ Pool, Reac, Enz, MMEnz,
+ Func, Function,
+ Gsolve, Ksolve,
+ Stats (to do stats on outputs)
+
+ Table2 (to plot chem. signals) 18 1 second
+
+ HDF5DataWriter 30 1 second
+ Postmaster (for parallel 31 0.01 seconds
+ computations)
+
+There are 32 available clock ticks. Numbers 20 to 29 are
+unassigned so you can use them for whatever purpose you like.
+
+If you want fine control over the scheduling, there are three things
+you can do.
+
+ * Alter the 'tick' field on the object
+ * Alter the dt associated with a given tick, using the
+ **moose.setClock( tick, newdt)** command
+ * Go through a wildcard path of objects reassigning there clock ticks,
+ using **moose.useClock( path, newtick, function)**.
+
+Here we discuss these in more detail.
+
+**Altering the 'tick' field**
+
+Every object knows which tick and dt it uses::
+
+ >>> a = moose.Pool( '/a' )
+ >>> print a.tick, a.dt
+ 13 0.1
+
+The ``tick`` field on every object can be changed, and the object will
+adopt whatever clock dt is used for that tick. The ``dt`` field is
+readonly, because changing it would have side-effects on every object
+associated with the current tick.
+
+Ticks **-1** and **-2** are special: They both tell the object that it is
+disabled (not scheduled for any operations). An object with a
+tick of **-1** will be left alone entirely. A tick of **-2** is used in
+solvers to indicate that should the solver be removed, the object will
+revert to its default tick.
+
+**Altering the dt associated with a given tick**
+
+We initialize the ticks and set their ``dt`` values using the
+``setClock`` function. ::
+
+ >>> moose.setClock(0, 0.025e-3)
+ >>> moose.setClock(1, 0.025e-3)
+ >>> moose.setClock(2, 0.25e-3)
+
+This will initialize tick #0 and tick #1 with ``dt = 25`` μs and tick #2
+with ``dt = 250`` μs. Thus all the elements scheduled on ticks #0 and 1
+will be updated every 25 μs and those on tick #2 every 250 μs. We use
+the faster clocks for the model components where finer timescale is
+required for numerical accuracy and the slower clock to sample the
+values of ``Vm``.
+
+Note that if you alter the dt associated with a given tick, this will
+affect the update time for *all* the objects using that clock tick. If
+you're unsure that you want to do this, use one of the vacant ticks.
+
+
+**Assigning clock ticks to all objects in a wildcard path**
+
+To assign tick #2 to the table for recording ``Vm``, we pass its
+whole path to the ``useClock`` function. ::
+
+ >>> moose.useClock(2, '/data/soma_Vm', 'process')
+
+Read this as "use tick # 2 on the element at path ``/data/soma_Vm`` to
+call its ``process`` method at every step". Every class that is supposed
+to update its state or take some action during simulation implements a
+``process`` method. And in most cases that is the method we want the
+ticks to call at every time step. A less common method is ``init``,
+which is implemented in some classes to interleave actions or updates
+that must be executed in a specific order [4]_. The ``Compartment``
+class is one such case where a neuronal compartment has to know the
+``Vm`` of its neighboring compartments before it can calculate its
+``Vm`` for the next step. This is done with: ::
+
+ >>> moose.useClock(0, soma.path, 'init')
+
+Here we used the ``path`` field instead of writing the path explicitly.
+
+Next we assign tick #1 to process method of everything under ``/model``. ::
+
+ >>> moose.useClock(1, '/model/##', 'process')
+
+Here the second argument is an example of wild-card path. The ``##``
+matches everything under the path preceding it at any depth. Thus if we
+had some other objects under ``/model/soma``, ``process`` method of
+those would also have been scheduled on tick #1. This is very useful for
+complex models where it is tedious to scheduled each element
+individually. In this case we could have used ``/model/#`` as well for
+the path. This is a single level wild-card which matches only the
+children of ``/model`` but does not go farther down in the hierarchy.
+
+.. _quickstart-running:
+
+Running the simulation
+======================
+
+Once the model is all set up, we can put the model to its
+initial state using ::
+
+ >>> moose.reinit()
+
+You may remember that we had changed initVm from ``-0.06`` to ``-0.07``.
+The reinit call we initialize ``Vm`` to that value. You can verify that ::
+
+ >>> print soma.Vm
+ -0.07
+
+Finally, we run the simulation for 300 ms ::
+
+ >>> moose.start(300e-3)
+
+The data will be recorded by the ``soma_vm`` table, which is referenced
+by the variable ``vmtab``. The ``Table`` class provides a numpy array
+interface to its content. The field is ``vector``. So you can easily plot
+the membrane potential using the `matplotlib <http://matplotlib.org/>`__
+library. ::
+
+ >>> import pylab
+ >>> t = pylab.linspace(0, 300e-3, len(vmtab.vector))
+ >>> pylab.plot(t, vmtab.vector)
+ >>> pylab.show()
+
+The first line imports the pylab submodule from matplotlib. This useful
+for interactive plotting. The second line creates the time points to
+match our simulation time and length of the recorded data. The third
+line plots the ``Vm`` and the fourth line makes it visible. Does the
+plot match your expectation?
+
+.. _quickstart-details:
+
+Some more details
+=================
+
+``vec``, ``melement`` and ``element``
+-----------------------------------------
+
+MOOSE elements are instances of the class ``melement``. ``Compartment``,
+``PulseGen`` and other MOOSE classes are derived classes of
+``melement``. All ``melement`` instances are contained in array-like
+structures called ``vec``. Each ``vec`` object has a numerical
+``id_`` field uniquely identifying it. An ``vec`` can have one or
+more elements. You can create an array of elements ::
+
+ >>> comp_array = moose.vec('/model/comp', n=3, dtype='Compartment')
+
+This tells MOOSE to create an ``vec`` of 3 ``Compartment`` elements
+with path ``/model/comp``. For ``vec`` objects with multiple
+elements, the index in the ``vec`` is part of the element path. ::
+
+ >>> print comp_array.path, type(comp_array)
+
+shows that ``comp_array`` is an instance of ``vec`` class. You can
+loop through the elements in an ``vec`` like a Python list ::
+
+ >>> for comp in comp_array:
+ ... print comp.path, type(comp)
+ ...
+
+shows ::
+
+ /model/comp[0] <type 'moose.melement'>
+ /model/comp[1] <type 'moose.melement'>
+ /model/comp[2] <type 'moose.melement'>
+
+Thus elements are instances of class ``melement``. All elements in an
+``vec`` share the ``id_`` of the ``vec`` which can retrieved by
+``melement.getId()``.
+
+A frequent use case is that after loading a model from a file one knows
+the paths of various model components but does not know the appropriate
+class name for them. For this scenario there is a function called
+``element`` which converts ("casts" in programming jargon) a path or any
+moose object to its proper MOOSE class. You can create additional
+references to ``soma`` in the example this way ::
+
+ x = moose.element('/model/soma')
+
+Any MOOSE class can be extended in Python. But any additional attributes
+added in Python are invisible to MOOSE. So those can be used for
+functionalities at the Python level only. You can see
+``moose-examples/squid/squid.py`` for an example.
+
+``Finfos``
+----------
+
+The following kinds of ``Finfo`` are accessible in Python
+
+- **``valueFinfo``** : simple values. For each readable ``valueFinfo``
+ ``XYZ`` there is a ``destFinfo`` ``getXYZ`` that can be used for
+ reading the value at run time. If ``XYZ`` is writable then there will
+ also be ``destFinfo`` to set it: ``setXYZ``. Example:
+ ``Compartment.Rm``
+- **``lookupFinfo``** : lookup tables. These fields act like Python
+ dictionaries but iteration is not supported. Example:
+ ``Neutral.neighbors``.
+- **``srcFinfo``** : source of a message. Example:
+ ``PulseGen.output``.
+- **``destFinfo``** : destination of a message. Example:
+ ``Compartment.injectMsg``. Apart from being used in setting up
+ messages, these are accessible as functions from Python.
+ ``HHGate.setupAlpha`` is an example.
+- **``sharedFinfo``** : a composition of source and destination fields.
+ Example: ``Compartment.channel``.
+
+.. _quickstart-moving-on:
+
+Moving on
+=========
+
+Now you know the basics of pymoose and how to access the help
+system. You can figure out how to do specific things by looking at the
+:doc:`moose_cookbook`. In addition, the ``moose-examples/snippets`` directory
+in your MOOSE installation has small executable python scripts that
+show usage of specific classes or functionalities. Beyond that you can
+browse the code in the ``moose-examples`` directory to see some more complex
+models.
+
+MOOSE is backward compatible with GENESIS and most GENESIS classes have
+been reimplemented in MOOSE. There is slight change in naming (MOOSE
+uses CamelCase), and setting up messages are different. But `GENESIS
+documentation <http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual.html>`__
+is still a good source for documentation on classes that have been
+ported from GENESIS.
+
+If the built-in MOOSE classes do not satisfy your needs entirely, you
+are welcome to add new classes to MOOSE. The API documentation will
+help you get started.
+
+
+.. [1]
+ To list the classes only, use ``moose.le('/classes')``
+
+.. [2]
+ MOOSE is unit agnostic and things should work fine as long as you use
+ values all converted to a consistent unit system.
+
+.. [3]
+ This apparently convoluted implementation is for performance reason.
+ Can you figure out why? *Hint: the table is driven by a slower clock
+ than the compartment.*
+
+.. [4]
+ In principle any function available in a MOOSE class can be executed
+ periodically this way as long as that class exposes the function for
+ scheduling following the MOOSE API. So you have to consult the class'
+ documentation for any nonstandard methods that can be scheduled this
+ way.
diff --git a/moose-examples/docs/source/user/py/references/index_ref.rst b/moose-examples/docs/source/user/py/references/index_ref.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/moose-examples/paper-2015/rxdSpineSize.py b/moose-examples/paper-2015/rxdSpineSize.py
index 77a9fec80c87a5998d69d09a9682055f3957d75f..9d9a4e09936f755c1b8cf48a60aa434ad0c5a41e 100644
--- a/moose-examples/paper-2015/rxdSpineSize.py
+++ b/moose-examples/paper-2015/rxdSpineSize.py
@@ -22,6 +22,7 @@ import moogli
import moogli.extensions.moose
import matplotlib
+doMoo = True
PI = 3.141592653
ScalingForTesting = 10
RM = 1.0 / ScalingForTesting
@@ -45,8 +46,8 @@ spineAngleDistrib = 0.0
def makeCellProto( name ):
elec = moose.Neuron( '/library/' + name )
ecompt = []
- soma = rd.buildCompt( elec, 'soma', somaDia, somaDia, -somaDia, RM, RA, CM )
- dend = rd.buildCompt( elec, 'dend', dendLen, dendDia, 0, RM, RA, CM )
+ soma = rd.buildCompt( elec, 'soma', dx=somaDia, dia=somaDia, x=-somaDia, RM=RM, RA=RA, CM=CM )
+ dend = rd.buildCompt( elec, 'dend', dx=dendLen, dia=dendDia, x=0, RM=RM, RA=RA, CM=CM )
moose.connect( soma, 'axial', dend, 'raxial' )
elec.buildSegmentTree()
@@ -57,12 +58,7 @@ def makeChemProto( name ):
print(('making ', i))
compt = moose.CubeMesh( chem.path + '/' + i[0] )
compt.volume = i[1]
- #x = moose.Pool( compt.path + '/x' )
- #y = moose.BufPool( compt.path + '/y' )
z = moose.Pool( compt.path + '/z' )
- #x.concInit = 0.0
- #x.diffConst = diffConst
- #y.concInit = concInit
z.concInit = 0.0
z.diffConst = diffConst
nInit = comptVol * 6e23 * concInit
@@ -83,41 +79,33 @@ def makeChemProto( name ):
moose.connect( reac, 'sub', x, 'reac' )
moose.connect( reac, 'prd', z, 'reac' )
-def makeSpineProto2( name ):
- spine = moose.Neutral( '/library/' + name )
- shaft = rd.buildCompt( spine, 'shaft', 0.5e-6, 0.4e-6, 0, RM, RA, CM )
- head = rd.buildCompt( spine, 'head', 0.5e-6, 0.5e-6, 0.5e-6, RM, RA, CM )
- moose.connect( shaft, 'axial', head, 'raxial' )
-
def makeModel():
moose.Neutral( '/library' )
makeCellProto( 'cellProto' )
makeChemProto( 'cProto' )
- makeSpineProto2( 'spine' )
- rdes = rd.rdesigneur( useGssa = False, \
- combineSegments = False, \
- stealCellFromLibrary = True, \
- meshLambda = 1e-6, \
- cellProto = [['cellProto', 'elec' ]] ,\
- spineProto = [['spineProto', 'spine' ]] ,\
- chemProto = [['cProto', 'chem' ]] ,\
- spineDistrib = [ \
- ['spine', '#', \
- 'spacing', str( spineSpacing ), \
- 'spacingDistrib', str( spineSpacingDistrib ), \
- 'angle', str( spineAngle ), \
- 'angleDistrib', str( spineAngleDistrib ), \
- 'size', str( spineSize ), \
- 'sizeDistrib', str( spineSizeDistrib ) ] \
- ], \
- chemDistrib = [ \
- [ "chem", "dend", "install", "1" ] \
+ rdes = rd.rdesigneur( useGssa = False,
+ turnOffElec = True,
+ combineSegments = False,
+ stealCellFromLibrary = True,
+ diffusionLength = 1e-6,
+ cellProto = [['cellProto', 'elec' ]] ,
+ spineProto = [['makePassiveSpine()', 'spine' ]] ,
+ chemProto = [['cProto', 'chem' ]] ,
+ spineDistrib = [
+ ['spine', '#',
+ str( spineSpacing ), str( spineSpacingDistrib ),
+ str( spineSize ), str( spineSizeDistrib ),
+ str( spineAngle ), str( spineAngleDistrib )
+ ]
],
- adaptorList = [ \
- [ 'psd/z', 'n', 'spine', 'psdArea', 10.0e-15, 300e-15 ], \
- ] \
+ chemDistrib = [[ "chem", "#dend#,#psd#", "install", "1" ]],
+ adaptorList = [
+ [ 'psd/z', 'n', 'spine', 'psdArea', 50.0e-15, 500e-15 ],
+ ]
)
+ moose.seed(1234)
rdes.buildModel( '/model' )
+ print (('built model'))
x = moose.vec( '/model/chem/dend/x' )
x.concInit = 0.0
for i in range( 0,20 ):
@@ -177,12 +165,12 @@ def main():
pylab.legend()
pylab.show()
- app = QtGui.QApplication(sys.argv)
- #widget = mv.MoogliViewer( '/model' )
- morphology = moogli.read_morphology_from_moose( name="", path = '/model/elec' )
- widget = moogli.MorphologyViewerWidget( morphology )
- widget.show()
- return app.exec_()
+ if doMoo:
+ app = QtGui.QApplication(sys.argv)
+ morphology = moogli.read_morphology_from_moose( name="", path = '/model/elec' )
+ widget = moogli.MorphologyViewerWidget( morphology )
+ widget.show()
+ return app.exec_()
quit()
# Run the 'main' if this script is executed standalone.
@@ -202,24 +190,18 @@ def showVisualization():
makePlot( 'head_z', moose.vec( '/model/chem/spine/z' ), 'getN' )
psdZ = makePlot( 'psd_z', moose.vec( '/model/chem/psd/z' ), 'getN' )
diaTab = makePlot( 'headDia', eHead, 'getDiameter' )
- # print diaTab[0].vector[-1]
- # return
dendrite = moose.element("/model/elec/dend")
dendrites = [dendrite.path + "/" + str(i) for i in range(len(dendZ))]
- # print dendrites
moose.reinit()
spineHeads = moose.wildcardFind( '/model/elec/#head#')
- # print moose.wildcardFind( '/model/elec/##')
-
- # print "dendZ", readValues(dendZ)
- # print dendrite
- app = QtGui.QApplication(sys.argv)
- viewer = create_viewer("/model/elec", dendrite, dendZ, diaTab, psdZ)
- viewer.showMaximized()
- viewer.start()
- return app.exec_()
+ if doMoo:
+ app = QtGui.QApplication(sys.argv)
+ viewer = create_viewer("/model/elec", dendrite, dendZ, diaTab, psdZ)
+ viewer.showMaximized()
+ viewer.start()
+ return app.exec_()
def create_viewer(path, moose_dendrite, dendZ, diaTab, psdZ):
@@ -290,4 +272,7 @@ def create_viewer(path, moose_dendrite, dendZ, diaTab, psdZ):
if __name__ == '__main__':
- showVisualization()
+ if doMoo:
+ showVisualization()
+ else:
+ main()
diff --git a/moose-examples/snippets/MULTI/TuringInNeuron.py b/moose-examples/snippets/MULTI/TuringInNeuron.py
deleted file mode 100644
index 7f1c7a1e4d4bd15d887747a33d16430f894f2f8a..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/TuringInNeuron.py
+++ /dev/null
@@ -1,201 +0,0 @@
-# __DEPRECATED__ __BROKEN__
-#########################################################################
-## This program is part of 'MOOSE', the
-## Messaging Object Oriented Simulation Environment.
-## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
-## It is made available under the terms of the
-## GNU Lesser General Public License version 2.1
-## See the file COPYING.LIB for the full notice.
-#########################################################################
-
-# This example illustrates how to set up a Turing pattern in 1-D using
-# reaction diffusion calculations. The runtime is kept short so that the
-# pattern doesn't make it all the way to the end of the system.
-
-import math
-import pylab
-import numpy
-import moose
-import proto18
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- model = moose.element( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "Neutral" )
- return cellId
-
-def makeChemModel( cellId ):
- # create container for model
- r0 = 1e-6 # m
- r1 = 1e-6 # m
- num = 2800
- diffLength = 1e-6 # m
- diffConst = 5e-12 # m^2/sec
- motorRate = 1e-6 # m/sec
- concA = 1 # millimolar
-
- model = moose.element( '/model' )
- compartment = moose.NeuroMesh( '/model/compartment' )
- # FIXME: No attribute cell
- compartment.cell = cellId
- compartment.diffLength = diffLength
- print(("cell NeuroMesh parameters: numSeg and numDiffCompt: ", compartment.numSegments, compartment.numDiffCompts))
-
- print(("compartment.numDiffCompts == num: ", compartment.numDiffCompts, num))
- assert( compartment.numDiffCompts == num )
-
- # create molecules and reactions
- a = moose.Pool( '/model/compartment/a' )
- b = moose.Pool( '/model/compartment/b' )
- s = moose.Pool( '/model/compartment/s' )
- e1 = moose.MMenz( '/model/compartment/e1' )
- e2 = moose.MMenz( '/model/compartment/e2' )
- e3 = moose.MMenz( '/model/compartment/e3' )
- r1 = moose.Reac( '/model/compartment/r1' )
- moose.connect( e1, 'sub', s, 'reac' )
- moose.connect( e1, 'prd', a, 'reac' )
- moose.connect( a, 'nOut', e1, 'enzDest' )
- e1.Km = 1
- e1.kcat = 1
-
- moose.connect( e2, 'sub', s, 'reac' )
- moose.connect( e2, 'prd', b, 'reac' )
- moose.connect( a, 'nOut', e2, 'enzDest' )
- e2.Km = 1
- e2.kcat = 0.5
-
- moose.connect( e3, 'sub', a, 'reac' )
- moose.connect( e3, 'prd', s, 'reac' )
- moose.connect( b, 'nOut', e3, 'enzDest' )
- e3.Km = 0.1
- e3.kcat = 1
-
- moose.connect( r1, 'sub', b, 'reac' )
- moose.connect( r1, 'prd', s, 'reac' )
- r1.Kf = 0.3 # 1/sec
- r1.Kb = 0 # 1/sec
-
- # Assign parameters
- a.diffConst = diffConst/10
- b.diffConst = diffConst
- s.diffConst = 0
- #b.motorConst = motorRate
-
- # Make solvers
- ksolve = moose.Ksolve( '/model/compartment/ksolve' )
- dsolve = moose.Dsolve( '/model/compartment/dsolve' )
- stoich = moose.Stoich( '/model/compartment/stoich' )
- stoich.compartment = compartment
- #ksolve.numAllVoxels = compartment.numDiffCompts
- stoich.ksolve = ksolve
- stoich.dsolve = dsolve
- stoich.path = "/model/compartment/##"
- assert( dsolve.numPools == 3 )
- a.vec.concInit = [0.1]*num
- a.vec[0].concInit += 0.5
- a.vec[400].concInit += 0.5
- a.vec[800].concInit += 0.5
- a.vec[1200].concInit += 0.5
- a.vec[1600].concInit += 0.5
- a.vec[2000].concInit += 0.5
- a.vec[2400].concInit += 0.5
- #a.vec[num/2].concInit -= 0.1
- b.vec.concInit = [0.1]*num
- s.vec.concInit = [1]*num
-
-def displayPlots( num ):
- a = moose.element( '/model/compartment/a' )
- b = moose.element( '/model/compartment/b' )
- print(('/newplot\n/plotname a' + str(num)))
- for x in a.vec.conc:
- print(x)
- print(('/newplot\n/plotname b' + str(num)))
- for y in b.vec.conc:
- print(y)
- """
- print '/newplot\n/plotname bvol'
- for z in a.vec.volume:
- print z * 1e18
- print '/newplot\n/plotname aInit'
- for x in a.vec.concInit:
- print x
- pos = numpy.arange( 0, a.vec.conc.size, 1.0 )
- aconc = numpy.array( a.vec.conc )
- bconc = numpy.array( b.vec.conc )
- print "pos a, b = ", pos, b.vec.conc.size
- pylab.plot( pos[:100], aconc[:100], label='a' )
- pylab.plot( pos[:100], bconc[:100], label='b' )
- #pylab.plot( pos, a.vec.conc, label='a' )
- #pylab.plot( pos, b.vec.conc, label='b' )
- print "plotting done"
- pylab.legend()
- print "legend done"
- pylab.show()
- print "show done"
- """
-
-def main():
- runtime = 400
- dt4 = 0.02 # for the diffusion
- dt5 = 0.2 # for the reaction
- # Set up clocks. The dsolver to know before assigning stoich
- moose.setClock( 4, dt4 )
- moose.setClock( 5, dt5 )
- model = moose.Neutral( '/model' )
- cellId = loadElec()
- makeChemModel( cellId )
- moose.useClock( 4, '/model/compartment/dsolve', 'process' )
- # Ksolve must be scheduled after dsolve.
- moose.useClock( 5, '/model/compartment/ksolve', 'process' )
- print("finished loading")
- moose.reinit()
- for i in range( 10 ):
- moose.start( runtime / 10 ) # Run the model for 10 seconds.
- # print 'done', i
- displayPlots( i )
- print("finished running")
-
- """
- a = moose.element( '/model/compartment/a' )
- b = moose.element( '/model/compartment/b' )
- s = moose.element( '/model/compartment/s' )
-
- atot = sum( a.vec.conc )
- btot = sum( b.vec.conc )
- stot = sum( s.vec.conc )
- print "a = ", a.vec.conc
- print "b = ", b.vec.conc
- print "s = ", s.vec.conc
-
- print 'tot = ', atot, btot, atot + btot + stot
- displayPlots()
- """
-
- """
- dsolve = moose.element( '/model/compartment/dsolve' )
- x = dsolve.nVec[0]
- print dsolve.numPools, x, sum(x)
- print dsolve.nVec[1], sum( dsolve.nVec[1] )
- print dsolve.nVec[2], sum( dsolve.nVec[2] )
- print dsolve.nVec[3], sum( dsolve.nVec[3] )
- """
-
- quit()
-
-
-# Run the 'main' if this script is executed standalone.
-if __name__ == '__main__':
- main()
diff --git a/moose-examples/snippets/MULTI/ca1_asym.p b/moose-examples/snippets/MULTI/ca1_asym.p
deleted file mode 100644
index 42bd21dba471fa0e248f56b8db70afb83f309972..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/ca1_asym.p
+++ /dev/null
@@ -1,100 +0,0 @@
-// genesis
-// cell parameter file for the 1991 Traub CA1 hippocampal cell
-// "phi" parameter reduced by e-3
-*cartesian
-*relative
-
-*set_global RM 1.0 //ohm*m^2
-*set_global RA 1.0 //ohm*m
-*set_global CM 0.03 //F/m^2
-*set_global EREST_ACT -0.06 // volts
-
-// The format for each compartment parameter line is :
-// name parent x y z d ch dens ...
-// For channels, "dens" = maximum conductance per unit area of compartment
-
-/* NOTE: The format of the cell descriptor files does not allow for
- continuation to another line. The following long line lists the
- soma channels with their "density" parameters.
-
- Ca_conc -17.402e12
- Not really a channel, but a "Ca_concen" object. Normally, the B
- field is set to "dens"/compt_volume (m^3), but the negative sign
- causes the absolute value to be used with no scaling by volume.
- Na 300
- Ca 40
- K_DR 150
- K_AHP 8
- K_C 100
- K_A 50
-*/
-
-basal_3 none 0 220 0 3.84 Ca_conc 8.96e-3 Ca 50 K_AHP 8 K_C 50
-basal_5 . 0 220 0 3.84 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50
-basal_6 . 0 220 0 3.84 Ca_conc 8.96e-3 Na 200 Ca 120 K_DR 200 K_AHP 8 K_C 100
-basal_8 . 0 110 0 3.84 Ca_conc -34.53e12 Na 150 Ca 80 K_DR 100 K_AHP 8 K_C 200
-
-soma basal_8 0 125 0 8.46 Ca_conc -17.402e12 Na 300 Ca 40 K_DR 250 K_AHP 8 K_C 100 K_A 50
-
-
-apical_10 soma 0 120 0 4.0 Ca_conc -26.404e12 Na 150 Ca 80 K_DR 100 K_AHP 8 K_C 200 glu 700 NMDA 200
-apical_11 apical_10 0 120 0 3 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 80 K_DR 60 K_A 100 glu 700 NMDA 200
-apical_12 apical_11 0 120 0 3 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 60 K_DR 60 K_A 100 glu 700 NMDA 200
-apical_13 apical_12 0 120 0 2.6 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 50 K_DR 60 K_A 100 glu 700 NMDA 200
-apical_14 apical_13 0 120 0 2.6 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-apical_15 apical_14 0 120 0 2.6 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-apical_16 apical_15 0 120 0 2.6 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-apical_17 apical_16 0 120 0 2.6 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-apical_18 apical_17 0 120 0 2.6 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-apical_19 apical_18 0 120 0 2.6 Ca_conc 8.96e-3
-
-lat_11_1 apical_10 -60 60 0 2 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 80 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_11_2 lat_11_1 -60 60 0 1.8 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_11_3 lat_11_2 0 80 0 1.5 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_11_4 lat_11_3 0 80 0 1.5 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-
-lat_13_1 apical_12 40 40 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_13_2 lat_13_1 40 40 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-
-lat_14_1 lat_13_2 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_2 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_3 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_4 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_5 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_6 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_7 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_8 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_9 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_10 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_11 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_12 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_14_13 . 0 10 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_15_1 . 0 30 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-lat_15_2 . 0 60 0 1.0 Ca_conc 8.96e-3 Ca 70 K_AHP 8 K_C 50 Na 40 K_DR 60 K_A 100 glu 700 NMDA 200
-
-spine_neck_14_1 lat_14_1 0.5 0 0 0.1
-spine_head_14_1 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_2 lat_14_2 0.5 0 0 0.1
-spine_head_14_2 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_3 lat_14_3 0.5 0 0 0.1
-spine_head_14_3 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_4 lat_14_4 0.5 0 0 0.1
-spine_head_14_4 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_5 lat_14_5 0.5 0 0 0.1
-spine_head_14_5 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_6 lat_14_6 0.5 0 0 0.1
-spine_head_14_6 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_7 lat_14_7 0.5 0 0 0.1
-spine_head_14_7 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_8 lat_14_8 0.5 0 0 0.1
-spine_head_14_8 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_9 lat_14_9 0.5 0 0 0.1
-spine_head_14_9 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_10 lat_14_10 0.5 0 0 0.1
-spine_head_14_10 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_11 lat_14_11 0.5 0 0 0.1
-spine_head_14_11 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_12 lat_14_12 0.5 0 0 0.1
-spine_head_14_12 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
-spine_neck_14_13 lat_14_13 0.5 0 0 0.1
-spine_head_14_13 . 0.5 0 0 0.5 NMDA_Ca_conc 8.96e-3 glu 700 Ca_NMDA 20 NMDA 200 Ca 60
diff --git a/moose-examples/snippets/MULTI/diffonly.g b/moose-examples/snippets/MULTI/diffonly.g
deleted file mode 100644
index 9b485d79037bbd11e4a0991fc939804145292393..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/diffonly.g
+++ /dev/null
@@ -1,160 +0,0 @@
-//genesis
-// kkit Version 11 flat dumpfile
-
-// Saved on Tue Aug 27 21:53:07 2013
-
-include kkit {argv 1}
-
-FASTDT = 0.0001
-SIMDT = 0.01
-CONTROLDT = 5
-PLOTDT = 1
-MAXTIME = 100
-TRANSIENT_TIME = 2
-VARIABLE_DT_FLAG = 0
-DEFAULT_VOL = 1e-20
-VERSION = 11.0
-setfield /file/modpath value /home2/bhalla/scripts/modules
-kparms
-
-//genesis
-
-initdump -version 3 -ignoreorphans 1
-simobjdump doqcsinfo filename accessname accesstype transcriber developer \
- citation species tissue cellcompartment methodology sources \
- model_implementation model_validation x y z
-simobjdump table input output alloced step_mode stepsize x y z
-simobjdump xtree path script namemode sizescale
-simobjdump xcoredraw xmin xmax ymin ymax
-simobjdump xtext editable
-simobjdump xgraph xmin xmax ymin ymax overlay
-simobjdump xplot pixflags script fg ysquish do_slope wy
-simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
- link savename file version md5sum mod_save_flag x y z
-simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
- z
-simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
- geomname xtree_fg_req xtree_textfg_req x y z
-simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
-simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
- keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
-simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
- trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
-simobjdump xtab input output alloced step_mode stepsize notes editfunc \
- xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
-simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
- xtree_textfg_req x y z
-simobjdump transport input output alloced step_mode stepsize dt delay clock \
- kf xtree_fg_req xtree_textfg_req x y z
-simobjdump proto x y z
-simobjdump text str
-simundump geometry /kinetics/geometry 0 1e-18 3 sphere "" white black 2 -6 0
-simundump geometry /kinetics/geometry[1] 0 1e-19 3 sphere "" white black 0 -8 \
- 0
-simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black -3 \
- -6 0
-simundump geometry /kinetics/geometry[3] 0 1e-18 3 sphere "" white black 0 0 \
- 0
-simundump text /kinetics/notes 0 ""
-call /kinetics/notes LOAD \
-""
-simundump text /kinetics/geometry/notes 0 ""
-call /kinetics/geometry/notes LOAD \
-""
-simundump text /kinetics/geometry[1]/notes 0 ""
-call /kinetics/geometry[1]/notes LOAD \
-""
-simundump text /kinetics/geometry[2]/notes 0 ""
-call /kinetics/geometry[2]/notes LOAD \
-""
-simundump text /kinetics/geometry[3]/notes 0 ""
-call /kinetics/geometry[3]/notes LOAD \
-""
-simundump group /kinetics/DEND 0 yellow black x 0 0 "" DEND defaultfile.g 0 0 \
- 0 -3 -3 0
-simundump text /kinetics/DEND/notes 0 ""
-call /kinetics/DEND/notes LOAD \
-""
-simundump kpool /kinetics/DEND/Ca 0 1e-10 0.08 0.08 48 48 0 0 600 0 \
- /kinetics/geometry blue yellow -4 4 0
-simundump text /kinetics/DEND/Ca/notes 0 ""
-call /kinetics/DEND/Ca/notes LOAD \
-""
-simundump kpool /kinetics/DEND/Ca_CaM 0 1e-11 1 1 600 600 0 0 600 0 \
- /kinetics/geometry[3] blue yellow -2 -1 0
-simundump text /kinetics/DEND/Ca_CaM/notes 0 ""
-call /kinetics/DEND/Ca_CaM/notes LOAD \
-""
-simundump group /kinetics/SPINE 0 28 black x 0 0 "" SPINE defaultfile.g 0 0 0 \
- 0 -3 0
-simundump text /kinetics/SPINE/notes 0 ""
-call /kinetics/SPINE/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/Ca 0 1e-10 0.08 0.08 4.8 4.8 0 0 60 0 \
- /kinetics/geometry[1] blue 28 -2 4 0
-simundump text /kinetics/SPINE/Ca/notes 0 ""
-call /kinetics/SPINE/Ca/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaM 0 1e-11 5 5 300 300 0 0 60 0 \
- /kinetics/geometry[1] 55 28 -2 2 0
-simundump text /kinetics/SPINE/CaM/notes 0 ""
-call /kinetics/SPINE/CaM/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/Ca_CaM 0 1e-11 0 0 0 0 0 0 60 0 \
- /kinetics/geometry[1] blue 28 1 -1 0
-simundump text /kinetics/SPINE/Ca_CaM/notes 0 ""
-call /kinetics/SPINE/Ca_CaM/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/kreac 0 0.1 0.1 "" white 28 -1 0 0
-simundump text /kinetics/SPINE/kreac/notes 0 ""
-call /kinetics/SPINE/kreac/notes LOAD \
-""
-simundump group /kinetics/PSD 0 0 black x 0 0 "" PSD defaultfile.g 0 0 0 3 -3 \
- 0
-simundump text /kinetics/PSD/notes 0 ""
-call /kinetics/PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/Ca 0 1e-10 0.08 0.08 0.48 0.48 0 0 6 0 \
- /kinetics/geometry[2] blue 0 1 4 0
-simundump text /kinetics/PSD/Ca/notes 0 ""
-call /kinetics/PSD/Ca/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaM 0 1e-11 5 5 30 30 0 0 6 0 \
- /kinetics/geometry[2] 53 0 1 2 0
-simundump text /kinetics/PSD/CaM/notes 0 ""
-call /kinetics/PSD/CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/Ca_CaM 0 1e-11 0 0 0 0 0 0 6 0 \
- /kinetics/geometry[2] blue 0 4 -1 0
-simundump text /kinetics/PSD/Ca_CaM/notes 0 ""
-call /kinetics/PSD/Ca_CaM/notes LOAD \
-""
-simundump kreac /kinetics/PSD/kreac 0 0.1 0.1 "" white 0 2 0 0
-simundump text /kinetics/PSD/kreac/notes 0 ""
-call /kinetics/PSD/kreac/notes LOAD \
-""
-simundump xgraph /graphs/conc1 0 0 100 0 1 0
-simundump xgraph /graphs/conc2 0 0 100 0 1 0
-simundump xgraph /moregraphs/conc3 0 0 100 0 1 0
-simundump xgraph /moregraphs/conc4 0 0 100 0 1 0
-simundump xcoredraw /edit/draw 0 -6 6 -10 6
-simundump xtree /edit/draw/tree 0 \
- /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \
- "edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>" auto 0.6
-simundump xtext /file/notes 0 1
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/Ca REAC A B
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/CaM REAC A B
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/Ca_CaM REAC B A
-addmsg /kinetics/SPINE/Ca /kinetics/SPINE/kreac SUBSTRATE n
-addmsg /kinetics/SPINE/CaM /kinetics/SPINE/kreac SUBSTRATE n
-addmsg /kinetics/SPINE/Ca_CaM /kinetics/SPINE/kreac PRODUCT n
-addmsg /kinetics/PSD/kreac /kinetics/PSD/Ca REAC A B
-addmsg /kinetics/PSD/kreac /kinetics/PSD/CaM REAC A B
-addmsg /kinetics/PSD/kreac /kinetics/PSD/Ca_CaM REAC B A
-addmsg /kinetics/PSD/Ca /kinetics/PSD/kreac SUBSTRATE n
-addmsg /kinetics/PSD/CaM /kinetics/PSD/kreac SUBSTRATE n
-addmsg /kinetics/PSD/Ca_CaM /kinetics/PSD/kreac PRODUCT n
-enddump
-// End of dump
-
-complete_loading
diff --git a/moose-examples/snippets/MULTI/diffusionOnly.py b/moose-examples/snippets/MULTI/diffusionOnly.py
deleted file mode 100644
index 9797c50dc9b9e38fbc53cccecf0b39ed1d990586..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/diffusionOnly.py
+++ /dev/null
@@ -1,437 +0,0 @@
-# __DEPRECATED__ __BROKEN__
-# minimal.py ---
-# Upi Bhalla, NCBS Bangalore 2013.
-#
-# Commentary:
-#
-# Testing system for loading in arbitrary multiscale models based on
-# model definition files.
-# This version has a minimal model with Ca in all 3 compartments,
-# and CaM (just one step) in SPINE and PSD, with a nominal product Ca.CaM.
-# In this diffusionOnly version there is no reaction. To be more precise,
-# the loaded in minimal.g model has the Ca-binding reaction, but it is
-# deleted when the file is loaded in.
-# Incoming Ca from synaptic events comes to the PSD.
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-sys.path.append('../../python')
-import os
-os.environ['NUMPTHREADS'] = '1'
-import math
-
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "hsolve" )
- return cellId
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if ( moose.exists( objpath ) ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- moose.connect( tab, 'requestOut', obj, field )
-
-
-def dumpPlots( fname ):
- if ( os.path.exists( fname ) ):
- os.remove( fname )
- for x in moose.wildcardFind( '/graphs/#[ISA=Table]' ):
- moose.element( x[0] ).xplot( fname, x[0].name )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- moose.element( x[0] ).xplot( fname, x[0].name + '_e' )
-
-def moveCompt( path, oldParent, newParent ):
- meshEntries = moose.element( newParent.path + '/mesh' )
- # Set up vol messaging from new compts to all their child objects.
- for x in moose.wildcardFind( path + '/##[ISA=PoolBase]' ):
- moose.connect( meshEntries, 'mesh', x, 'mesh', 'OneToOne' )
- #print 'path = ', path, ', oldparent = ', oldParent.path
- orig = moose.element( path )
- moose.move( orig, newParent )
- moose.delete( moose.vec( oldParent.path ) )
- chem = moose.element( '/model/chem' )
- moose.move( newParent, chem )
-
-def loadChem( neuroCompt, spineCompt, psdCompt ):
- # We need the compartments to come in with a volume of 1 to match the
- # original CubeMesh.
- assert( neuroCompt.volume == 1.0 )
- assert( spineCompt.volume == 1.0 )
- assert( psdCompt.volume == 1.0 )
- assert( neuroCompt.mesh.num == 1 )
- print(('volume = ', neuroCompt.mesh[0].volume))
- #assert( neuroCompt.mesh[0].volume == 1.0 )
- #an unfortunate mismatch
- # So we'll have to resize the volumes of the current compartments to the
- # new ones.
-
- modelId = moose.loadModel( 'diffonly.g', '/model', 'ee' )
- #moose.le( '/model/model' )
- #moose.le( '/model/model/kinetics' )
- #moose.le( '/model/model/kinetics/PSD' )
- #moose.le( '/model/model/kinetics/SPINE' )
- moose.delete( moose.vec( '/model/model/kinetics/PSD/kreac' ) )
- moose.delete( moose.vec( '/model/model/kinetics/SPINE/kreac' ) )
- #moose.le( '/model/model/kinetics/PSD' )
- #moose.le( '/model/model/kinetics/SPINE' )
- pCaCaM = moose.element( '/model/model/kinetics/PSD/Ca_CaM' )
- pCaCaM.concInit = 0.001
- dCaCaM = moose.element( '/model/model/kinetics/PSD/Ca_CaM' )
- sCaCaM = moose.element( '/model/model/kinetics/SPINE/Ca_CaM' )
- print(("CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit))
- #moose.delete( moose.vec( '/model/model/kinetics/SPINE/Ca_CaM' ) )
- #CaCaM2 = moose.element( '/model/model/kinetics/SPINE/Ca_CaM' )
- #CaCaM2.concInit = 0.001
- chem = moose.element( '/model/model' )
- chem.name = 'chem'
- oldS = moose.element( '/model/chem/compartment_1' )
- oldP = moose.element( '/model/chem/compartment_2' )
- oldN = moose.element( '/model/chem/kinetics' )
- print(('oldvols[p,s,d] = ', oldP.volume, oldS.volume, oldN.volume))
- print(('newvols[p,s,d] = ', psdCompt.mesh[0].volume, spineCompt.mesh[0].volume, neuroCompt.mesh[0].volume))
- oldN.volume = neuroCompt.mesh[0].volume
- oldS.volume = spineCompt.mesh[0].volume
- oldP.volume = psdCompt.mesh[0].volume
- print('after redoing vols')
- print(("CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit))
- moveCompt( '/model/chem/kinetics/SPINE', oldS, spineCompt )
- moveCompt( '/model/chem/kinetics/PSD', oldP, psdCompt )
- # Need to do the DEND last because the oldN is /kinetics,
- # and it will be deleted.
- moveCompt( '/model/chem/kinetics/DEND', oldN, neuroCompt )
- print('after moving to new compts')
- print(("CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit))
-
-def makeNeuroMeshModel():
- diffLength = 20e-6 # But we only want diffusion over part of the model.
- numSyn = 13
- elec = loadElec()
- synInput = moose.SpikeGen( '/model/elec/synInput' )
- synInput.refractT = 47e-3
- synInput.threshold = -1.0
- synInput.edgeTriggered = 0
- synInput.Vm( 0 )
-
- synInput.refractT = 47e-3
- for i in range( numSyn ):
- name = '/model/elec/spine_head_14_' + str( i + 1 )
- r = moose.element( name + '/glu' )
- r.synapse.num = 1
- syn = moose.element( r.path + '/synapse' )
- moose.connect( synInput, 'spikeOut', syn, 'addSpike', 'Single' )
- syn.weight = 0.2 * i * ( numSyn - 1 - i )
- syn.delay = i * 1.0e-3
-
- neuroCompt = moose.NeuroMesh( '/model/neuroMesh' )
- #print 'neuroMeshvolume = ', neuroCompt.mesh[0].volume
- neuroCompt.separateSpines = 1
- neuroCompt.diffLength = diffLength
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/spineMesh' )
- #print 'spineMeshvolume = ', spineCompt.mesh[0].volume
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/psdMesh' )
- #print 'psdMeshvolume = ', psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- loadChem( neuroCompt, spineCompt, psdCompt )
-
- # Put in the solvers, see how they fare.
- nmksolve = moose.GslStoich( '/model/chem/neuroMesh/ksolve' )
- nmksolve.path = '/model/chem/neuroMesh/##'
- nmksolve.compartment = moose.element( '/model/chem/neuroMesh' )
- nmksolve.method = 'rk5'
- nm = moose.element( '/model/chem/neuroMesh/mesh' )
- moose.connect( nm, 'remesh', nmksolve, 'remesh' )
- #print "neuron: nv=", nmksolve.numLocalVoxels, ", nav=", nmksolve.numAllVoxels, nmksolve.numVarPools, nmksolve.numAllPools
-
- #print 'setting up smksolve'
- smksolve = moose.GslStoich( '/model/chem/spineMesh/ksolve' )
- smksolve.path = '/model/chem/spineMesh/##'
- smksolve.compartment = moose.element( '/model/chem/spineMesh' )
- smksolve.method = 'rk5'
- sm = moose.element( '/model/chem/spineMesh/mesh' )
- moose.connect( sm, 'remesh', smksolve, 'remesh' )
- #print "spine: nv=", smksolve.numLocalVoxels, ", nav=", smksolve.numAllVoxels, smksolve.numVarPools, smksolve.numAllPools
- #
- #print 'setting up pmksolve'
- pmksolve = moose.GslStoich( '/model/chem/psdMesh/ksolve' )
- pmksolve.path = '/model/chem/psdMesh/##'
- pmksolve.compartment = moose.element( '/model/chem/psdMesh' )
- pmksolve.method = 'rk5'
- pm = moose.element( '/model/chem/psdMesh/mesh' )
- moose.connect( pm, 'remesh', pmksolve, 'remesh' )
- #print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools
- #
- print(('neuroMeshvolume = ', neuroCompt.mesh[0].volume))
-
- #print 'Assigning the cell model'
- # Now to set up the model.
- #neuroCompt.cell = elec
- neuroCompt.cellPortion( elec, '/model/elec/lat_14_#,/model/elec/spine_neck#,/model/elec/spine_head#' )
- """
- ns = neuroCompt.numSegments
- #assert( ns == 11 ) # dend, 5x (shaft+head)
- ndc = neuroCompt.numDiffCompts
- #print 'numDiffCompts = ', ndc
- assert( ndc == 145 )
- ndc = neuroCompt.mesh.num
- #print 'NeuroMeshNum = ', ndc
- assert( ndc == 145 )
-
- sdc = spineCompt.mesh.num
- #print 'SpineMeshNum = ', sdc
- assert( sdc == 13 )
- pdc = psdCompt.mesh.num
- #print 'PsdMeshNum = ', pdc
- assert( pdc == 13 )
- """
-
- mesh = moose.vec( '/model/chem/neuroMesh/mesh' )
- #for i in range( ndc ):
- # print 's[', i, '] = ', mesh[i].volume
- mesh2 = moose.vec( '/model/chem/spineMesh/mesh' )
-# for i in range( sdc ):
-# print 's[', i, '] = ', mesh2[i].volume
- #print 'numPSD = ', moose.element( '/model/chem/psdMesh/mesh' ).localNumField
- mesh = moose.vec( '/model/chem/psdMesh/mesh' )
- #print 'psd mesh.volume = ', mesh.volume
- #for i in range( pdc ):
- # print 's[', i, '] = ', mesh[i].volume
- #
- # We need to use the spine solver as the master for the purposes of
- # these calculations. This will handle the diffusion calculations
- # between head and dendrite, and between head and PSD.
- smksolve.addJunction( nmksolve )
- #print "spine: nv=", smksolve.numLocalVoxels, ", nav=", smksolve.numAllVoxels, smksolve.numVarPools, smksolve.numAllPools
- smksolve.addJunction( pmksolve )
- #print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools
- ndc = neuroCompt.numDiffCompts
- #print 'numDiffCompts = ', ndc
- assert( ndc == 13 )
- ndc = neuroCompt.mesh.num
- #print 'NeuroMeshNum = ', ndc
- assert( ndc == 13 )
- sdc = spineCompt.mesh.num
- #print 'SpineMeshNum = ', sdc
- assert( sdc == 13 )
- pdc = psdCompt.mesh.num
- #print 'PsdMeshNum = ', pdc
- assert( pdc == 13 )
-
- """
- print 'neuroCompt'
- for i in range( ndc ):
- print i, neuroCompt.stencilIndex[i]
- print i, neuroCompt.stencilRate[i]
-
- print 'spineCompt'
- for i in range( sdc * 3 ):
- print i, spineCompt.stencilIndex[i]
- print i, spineCompt.stencilRate[i]
-
- print 'psdCompt'
- for i in range( pdc ):
- print i, psdCompt.stencilIndex[i]
- print i, psdCompt.stencilRate[i]
- print 'Spine parents:'
- pavoxel = spineCompt.parentVoxel
- for i in range( sdc ):
- print i, pavoxel[i]
- """
-
- # oddly, numLocalFields does not work.
- #moose.le( '/model/chem/neuroMesh' )
- ca = moose.element( '/model/chem/neuroMesh/DEND/Ca' )
- assert( ca.lastDimension == ndc )
- """
- CaNpsd = moose.vec( '/model/chem/psdMesh/PSD/PP1_PSD/CaN' )
- print 'numCaN in PSD = ', CaNpsd.nInit, ', vol = ', CaNpsd.volume
- CaNspine = moose.vec( '/model/chem/spineMesh/SPINE/CaN_BULK/CaN' )
- print 'numCaN in spine = ', CaNspine.nInit, ', vol = ', CaNspine.volume
- """
-
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/psdMesh/adaptCa', pdc )
- adaptCa = moose.vec( '/model/chem/psdMesh/adaptCa' )
- chemCa = moose.vec( '/model/chem/psdMesh/PSD/Ca' )
- assert( len( adaptCa ) == pdc )
- assert( len( chemCa ) == pdc )
- for i in range( pdc ):
- path = '/model/elec/spine_head_14_' + str( i + 1 ) + '/NMDA_Ca_conc'
- elecCa = moose.element( path )
- moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
- moose.connect( adaptCa, 'outputSrc', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 80e-6 # 80 nM offset in chem.
- adaptCa.scale = 1e-5 # 520 to 0.0052 mM
- #print adaptCa.outputOffset
- #print adaptCa.scale
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'elec/somaCa' )
- addPlot( '/model/elec/basal_3', 'getVm', 'elec/basal3Vm' )
- addPlot( '/model/elec/apical_14', 'getVm', 'elec/apical_14Vm' )
- addPlot( '/model/elec/apical_14/Ca_conc', 'getCa', 'elec/apical_14Ca' )
- addPlot( '/model/elec/spine_head_14_7', 'getVm', 'elec/spine_7Vm' )
- addPlot( '/model/elec/spine_head_14_7/NMDA_Ca_conc', 'getCa', 'elec/spine_7Ca' )
- addPlot( '/model/elec/spine_head_14_13/NMDA_Ca_conc', 'getCa', 'elec/spine_13Ca' )
-
-def makeChemPlots():
- spineMesh = moose.element( '/model/chem/spineMesh' )
- middleSpine = 6
- midSpineVoxel = spineMesh.parentVoxel[middleSpine]
- graphs = moose.Neutral( '/graphs' )
- addPlot( '/model/chem/psdMesh/PSD/Ca[0]', 'getConc', 'pCa0' )
- addPlot( '/model/chem/psdMesh/PSD/Ca[6]', 'getConc', 'pCa6' )
- addPlot( '/model/chem/psdMesh/PSD/Ca[12]', 'getConc', 'pCa12' )
-
- addPlot( '/model/chem/spineMesh/SPINE/Ca[0]', 'getConc', 'sCa0' )
- addPlot( '/model/chem/spineMesh/SPINE/Ca[6]', 'getConc', 'sCa6' )
- addPlot( '/model/chem/spineMesh/SPINE/Ca[12]', 'getConc', 'sCa12' )
-
- addPlot( '/model/chem/neuroMesh/DEND/Ca[0]', 'getConc', 'dend0Ca' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca[' + str( midSpineVoxel ) + ']', 'getConc', 'dendMidCa' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca[' + str( midSpineVoxel+2 ) + ']', 'getConc', 'dendMid2' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca[' + str( midSpineVoxel+4 ) + ']', 'getConc', 'dendMid4' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca[' + str( midSpineVoxel+6 ) + ']', 'getConc', 'dendMid6' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca[144]', 'getConc', 'dend144Ca' )
-
- addPlot( '/model/chem/psdMesh/PSD/CaM[0]', 'getConc', 'pCaM0' )
- addPlot( '/model/chem/psdMesh/PSD/CaM[6]', 'getConc', 'pCaM6' )
- addPlot( '/model/chem/psdMesh/PSD/CaM[12]', 'getConc', 'pCaM12' )
-
- addPlot( '/model/chem/spineMesh/SPINE/CaM[0]', 'getConc', 'sCaM0' )
- addPlot( '/model/chem/spineMesh/SPINE/CaM[6]', 'getConc', 'sCaM6' )
- addPlot( '/model/chem/spineMesh/SPINE/CaM[12]', 'getConc', 'sCaM12' )
-
- addPlot( '/model/chem/psdMesh/PSD/Ca_CaM[0]', 'getConc', 'pCaCaM0' )
- addPlot( '/model/chem/psdMesh/PSD/Ca_CaM[6]', 'getConc', 'pCaCaM6' )
- addPlot( '/model/chem/psdMesh/PSD/Ca_CaM[12]', 'getConc', 'pCaCaM12' )
-
- addPlot( '/model/chem/spineMesh/SPINE/Ca_CaM[0]', 'getConc', 'sCaCaM0' )
- addPlot( '/model/chem/spineMesh/SPINE/Ca_CaM[6]', 'getConc', 'sCaCaM6' )
- addPlot( '/model/chem/spineMesh/SPINE/Ca_CaM[12]', 'getConc', 'sCaCaM12' )
-
- addPlot( '/model/chem/neuroMesh/DEND/Ca_CaM[0]', 'getConc', 'dCaCaM0' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca_CaM[' + str( midSpineVoxel ) + ']', 'getConc', 'dendMidCaCaM' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca_CaM[144]', 'getConc', 'dCaCaM144' )
-
-def testNeuroMeshMultiscale():
- elecDt = 50e-6
- chemDt = 1e-4
- plotDt = 5e-4
- plotName = 'diffonly.plot'
-
- makeNeuroMeshModel()
- """
- for i in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if ( i[0].diffConst > 0 ):
- grandpaname = i.parent[0].parent.name + '/'
- paname = i.parent[0].name + '/'
- print grandpaname + paname + i[0].name, i[0].diffConst
- moose.le( '/model/chem/spineMesh/ksolve' )
- print 'Neighbors:'
- for t in moose.element( '/model/chem/spineMesh/ksolve/junction' ).neighbors['masterJunction']:
- print 'masterJunction <-', t.path
- for t in moose.wildcardFind( '/model/chem/#Mesh/ksolve' ):
- k = moose.element( t[0] )
- print k.path + ' localVoxels=', k.numLocalVoxels, ', allVoxels= ', k.numAllVoxels
- """
-
- makeChemPlots()
- makeElecPlots()
- moose.setClock( 0, elecDt )
- moose.setClock( 1, elecDt )
- moose.setClock( 2, elecDt )
- moose.setClock( 5, chemDt )
- moose.setClock( 6, chemDt )
- moose.setClock( 7, plotDt )
- moose.setClock( 8, plotDt )
- moose.useClock( 0, '/model/elec/##[ISA=Compartment]', 'init' )
- moose.useClock( 1, '/model/elec/##[ISA=SpikeGen]', 'process' )
- moose.useClock( 2, '/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
- moose.useClock( 5, '/model/chem/##[ISA=PoolBase],/model/##[ISA=ReacBase],/model/##[ISA=EnzBase]', 'process' )
- moose.useClock( 6, '/model/chem/##[ISA=Adaptor]', 'process' )
- moose.useClock( 7, '/graphs/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#', 'process' )
- moose.useClock( 5, '/model/chem/#Mesh/ksolve', 'init' )
- moose.useClock( 6, '/model/chem/#Mesh/ksolve', 'process' )
- hsolve = moose.HSolve( '/model/elec/hsolve' )
- moose.useClock( 1, '/model/elec/hsolve', 'process' )
- hsolve.dt = elecDt
- hsolve.target = '/model/elec/compt'
- moose.reinit()
- moose.reinit()
- """
- print 'pre'
- eca = moose.vec( '/model/chem/psdMesh/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'dend'
- eca = moose.vec( '/model/chem/neuroMesh/DEND/Ca' )
- for i in ( 0, 1, 2, 30, 60, 90, 120, 144 ):
- print i, eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
-
- print 'PSD'
- eca = moose.vec( '/model/chem/psdMesh/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'spine'
- eca = moose.vec( '/model/chem/spineMesh/SPINE/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- """
-
- moose.start( 0.5 )
- dumpPlots( plotName )
- print('All done')
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# loadMulti.py ends here.
diff --git a/moose-examples/snippets/MULTI/loadMulti.py b/moose-examples/snippets/MULTI/loadMulti.py
deleted file mode 100644
index 128acd3b4aa8aff8ca88cae654e9663848ebc3cc..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/loadMulti.py
+++ /dev/null
@@ -1,371 +0,0 @@
-# __DEPRECATED__ __BROKEN__
-# loadMulti.py ---
-# Upi Bhalla, NCBS Bangalore 2013.
-#
-# Commentary:
-#
-# Testing system for loading in arbirary multiscale models based on
-# model definition files.
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-import os
-import math
-
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "Neutral" )
- return cellId
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if moose.exists( objpath ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- if obj.className == 'Neutral':
- print(("addPlot failed: object is a Neutral: ", objpath))
- return moose.element( '/' )
- else:
- #print "object was found: ", objpath, obj.className
- moose.connect( tab, 'requestOut', obj, field )
- return tab
- else:
- print(("addPlot failed: object not found: ", objpath))
- return moose.element( '/' )
-
-def dumpPlots( fname ):
- if ( os.path.exists( fname ) ):
- os.remove( fname )
- for x in moose.wildcardFind( '/graphs/#[ISA=Table]' ):
- moose.element( x[0] ).xplot( fname, x[0].name )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- moose.element( x[0] ).xplot( fname, x[0].name + '_e' )
-
-def loadChem( diffLength ):
- chem = moose.Neutral( '/model/chem' )
- neuroCompt = moose.NeuroMesh( '/model/chem/kinetics' )
- neuroCompt.separateSpines = 1
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/chem/compartment_1' )
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/chem/compartment_2' )
- #print 'Meshvolume[neuro, spine, psd] = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- modelId = moose.loadModel( 'psd_merged31d.g', '/model/chem', 'ee' )
- neuroCompt.name = 'dend'
- spineCompt.name = 'spine'
- psdCompt.name = 'psd'
-
-
-def makeNeuroMeshModel():
- diffLength = 10e-6 # But we only want diffusion over part of the model.
- numSyn = 13
- elec = loadElec()
- synInput = moose.SpikeGen( '/model/elec/synInput' )
- synInput.threshold = -1.0
- synInput.edgeTriggered = 0
- synInput.Vm( 0 )
- synInput.refractT = 47e-3
-
- for i in range( numSyn ):
- name = '/model/elec/spine_head_14_' + str( i + 1 )
- r = moose.element( name + '/glu' )
- r.synapse.num = 1
- syn = moose.element( r.path + '/synapse' )
- moose.connect( synInput, 'spikeOut', syn, 'addSpike', 'Single' )
- syn.weight = 0.2 * i * ( numSyn - 1 - i )
- syn.delay = i * 1.0e-3
-
- loadChem( diffLength )
- neuroCompt = moose.element( '/model/chem/dend' )
- neuroCompt.diffLength = diffLength
- neuroCompt.cellPortion( elec, '/model/elec/#' )
- for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if (x.diffConst > 0):
- x.diffConst = 1e-11
- for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- x.diffConst = 1e-10
-
- # Put in dend solvers
- ns = neuroCompt.numSegments
- ndc = neuroCompt.numDiffCompts
- print(('ns = ', ns, ', ndc = ', ndc))
- assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
- assert( ns == 36 ) # dend, 5x (shaft+head)
- assert( ndc == 278 )
- nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
- nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
- nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
- nmstoich.compartment = neuroCompt
- nmstoich.ksolve = nmksolve
- nmstoich.dsolve = nmdsolve
- nmstoich.path = "/model/chem/dend/##"
- print(('done setting path, numPools = ', nmdsolve.numPools))
- assert( nmdsolve.numPools == 1 )
- # oddly, numLocalFields does not work.
- ca = moose.element( '/model/chem/dend/DEND/Ca' )
- assert( ca.numData == ndc )
-
- # Put in spine solvers. Note that these get info from the neuroCompt
- spineCompt = moose.element( '/model/chem/spine' )
- sdc = spineCompt.mesh.num
- print(('sdc = ', sdc))
- assert( sdc == 13 )
- smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
- smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
- smstoich = moose.Stoich( '/model/chem/spine/stoich' )
- smstoich.compartment = spineCompt
- smstoich.ksolve = smksolve
- smstoich.dsolve = smdsolve
- smstoich.path = "/model/chem/spine/##"
- assert( smstoich.numAllPools == 36 )
-
- # Put in PSD solvers. Note that these get info from the neuroCompt
- psdCompt = moose.element( '/model/chem/psd' )
- pdc = psdCompt.mesh.num
- assert( pdc == 13 )
- pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
- pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
- pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
- pmstoich.compartment = psdCompt
- pmstoich.ksolve = pmksolve
- pmstoich.dsolve = pmdsolve
- pmstoich.path = "/model/chem/psd/##"
- print(('numAllPools = ', pmstoich.numAllPools))
- assert( pmstoich.numAllPools == 56 )
- foo = moose.element( '/model/chem/psd/Ca' )
- bar = moose.element( '/model/chem/psd/I1_p' )
- print(('PSD: numfoo = ', foo.numData, 'numbar = ', bar.numData))
- print(('PSD: numAllVoxels = ', pmksolve.numAllVoxels))
-
- # Put in junctions between diffusion solvers
- nmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
-
- """
- CaNpsd = moose.vec( '/model/chem/psdMesh/PSD/PP1_PSD/CaN' )
- print 'numCaN in PSD = ', CaNpsd.nInit, ', vol = ', CaNpsd.volume
- CaNspine = moose.vec( '/model/chem/spine/SPINE/CaN_BULK/CaN' )
- print 'numCaN in spine = ', CaNspine.nInit, ', vol = ', CaNspine.volume
- """
-
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/psd/adaptCa', pdc )
- adaptCa = moose.vec( '/model/chem/psd/adaptCa' )
- chemCa = moose.vec( '/model/chem/psd/Ca' )
- print( 'aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = "
- , len( chemCa ), ", numData = ", chemCa.numData
- )
- assert( len( adaptCa ) == pdc )
- assert( len( chemCa ) == pdc )
- for i in range( pdc ):
- path = '/model/elec/spine_head_14_' + str( i + 1 ) + '/NMDA_Ca_conc'
- elecCa = moose.element( path )
- moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
- moose.connect( adaptCa, 'output', chemCa, 'setConc', 'OneToOne' )
- adaptCa[i].inputOffset = 0.0 #
- adaptCa[i].outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa[i].scale = 1e-5 # 520 to 0.0052 mM
-
- """
- aGluR = moose.Adaptor( '/model/chem/psd/adaptGluR', 5 )
- adaptGluR = moose.vec( '/model/chem/psd/adaptGluR' )
- chemR = moose.vec( '/model/chem/psd/psdGluR' )
- assert( len( adaptGluR ) == 5 )
- for i in range( 5 ):
- path = '/model/elec/head' + str( i ) + '/gluR'
- elecR = moose.element( path )
- moose.connect( adaptGluR[i], 'outputSrc', elecR, 'setGbar', 'Single' )
- #moose.connect( chemR, 'nOut', adaptGluR, 'input', 'OneToOne' )
- # Ksolve isn't sending nOut. Not good. So have to use requestOut.
- moose.connect( adaptGluR, 'requestOut', chemR, 'getN', 'OneToOne' )
- adaptGluR.outputOffset = 1e-7 # pS
- adaptGluR.scale = 1e-6 / 100 # from n to pS
-
- adaptK = moose.Adaptor( '/model/chem/dend/adaptK' )
- chemK = moose.element( '/model/chem/dend/kChan' )
- elecK = moose.element( '/model/elec/compt/K' )
- moose.connect( adaptK, 'requestOut', chemK, 'getConc', 'OneToAll' )
- moose.connect( adaptK, 'outputSrc', elecK, 'setGbar', 'Single' )
- adaptK.scale = 0.3 # from mM to Siemens
- """
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'elec/somaCa' )
- addPlot( '/model/elec/basal_3', 'getVm', 'elec/basal3Vm' )
- addPlot( '/model/elec/apical_14', 'getVm', 'elec/apical_14Vm' )
- addPlot( '/model/elec/apical_14/Ca_conc', 'getCa', 'elec/apical_14Ca' )
- addPlot( '/model/elec/spine_head_14_7', 'getVm', 'elec/spine_7Vm' )
- addPlot( '/model/elec/spine_head_14_7/NMDA_Ca_conc', 'getCa', 'elec/spine_7Ca' )
- addPlot( '/model/elec/spine_head_14_13/NMDA_Ca_conc', 'getCa', 'elec/spine_13Ca' )
-
-def makeChemPlots():
- spineMesh = moose.element( '/model/chem/spine' )
- middleSpine = 6
- # handy lookup function to find which voxel # the spine is on.
- midSpineVoxel = spineMesh.parentVoxel[middleSpine]
- print((spineMesh.parentVoxel))
- graphs = moose.Neutral( '/graphs' )
- addPlot( '/model/chem/psd/tot_PSD_R[0]', 'getN', 'psd0R' )
- addPlot( '/model/chem/psd/tot_PSD_R[1]', 'getN', 'psd1R' )
- addPlot( '/model/chem/psd/tot_PSD_R[2]', 'getN', 'psd2R' )
- addPlot( '/model/chem/psd/CaM_dash_Ca4[0]', 'getConc', 'psdCaM0' )
- addPlot( '/model/chem/psd/CaM_dash_Ca4[6]', 'getConc', 'psdCaM6' )
- addPlot( '/model/chem/psd/CaM_CaN[0]', 'getConc', 'CaM_CaN' )
- addPlot( '/model/chem/psd/PP1_dash_active[0]', 'getConc', 'PP1_active0' )
- addPlot( '/model/chem/psd/PP1_dash_active[6]', 'getConc', 'psdPP1_active6' )
- addPlot( '/model/chem/psd/actCaMKII[6]', 'getConc', 'psdCaMKII6' )
- addPlot( '/model/chem/spine/actCaMKII[6]', 'getConc', 'spineCaMKII6' )
- addPlot( '/model/chem/psd/Ca[0]', 'getConc', 'psd0Ca' )
- addPlot( '/model/chem/psd/Ca[6]', 'getConc', 'psd6Ca' )
- addPlot( '/model/chem/psd/Ca[12]', 'getConc', 'psd12Ca' )
-
- addPlot( '/model/chem/spine/Ca[0]', 'getConc', 'spine0Ca' )
- addPlot( '/model/chem/spine/Ca[6]', 'getConc', 'spine6Ca' )
- addPlot( '/model/chem/spine/Ca[12]', 'getConc', 'spine12Ca' )
-
- addPlot( '/model/chem/dend/DEND/Ca[0]', 'getConc', 'dend0Ca' )
- path = '/model/chem/dend/DEND/Ca['
- addPlot( path + str( midSpineVoxel ) + ']', 'getConc', 'dendMidCa' )
- addPlot( path + str( midSpineVoxel+2 ) + ']', 'getConc', 'dendMid2Ca' )
- addPlot( path + str( midSpineVoxel+4 ) + ']', 'getConc', 'dendMid4Ca' )
- addPlot( path + str( midSpineVoxel+6 ) + ']', 'getConc', 'dendMid6Ca' )
- addPlot( '/model/chem/dend/DEND/Ca[144]', 'getConc', 'dend144Ca' )
-
- #addPlot( '/n/dend/Ca', 'getConc', 'dendCa' )
- #addPlot( '/n/dend/inact_kinase', 'getConc', 'inactDendKinase' )
- #addPlot( '/n/psd/psdGluR', 'getN', 'psdGluR' )
- addPlot( '/model/chem/psd/CaMKII_dash_CaM[6]', 'getConc', 'psdCaM_CaMKII6' )
- addPlot( '/model/chem/spine/CaMKII_dash_CaM[6]', 'getConc', 'spineCaM_CaMKII6' )
- addPlot( '/model/chem/spine/NMDAR[6]', 'getConc', 'psd_NMDAR6' )
-
-
-def testNeuroMeshMultiscale():
- elecDt = 50e-6
- chemDt = 1e-2
- cplotDt = 1e-2
- eplotDt = 1e-3
- plotName = 'nm.plot'
-
- makeNeuroMeshModel()
- print("after model is completely done")
- for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ):
- print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
-
- """
- for i in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if ( i[0].diffConst > 0 ):
- grandpaname = i.parent[0].parent.name + '/'
- paname = i.parent[0].name + '/'
- print grandpaname + paname + i[0].name, i[0].diffConst
- print 'Neighbors:'
- for t in moose.element( '/model/chem/spine/ksolve/junction' ).neighbors['masterJunction']:
- print 'masterJunction <-', t.path
- for t in moose.wildcardFind( '/model/chem/#/ksolve' ):
- k = moose.element( t[0] )
- print k.path + ' localVoxels=', k.numLocalVoxels, ', allVoxels= ', k.numAllVoxels
- """
- """
- moose.useClock( 4, '/model/chem/dend/dsolve', 'process' )
- moose.useClock( 5, '/model/chem/dend/ksolve', 'process' )
- moose.useClock( 5, '/model/chem/spine/ksolve', 'process' )
- moose.useClock( 5, '/model/chem/psd/ksolve', 'process' )
- """
-
- makeChemPlots()
- makeElecPlots()
- moose.setClock( 0, elecDt )
- moose.setClock( 1, elecDt )
- moose.setClock( 2, elecDt )
- moose.setClock( 4, chemDt )
- moose.setClock( 5, chemDt )
- moose.setClock( 6, chemDt )
- moose.setClock( 7, cplotDt )
- moose.setClock( 8, eplotDt )
- moose.useClock( 0, '/model/elec/##[ISA=Compartment]', 'init' )
- moose.useClock( 1, '/model/elec/##[ISA=Compartment]', 'process' )
- moose.useClock( 1, '/model/elec/##[ISA=SpikeGen]', 'process' )
- moose.useClock( 2, '/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
- moose.useClock( 4, '/model/chem/#/dsolve', 'process' )
- moose.useClock( 5, '/model/chem/#/ksolve', 'process' )
- moose.useClock( 6, '/model/chem/psd/adaptCa', 'process' )
- moose.useClock( 7, '/graphs/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#', 'process' )
- #hsolve = moose.HSolve( '/model/elec/hsolve' )
- #moose.useClock( 1, '/model/elec/hsolve', 'process' )
- #hsolve.dt = elecDt
- #hsolve.target = '/model/elec/compt'
- #moose.reinit()
- moose.reinit()
- """
- print 'pre'
- eca = moose.vec( '/model/chem/psd/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'dend'
- eca = moose.vec( '/model/chem/dend/DEND/Ca' )
- #for i in ( 0, 1, 2, 30, 60, 90, 120, 144 ):
- for i in range( 13 ):
- print i, eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
-
- print 'PSD'
- eca = moose.vec( '/model/chem/psd/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'spine'
- eca = moose.vec( '/model/chem/spine/SPINE/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- """
-
- moose.start( 0.5 )
- dumpPlots( plotName )
- print('All done')
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# loadMulti.py ends here.
diff --git a/moose-examples/snippets/MULTI/midchan.py b/moose-examples/snippets/MULTI/midchan.py
deleted file mode 100644
index af26757d85ccb6d0b229a191deef18363726c4a7..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/midchan.py
+++ /dev/null
@@ -1,318 +0,0 @@
-# midchan.py ---
-# Upi Bhalla, NCBS Bangalore 2014.
-#
-# Commentary:
-#
-# This loads in a medium-detail model incorporating
-# reac-diff and elec signaling in neurons. The reac-diff model
-# has just Ca and CaM in it, and there are no-cross-compartment
-# reactions though Ca diffuses everywhere. The elec model controls the
-# Ca levels in the chem compartments.
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-sys.path.append('../../python')
-import os
-os.environ['NUMPTHREADS'] = '1'
-import math
-import numpy
-import matplotlib.pyplot as plt
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- moose.setCwe( '/library' )
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "Neutral" )
- return cellId
-
-def loadChem( diffLength ):
- chem = moose.Neutral( '/model/chem' )
- neuroCompt = moose.NeuroMesh( '/model/chem/kinetics' )
- neuroCompt.separateSpines = 1
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/chem/compartment_1' )
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/chem/compartment_2' )
- #print 'Meshvolume[neuro, spine, psd] = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- modelId = moose.loadModel( 'minimal.g', '/model/chem', 'ee' )
- #modelId = moose.loadModel( 'psd_merged31d.g', '/model/chem', 'ee' )
- neuroCompt.name = 'dend'
- spineCompt.name = 'spine'
- psdCompt.name = 'psd'
-
-def makeNeuroMeshModel():
- diffLength = 10e-6 # Aim for 2 soma compartments.
- elec = loadElec()
- loadChem( diffLength )
- neuroCompt = moose.element( '/model/chem/dend' )
- neuroCompt.diffLength = diffLength
- neuroCompt.cellPortion( elec, '/model/elec/#' )
- for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if (x.diffConst > 0):
- x.diffConst = 1e-11
- for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- x.diffConst = 1e-10
-
- # Put in dend solvers
- ns = neuroCompt.numSegments
- ndc = neuroCompt.numDiffCompts
- print(('ns = ', ns, ', ndc = ', ndc))
- assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
- assert( ns == 36 ) #
- assert( ndc == 278 ) #
- nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
- nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
- nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
- nmstoich.compartment = neuroCompt
- nmstoich.ksolve = nmksolve
- nmstoich.dsolve = nmdsolve
- nmstoich.path = "/model/chem/dend/##"
- print(('done setting path, numPools = ', nmdsolve.numPools))
- assert( nmdsolve.numPools == 1 )
- assert( nmdsolve.numAllVoxels == ndc )
- assert( nmstoich.numAllPools == 1 )
- # oddly, numLocalFields does not work.
- ca = moose.element( '/model/chem/dend/DEND/Ca' )
- assert( ca.numData == ndc )
-
- # Put in spine solvers. Note that these get info from the neuroCompt
- spineCompt = moose.element( '/model/chem/spine' )
- sdc = spineCompt.mesh.num
- print('sdc = ', sdc)
- assert( sdc == 13 )
- smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
- smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
- smstoich = moose.Stoich( '/model/chem/spine/stoich' )
- smstoich.compartment = spineCompt
- smstoich.ksolve = smksolve
- smstoich.dsolve = smdsolve
- smstoich.path = "/model/chem/spine/##"
- print('spine num Pools = ', smstoich.numAllPools)
- assert( smstoich.numAllPools == 3 )
- assert( smdsolve.numPools == 3 )
- assert( smdsolve.numAllVoxels == sdc )
-
- # Put in PSD solvers. Note that these get info from the neuroCompt
- psdCompt = moose.element( '/model/chem/psd' )
- pdc = psdCompt.mesh.num
- assert( pdc == 13 )
- pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
- pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
- pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
- pmstoich.compartment = psdCompt
- pmstoich.ksolve = pmksolve
- pmstoich.dsolve = pmdsolve
- pmstoich.path = "/model/chem/psd/##"
- assert( pmstoich.numAllPools == 3 )
- assert( pmdsolve.numPools == 3 )
- assert( pmdsolve.numAllVoxels == pdc )
- foo = moose.element( '/model/chem/psd/Ca' )
- print('PSD: numfoo = ', foo.numData)
- print('PSD: numAllVoxels = ', pmksolve.numAllVoxels)
-
- # Put in junctions between the diffusion solvers
- nmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
-
-
- ##################################################################
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/spine/adaptCa', sdc )
- adaptCa = moose.vec( '/model/chem/spine/adaptCa' )
- chemCa = moose.vec( '/model/chem/spine/Ca' )
- assert( len( adaptCa ) == sdc )
- assert( len( chemCa ) == sdc )
- for i in range( sdc ):
- elecCa = moose.element( '/model/elec/spine_head_14_' + str(i+1) + '/NMDA_Ca_conc' )
- #print elecCa
- moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
- moose.connect( adaptCa, 'output', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 1e-4 # 520 to 0.0052 mM
-
-
- moose.le( '/model/chem/dend/DEND' )
- compts = neuroCompt.elecComptList
- begin = neuroCompt.startVoxelInCompt
- end = neuroCompt.endVoxelInCompt
- aCa = moose.Adaptor( '/model/chem/dend/DEND/adaptCa', len( compts))
- adaptCa = moose.vec( '/model/chem/dend/DEND/adaptCa' )
- chemCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- assert( len( chemCa ) == ndc )
- for i in zip( compts, adaptCa, begin, end ):
- name = i[0].path + '/Ca_conc'
- if ( moose.exists( name ) ):
- elecCa = moose.element( name )
- #print i[2], i[3], ' ', elecCa
- #print i[1]
- moose.connect( elecCa, 'concOut', i[1], 'input', 'Single' )
- for j in range( i[2], i[3] ):
- moose.connect( i[1], 'output', chemCa[j], 'setConc', 'Single' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 20e-6 # 10 arb units to 2 uM.
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if moose.exists( objpath ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- if obj.className == 'Neutral':
- print(("addPlot failed: object is a Neutral: ", objpath))
- return moose.element( '/' )
- else:
- #print "object was found: ", objpath, obj.className
- moose.connect( tab, 'requestOut', obj, field )
- return tab
- else:
- print(("addPlot failed: object not found: ", objpath))
- return moose.element( '/' )
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/spine_head_14_4', 'getVm', 'elec/spineVm' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'elec/somaCa' )
- addPlot( '/model/elec/lat_11_2/Ca_conc', 'getCa', 'elec/lat11Ca' )
- addPlot( '/model/elec/spine_head_14_4/NMDA_Ca_conc', 'getCa', 'elec/spine4Ca' )
- addPlot( '/model/elec/spine_head_14_12/NMDA_Ca_conc', 'getCa', 'elec/spine12Ca' )
-
-def makeChemPlots():
- graphs = moose.Neutral( '/graphs' )
- chem = moose.Neutral( '/graphs/chem' )
- addPlot( '/model/chem/psd/Ca_CaM', 'getConc', 'chem/psdCaCam' )
- addPlot( '/model/chem/psd/Ca', 'getConc', 'chem/psdCa' )
- addPlot( '/model/chem/spine/Ca_CaM', 'getConc', 'chem/spineCaCam' )
- addPlot( '/model/chem/spine/Ca[3]', 'getConc', 'chem/spine4Ca' )
- addPlot( '/model/chem/spine/Ca[11]', 'getConc', 'chem/spine12Ca' )
- addPlot( '/model/chem/dend/DEND/Ca', 'getConc', 'chem/dendCa' )
- addPlot( '/model/chem/dend/DEND/Ca[20]', 'getConc', 'chem/dendCa20' )
-
-def testNeuroMeshMultiscale():
- elecDt = 50e-6
- chemDt = 0.005
- ePlotDt = 0.5e-3
- cPlotDt = 0.005
- plotName = 'nm.plot'
-
- makeNeuroMeshModel()
- print("after model is completely done")
- for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ):
- print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
-
- makeChemPlots()
- makeElecPlots()
- moose.setClock( 0, elecDt )
- moose.setClock( 1, elecDt )
- moose.setClock( 2, elecDt )
- moose.setClock( 4, chemDt )
- moose.setClock( 5, chemDt )
- moose.setClock( 6, chemDt )
- moose.setClock( 7, cPlotDt )
- moose.setClock( 8, ePlotDt )
- moose.useClock( 0, '/model/elec/##[ISA=Compartment]', 'init' )
- moose.useClock( 1, '/model/elec/##[ISA=Compartment]', 'process' )
- moose.useClock( 1, '/model/elec/##[ISA=SpikeGen]', 'process' )
- moose.useClock( 2, '/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
- #moose.useClock( 5, '/model/chem/##[ISA=PoolBase],/model/##[ISA=ReacBase],/model/##[ISA=EnzBase]', 'process' )
- #moose.useClock( 4, '/model/chem/##[ISA=Adaptor]', 'process' )
- moose.useClock( 4, '/model/chem/#/dsolve', 'process' )
- moose.useClock( 5, '/model/chem/#/ksolve', 'process' )
- moose.useClock( 6, '/model/chem/spine/adaptCa', 'process' )
- moose.useClock( 6, '/model/chem/dend/DEND/adaptCa', 'process' )
- moose.useClock( 7, '/graphs/chem/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#', 'process' )
- moose.element( '/model/elec/soma' ).inject = 2e-10
- moose.element( '/model/chem/psd/Ca' ).concInit = 0.001
- moose.element( '/model/chem/spine/Ca' ).concInit = 0.002
- moose.element( '/model/chem/dend/DEND/Ca' ).concInit = 0.003
- moose.reinit()
-
- moose.start( 0.25 )
- plt.ion()
- fig = plt.figure( figsize=(8,8) )
- chem = fig.add_subplot( 311 )
- chem.set_ylim( 0, 0.002 )
- plt.ylabel( 'Conc (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/chem/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
- line1, = chem.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- elec = fig.add_subplot( 312 )
- plt.ylabel( 'Vm (V)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = elec.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- lenplot = fig.add_subplot( 313 )
- plt.ylabel( 'Ca (mM )' )
- plt.xlabel( 'Voxel#)' )
-
- spineCa = moose.vec( '/model/chem/spine/Ca' )
- dendCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- line1, = lenplot.plot( list(range( len( spineCa ))), spineCa.conc, label='spine' )
- line2, = lenplot.plot( list(range( len( dendCa ))), dendCa.conc, label='dend' )
-
- ca = [ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConc]') ]
- line3, = lenplot.plot( list(range( len( ca ))), ca, label='elec' )
-
- spineCaM = moose.vec( '/model/chem/spine/Ca_CaM' )
- line4, = lenplot.plot( list(range( len( spineCaM ))), spineCaM.conc, label='spineCaM' )
- psdCaM = moose.vec( '/model/chem/psd/Ca_CaM' )
- line5, = lenplot.plot( list(range( len( psdCaM ))), psdCaM.conc, label='psdCaM' )
- plt.legend()
-
-
- fig.canvas.draw()
- eval(input())
- print('All done')
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# minimal.py ends here.
diff --git a/moose-examples/snippets/MULTI/mincell.p b/moose-examples/snippets/MULTI/mincell.p
deleted file mode 100644
index 12fa81379b4b17e955f63aef6c8415f4693248f6..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/mincell.p
+++ /dev/null
@@ -1,36 +0,0 @@
-// genesis
-// cell parameter file for the 1991 Traub CA1 hippocampal cell
-// "phi" parameter reduced by e-3
-*cartesian
-*relative
-
-*set_global RM 1.0 //ohm*m^2
-*set_global RA 1.0 //ohm*m
-*set_global CM 0.03 //F/m^2
-*set_global EREST_ACT -0.06 // volts
-
-// The format for each compartment parameter line is :
-// name parent x y z d ch dens ...
-// For channels, "dens" = maximum conductance per unit area of compartment
-
-/* NOTE: The format of the cell descriptor files does not allow for
- continuation to another line. The following long line lists the
- soma channels with their "density" parameters.
-
- Ca_conc -17.402e12
- Not really a channel, but a "Ca_concen" object. Normally, the B
- field is set to "dens"/compt_volume (m^3), but the negative sign
- causes the absolute value to be used with no scaling by volume.
- Na 300
- Ca 40
- K_DR 150
- K_AHP 8
- K_C 100
- K_A 50
-*/
-
-
-soma none 0 10 0 8.46
-
-spine_neck soma 0.5 0 0 0.1
-spine_head . 0.5 0 0 0.5
diff --git a/moose-examples/snippets/MULTI/mincell2.p b/moose-examples/snippets/MULTI/mincell2.p
deleted file mode 100644
index 418e8e940b74dc97c447d242586b827e33be5b0d..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/mincell2.p
+++ /dev/null
@@ -1,37 +0,0 @@
-
-// genesis
-// cell parameter file for the 1991 Traub CA1 hippocampal cell
-// "phi" parameter reduced by e-3
-*cartesian
-*relative
-
-*set_global RM 1.0 //ohm*m^2
-*set_global RA 1.0 //ohm*m
-*set_global CM 0.03 //F/m^2
-*set_global EREST_ACT -0.06 // volts
-
-// The format for each compartment parameter line is :
-// name parent x y z d ch dens ...
-// For channels, "dens" = maximum conductance per unit area of compartment
-
-/* NOTE: The format of the cell descriptor files does not allow for
- continuation to another line. The following long line lists the
- soma channels with their "density" parameters.
-
- Ca_conc -17.402e12
- Not really a channel, but a "Ca_concen" object. Normally, the B
- field is set to "dens"/compt_volume (m^3), but the negative sign
- causes the absolute value to be used with no scaling by volume.
- Na 300
- Ca 40
- K_DR 150
- K_AHP 8
- K_C 100
- K_A 50
-*/
-
-
-soma none 0 10 0 8.46 Na 150 K_DR 400 Ca_conc 8.96e-3 Ca 50
-
-spine_neck soma 0.5 0 0 0.2 glu 700
-spine_head . 0.5 0 0 0.5 glu 700
diff --git a/moose-examples/snippets/MULTI/minchan.py b/moose-examples/snippets/MULTI/minchan.py
deleted file mode 100644
index e2c30afffcbfeb4b7e359a912824b66a7df7be18..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/minchan.py
+++ /dev/null
@@ -1,316 +0,0 @@
-# minimal.py ---
-# Upi Bhalla, NCBS Bangalore 2014.
-#
-# Commentary:
-#
-# Minimal model for loading rdesigneur: reac-diff elec signaling in neurons
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-sys.path.append('../../python')
-import os
-os.environ['NUMPTHREADS'] = '1'
-import math
-import numpy
-import matplotlib.pyplot as plt
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- moose.setCwe( '/library' )
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'mincell2.p', '/model/elec', "Neutral" )
- return cellId
-
-def loadChem( diffLength ):
- chem = moose.Neutral( '/model/chem' )
- neuroCompt = moose.NeuroMesh( '/model/chem/kinetics' )
- neuroCompt.separateSpines = 1
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/chem/compartment_1' )
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/chem/compartment_2' )
- #print 'Meshvolume[neuro, spine, psd] = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- modelId = moose.loadModel( 'minimal.g', '/model/chem', 'ee' )
- neuroCompt.name = 'dend'
- spineCompt.name = 'spine'
- psdCompt.name = 'psd'
-
-
-def makeNeuroMeshModel():
- diffLength = 6e-6 # Aim for 2 soma compartments.
- elec = loadElec()
- loadChem( diffLength )
- neuroCompt = moose.element( '/model/chem/dend' )
- neuroCompt.diffLength = diffLength
- neuroCompt.cellPortion( elec, '/model/elec/#' )
- for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if (x.diffConst > 0):
- x.diffConst = 1e-11
- for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- x.diffConst = 1e-10
-
- # Put in dend solvers
- ns = neuroCompt.numSegments
- ndc = neuroCompt.numDiffCompts
- print(('ns = ', ns, ', ndc = ', ndc))
- assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
- assert( ns == 1 ) # soma/dend only
- assert( ndc == 2 ) # split into 2.
- nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
- nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
- nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
- nmstoich.compartment = neuroCompt
- nmstoich.ksolve = nmksolve
- nmstoich.dsolve = nmdsolve
- nmstoich.path = "/model/chem/dend/##"
- print(('done setting path, numPools = ', nmdsolve.numPools))
- assert( nmdsolve.numPools == 1 )
- assert( nmdsolve.numAllVoxels == 2 )
- assert( nmstoich.numAllPools == 1 )
- # oddly, numLocalFields does not work.
- ca = moose.element( '/model/chem/dend/DEND/Ca' )
- assert( ca.numData == ndc )
-
- # Put in spine solvers. Note that these get info from the neuroCompt
- spineCompt = moose.element( '/model/chem/spine' )
- sdc = spineCompt.mesh.num
- print(('sdc = ', sdc))
- assert( sdc == 1 )
- smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
- smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
- smstoich = moose.Stoich( '/model/chem/spine/stoich' )
- smstoich.compartment = spineCompt
- smstoich.ksolve = smksolve
- smstoich.dsolve = smdsolve
- smstoich.path = "/model/chem/spine/##"
- assert( smstoich.numAllPools == 3 )
- assert( smdsolve.numPools == 3 )
- assert( smdsolve.numAllVoxels == 1 )
-
- # Put in PSD solvers. Note that these get info from the neuroCompt
- psdCompt = moose.element( '/model/chem/psd' )
- pdc = psdCompt.mesh.num
- assert( pdc == 1 )
- pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
- pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
- pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
- pmstoich.compartment = psdCompt
- pmstoich.ksolve = pmksolve
- pmstoich.dsolve = pmdsolve
- pmstoich.path = "/model/chem/psd/##"
- assert( pmstoich.numAllPools == 3 )
- assert( pmdsolve.numPools == 3 )
- assert( pmdsolve.numAllVoxels == 1 )
- foo = moose.element( '/model/chem/psd/Ca' )
- print(('PSD: numfoo = ', foo.numData))
- print(('PSD: numAllVoxels = ', pmksolve.numAllVoxels))
-
- # Put in junctions between the diffusion solvers
- nmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
-
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/dend/DEND/adaptCa', ndc )
- adaptCa = moose.vec( '/model/chem/dend/DEND/adaptCa' )
- chemCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- print(('aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData, "len( adaptCa ) = ", len( adaptCa )))
- assert( len( adaptCa ) == ndc )
- assert( len( chemCa ) == ndc )
- path = '/model/elec/soma/Ca_conc'
- elecCa = moose.element( path )
- print("==========")
- print(elecCa)
- print(adaptCa)
- print(chemCa)
- moose.connect( elecCa, 'concOut', adaptCa[0], 'input', 'Single' )
- moose.connect( adaptCa, 'output', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 1e-3 # 520 to 0.0052 mM
- #print adaptCa.outputOffset
- #print adaptCa.scale
-
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if moose.exists( objpath ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- if obj.className == 'Neutral':
- print(("addPlot failed: object is a Neutral: ", objpath))
- return moose.element( '/' )
- else:
- #print "object was found: ", objpath, obj.className
- moose.connect( tab, 'requestOut', obj, field )
- return tab
- else:
- print(("addPlot failed: object not found: ", objpath))
- return moose.element( '/' )
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/spine_head', 'getVm', 'elec/spineVm' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'elec/somaCa' )
-
-def makeChemPlots():
- graphs = moose.Neutral( '/graphs' )
- chem = moose.Neutral( '/graphs/chem' )
- addPlot( '/model/chem/psd/Ca_CaM', 'getConc', 'chem/psdCaCam' )
- addPlot( '/model/chem/psd/Ca', 'getConc', 'chem/psdCa' )
- addPlot( '/model/chem/spine/Ca_CaM', 'getConc', 'chem/spineCaCam' )
- addPlot( '/model/chem/spine/Ca', 'getConc', 'chem/spineCa' )
- addPlot( '/model/chem/dend/DEND/Ca', 'getConc', 'chem/dendCa' )
-
-def testNeuroMeshMultiscale():
- elecDt = 50e-6
- chemDt = 0.01
- ePlotDt = 0.5e-3
- cPlotDt = 0.01
- plotName = 'nm.plot'
-
- makeNeuroMeshModel()
- print("after model is completely done")
- for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ):
- print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
-
- """
- for i in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if ( i[0].diffConst > 0 ):
- grandpaname = i.parent[0].parent.name + '/'
- paname = i.parent[0].name + '/'
- print grandpaname + paname + i[0].name, i[0].diffConst
- print 'Neighbors:'
- for t in moose.element( '/model/chem/spine/ksolve/junction' ).neighbors['masterJunction']:
- print 'masterJunction <-', t.path
- for t in moose.wildcardFind( '/model/chem/#/ksolve' ):
- k = moose.element( t[0] )
- print k.path + ' localVoxels=', k.numLocalVoxels, ', allVoxels= ', k.numAllVoxels
- """
- '''
- moose.useClock( 4, '/model/chem/dend/dsolve', 'process' )
- moose.useClock( 5, '/model/chem/dend/ksolve', 'process' )
- moose.useClock( 5, '/model/chem/spine/ksolve', 'process' )
- moose.useClock( 5, '/model/chem/psd/ksolve', 'process' )
- '''
-
- makeChemPlots()
- makeElecPlots()
- moose.setClock( 0, elecDt )
- moose.setClock( 1, elecDt )
- moose.setClock( 2, elecDt )
- moose.setClock( 4, chemDt )
- moose.setClock( 5, chemDt )
- moose.setClock( 6, chemDt )
- moose.setClock( 7, cPlotDt )
- moose.setClock( 8, ePlotDt )
- moose.useClock( 0, '/model/elec/##[ISA=Compartment]', 'init' )
- moose.useClock( 1, '/model/elec/##[ISA=Compartment]', 'process' )
- moose.useClock( 1, '/model/elec/##[ISA=SpikeGen]', 'process' )
- moose.useClock( 2, '/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
- #moose.useClock( 5, '/model/chem/##[ISA=PoolBase],/model/##[ISA=ReacBase],/model/##[ISA=EnzBase]', 'process' )
- #moose.useClock( 4, '/model/chem/##[ISA=Adaptor]', 'process' )
- moose.useClock( 4, '/model/chem/#/dsolve', 'process' )
- moose.useClock( 5, '/model/chem/#/ksolve', 'process' )
- moose.useClock( 6, '/model/chem/dend/DEND/adaptCa', 'process' )
- moose.useClock( 7, '/graphs/chem/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#', 'process' )
- #hsolve = moose.HSolve( '/model/elec/hsolve' )
- #moose.useClock( 1, '/model/elec/hsolve', 'process' )
- #hsolve.dt = elecDt
- #hsolve.target = '/model/elec/compt'
- #moose.reinit()
- moose.element( '/model/elec/spine_head' ).inject = 5e-12
- moose.element( '/model/chem/psd/Ca' ).concInit = 0.001
- moose.element( '/model/chem/spine/Ca' ).concInit = 0.002
- moose.element( '/model/chem/dend/DEND/Ca' ).concInit = 0.003
- moose.reinit()
- """
- print 'pre'
- eca = moose.vec( '/model/chem/psd/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'dend'
- eca = moose.vec( '/model/chem/dend/DEND/Ca' )
- #for i in ( 0, 1, 2, 30, 60, 90, 120, 144 ):
- for i in range( 13 ):
- print i, eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
-
- print 'PSD'
- eca = moose.vec( '/model/chem/psd/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'spine'
- eca = moose.vec( '/model/chem/spine/SPINE/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- """
-
- moose.start( 0.5 )
- plt.ion()
- fig = plt.figure( figsize=(8,8) )
- chem = fig.add_subplot( 211 )
- chem.set_ylim( 0, 0.004 )
- plt.ylabel( 'Conc (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/chem/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
- line1, = chem.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- elec = fig.add_subplot( 212 )
- plt.ylabel( 'Vm (V)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = elec.plot( pos, x.vector, label=x.name )
- plt.legend()
- fig.canvas.draw()
- eval(input())
- pylab.show()
- print('All done')
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# minimal.py ends here.
diff --git a/moose-examples/snippets/MULTI/minimal.g b/moose-examples/snippets/MULTI/minimal.g
deleted file mode 100644
index a149f65050c8c76697dde87b0e3fa3dbca0fc5ab..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/minimal.g
+++ /dev/null
@@ -1,150 +0,0 @@
-//genesis
-// kkit Version 11 flat dumpfile
-
-// Saved on Sun Sep 22 23:33:41 2013
-
-include kkit {argv 1}
-
-FASTDT = 0.0001
-SIMDT = 0.01
-CONTROLDT = 5
-PLOTDT = 1
-MAXTIME = 100
-TRANSIENT_TIME = 2
-VARIABLE_DT_FLAG = 0
-DEFAULT_VOL = 1e-20
-VERSION = 11.0
-setfield /file/modpath value /home2/bhalla/scripts/modules
-kparms
-
-//genesis
-
-initdump -version 3 -ignoreorphans 1
-simobjdump doqcsinfo filename accessname accesstype transcriber developer \
- citation species tissue cellcompartment methodology sources \
- model_implementation model_validation x y z
-simobjdump table input output alloced step_mode stepsize x y z
-simobjdump xtree path script namemode sizescale
-simobjdump xcoredraw xmin xmax ymin ymax
-simobjdump xtext editable
-simobjdump xgraph xmin xmax ymin ymax overlay
-simobjdump xplot pixflags script fg ysquish do_slope wy
-simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
- link savename file version md5sum mod_save_flag x y z
-simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
- z
-simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
- geomname xtree_fg_req xtree_textfg_req x y z
-simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
-simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
- keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
-simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
- trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
-simobjdump xtab input output alloced step_mode stepsize notes editfunc \
- xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
-simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
- xtree_textfg_req x y z
-simobjdump transport input output alloced step_mode stepsize dt delay clock \
- kf xtree_fg_req xtree_textfg_req x y z
-simobjdump proto x y z
-simobjdump text str
-simundump geometry /kinetics/geometry 0 1e-18 3 sphere "" white black 2 -6 0
-simundump geometry /kinetics/geometry[1] 0 1e-19 3 sphere "" white black 0 -8 \
- 0
-simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black -3 \
- -6 0
-simundump text /kinetics/notes 0 ""
-call /kinetics/notes LOAD \
-""
-simundump text /kinetics/geometry/notes 0 ""
-call /kinetics/geometry/notes LOAD \
-""
-simundump text /kinetics/geometry[1]/notes 0 ""
-call /kinetics/geometry[1]/notes LOAD \
-""
-simundump text /kinetics/geometry[2]/notes 0 ""
-call /kinetics/geometry[2]/notes LOAD \
-""
-simundump group /kinetics/DEND 0 yellow black x 0 0 "" DEND defaultfile.g 0 0 \
- 0 -3 -3 0
-simundump text /kinetics/DEND/notes 0 ""
-call /kinetics/DEND/notes LOAD \
-""
-simundump kpool /kinetics/DEND/Ca 0 1e-10 0.08 0.08 48 48 0 0 600 0 \
- /kinetics/geometry blue yellow -4 4 0
-simundump text /kinetics/DEND/Ca/notes 0 ""
-call /kinetics/DEND/Ca/notes LOAD \
-""
-simundump group /kinetics/SPINE 0 28 black x 0 0 "" SPINE defaultfile.g 0 0 0 \
- 0 -3 0
-simundump text /kinetics/SPINE/notes 0 ""
-call /kinetics/SPINE/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/Ca 0 1e-10 0.08 0.08 4.8 4.8 0 0 60 0 \
- /kinetics/geometry[1] blue 28 -2 4 0
-simundump text /kinetics/SPINE/Ca/notes 0 ""
-call /kinetics/SPINE/Ca/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaM 0 1e-11 5 5 300 300 0 0 60 0 \
- /kinetics/geometry[1] 55 28 -2 2 0
-simundump text /kinetics/SPINE/CaM/notes 0 ""
-call /kinetics/SPINE/CaM/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/Ca_CaM 0 1e-11 0 0 0 0 0 0 60 0 \
- /kinetics/geometry[1] blue 28 1 -1 0
-simundump text /kinetics/SPINE/Ca_CaM/notes 0 ""
-call /kinetics/SPINE/Ca_CaM/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/kreac 0 0.1 0.1 "" white 28 -1 0 0
-simundump text /kinetics/SPINE/kreac/notes 0 ""
-call /kinetics/SPINE/kreac/notes LOAD \
-""
-simundump group /kinetics/PSD 0 0 black x 0 0 "" PSD defaultfile.g 0 0 0 3 -3 \
- 0
-simundump text /kinetics/PSD/notes 0 ""
-call /kinetics/PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/Ca 0 1e-10 0.08 0.08 0.48 0.48 0 0 6 0 \
- /kinetics/geometry[2] blue 0 1 4 0
-simundump text /kinetics/PSD/Ca/notes 0 ""
-call /kinetics/PSD/Ca/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaM 0 1e-11 5 5 30 30 0 0 6 0 \
- /kinetics/geometry[2] 53 0 1 2 0
-simundump text /kinetics/PSD/CaM/notes 0 ""
-call /kinetics/PSD/CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/Ca_CaM 0 1e-11 0 0 0 0 0 0 6 0 \
- /kinetics/geometry[2] blue 0 4 -1 0
-simundump text /kinetics/PSD/Ca_CaM/notes 0 ""
-call /kinetics/PSD/Ca_CaM/notes LOAD \
-""
-simundump kreac /kinetics/PSD/kreac 0 0.1 0.1 "" white 0 2 0 0
-simundump text /kinetics/PSD/kreac/notes 0 ""
-call /kinetics/PSD/kreac/notes LOAD \
-""
-simundump xgraph /graphs/conc1 0 0 100 0 1 0
-simundump xgraph /graphs/conc2 0 0 100 0 1 0
-simundump xgraph /moregraphs/conc3 0 0 100 0 1 0
-simundump xgraph /moregraphs/conc4 0 0 100 0 1 0
-simundump xcoredraw /edit/draw 0 -6 6 -10 6
-simundump xtree /edit/draw/tree 0 \
- /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \
- "edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>" auto 0.6
-simundump xtext /file/notes 0 1
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/Ca REAC A B
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/CaM REAC A B
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/Ca_CaM REAC B A
-addmsg /kinetics/SPINE/Ca /kinetics/SPINE/kreac SUBSTRATE n
-addmsg /kinetics/SPINE/CaM /kinetics/SPINE/kreac SUBSTRATE n
-addmsg /kinetics/SPINE/Ca_CaM /kinetics/SPINE/kreac PRODUCT n
-addmsg /kinetics/PSD/kreac /kinetics/PSD/Ca REAC A B
-addmsg /kinetics/PSD/kreac /kinetics/PSD/CaM REAC A B
-addmsg /kinetics/PSD/kreac /kinetics/PSD/Ca_CaM REAC B A
-addmsg /kinetics/PSD/Ca /kinetics/PSD/kreac SUBSTRATE n
-addmsg /kinetics/PSD/CaM /kinetics/PSD/kreac SUBSTRATE n
-addmsg /kinetics/PSD/Ca_CaM /kinetics/PSD/kreac PRODUCT n
-enddump
-// End of dump
-
-complete_loading
diff --git a/moose-examples/snippets/MULTI/minimal.py b/moose-examples/snippets/MULTI/minimal.py
deleted file mode 100644
index b5c018da1fb5d517465a8ff26797fc8811a9be2b..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/minimal.py
+++ /dev/null
@@ -1,302 +0,0 @@
-# minimal.py ---
-# Upi Bhalla, NCBS Bangalore 2014.
-#
-# Commentary:
-#
-# Minimal model for loading rdesigneur: reac-diff elec signaling in neurons
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-sys.path.append('../../python')
-import os
-os.environ['NUMPTHREADS'] = '1'
-import math
-import numpy
-import matplotlib.pyplot as plt
-import moose
-#import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'mincell.p', '/model/elec', "Neutral" )
- return cellId
-
-def loadChem( diffLength ):
- chem = moose.Neutral( '/model/chem' )
- neuroCompt = moose.NeuroMesh( '/model/chem/kinetics' )
- neuroCompt.separateSpines = 1
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/chem/compartment_1' )
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/chem/compartment_2' )
- #print 'Meshvolume[neuro, spine, psd] = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- modelId = moose.loadModel( 'minimal.g', '/model/chem', 'ee' )
- neuroCompt.name = 'dend'
- spineCompt.name = 'spine'
- psdCompt.name = 'psd'
-
-
-def makeNeuroMeshModel():
- diffLength = 20e-6 # Aim for just 3 compts.
- elec = loadElec()
- loadChem( diffLength )
- neuroCompt = moose.element( '/model/chem/dend' )
- neuroCompt.diffLength = diffLength
- neuroCompt.cellPortion( elec, '/model/elec/#' )
- for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if (x.diffConst > 0):
- x.diffConst = 1e-11
- for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- x.diffConst = 1e-10
-
- # Put in dend solvers
- ns = neuroCompt.numSegments
- ndc = neuroCompt.numDiffCompts
- print(('ns = ', ns, ', ndc = ', ndc))
- assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
- assert( ns == 1 ) # dend, 5x (shaft+head)
- assert( ndc == 1 )
- nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
- nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
- nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
- nmstoich.compartment = neuroCompt
- nmstoich.ksolve = nmksolve
- nmstoich.dsolve = nmdsolve
- nmstoich.path = "/model/chem/dend/##"
- print(('done setting path, numPools = ', nmdsolve.numPools))
- assert( nmdsolve.numPools == 1 )
- assert( nmdsolve.numAllVoxels == 1 )
- assert( nmstoich.numAllPools == 1 )
- # oddly, numLocalFields does not work.
- ca = moose.element( '/model/chem/dend/DEND/Ca' )
- assert( ca.numData == ndc )
-
- # Put in spine solvers. Note that these get info from the neuroCompt
- spineCompt = moose.element( '/model/chem/spine' )
- sdc = spineCompt.mesh.num
- print(('sdc = ', sdc))
- assert( sdc == 1 )
- smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
- smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
- smstoich = moose.Stoich( '/model/chem/spine/stoich' )
- smstoich.compartment = spineCompt
- smstoich.ksolve = smksolve
- smstoich.dsolve = smdsolve
- smstoich.path = "/model/chem/spine/##"
- assert( smstoich.numAllPools == 3 )
- assert( smdsolve.numPools == 3 )
- assert( smdsolve.numAllVoxels == 1 )
-
- # Put in PSD solvers. Note that these get info from the neuroCompt
- psdCompt = moose.element( '/model/chem/psd' )
- pdc = psdCompt.mesh.num
- assert( pdc == 1 )
- pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
- pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
- pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
- pmstoich.compartment = psdCompt
- pmstoich.ksolve = pmksolve
- pmstoich.dsolve = pmdsolve
- pmstoich.path = "/model/chem/psd/##"
- assert( pmstoich.numAllPools == 3 )
- assert( pmdsolve.numPools == 3 )
- assert( pmdsolve.numAllVoxels == 1 )
- foo = moose.element( '/model/chem/psd/Ca' )
- print(('PSD: numfoo = ', foo.numData))
- print(('PSD: numAllVoxels = ', pmksolve.numAllVoxels))
-
- """
- CaNpsd = moose.vec( '/model/chem/psdMesh/PSD/PP1_PSD/CaN' )
- print 'numCaN in PSD = ', CaNpsd.nInit, ', vol = ', CaNpsd.volume
- CaNspine = moose.vec( '/model/chem/spine/SPINE/CaN_BULK/CaN' )
- print 'numCaN in spine = ', CaNspine.nInit, ', vol = ', CaNspine.volume
- """
-
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/psd/adaptCa', pdc )
-
- adaptCa = moose.vec( '/model/chem/psd/adaptCa' )
- chemCa = moose.vec( '/model/chem/psd/Ca' )
- print(('aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData))
- assert( len( adaptCa ) == pdc )
- assert( len( chemCa ) == pdc )
- path = '/model/elec/spine_head'
- elecCa = moose.element( path )
- moose.connect( elecCa, 'VmOut', adaptCa[0], 'input', 'Single' )
- #moose.connect( adaptCa, 'outputSrc', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 1e-5 # 520 to 0.0052 mM
- #print adaptCa.outputOffset
- #print adaptCa.scale
-
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if moose.exists( objpath ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- if obj.className == 'Neutral':
- print(("addPlot failed: object is a Neutral: ", objpath))
- return moose.element( '/' )
- else:
- #print "object was found: ", objpath, obj.className
- moose.connect( tab, 'requestOut', obj, field )
- return tab
- else:
- print(("addPlot failed: object not found: ", objpath))
- return moose.element( '/' )
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/spine_head', 'getVm', 'elec/spineVm' )
-
-def makeChemPlots():
- graphs = moose.Neutral( '/graphs' )
- chem = moose.Neutral( '/graphs/chem' )
- addPlot( '/model/chem/psd/Ca_CaM', 'getConc', 'chem/psdCaCam' )
- addPlot( '/model/chem/psd/Ca', 'getConc', 'chem/psdCa' )
- addPlot( '/model/chem/spine/Ca_CaM', 'getConc', 'chem/spineCaCam' )
- addPlot( '/model/chem/spine/Ca', 'getConc', 'chem/spineCa' )
- addPlot( '/model/chem/dend/DEND/Ca', 'getConc', 'chem/dendCa' )
-
-def testNeuroMeshMultiscale():
- elecDt = 50e-6
- chemDt = 1e-1
- plotDt = 1e-1
- plotName = 'nm.plot'
-
- makeNeuroMeshModel()
- print("after model is completely done")
- for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ):
- print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
-
- """
- for i in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if ( i[0].diffConst > 0 ):
- grandpaname = i.parent[0].parent.name + '/'
- paname = i.parent[0].name + '/'
- print grandpaname + paname + i[0].name, i[0].diffConst
- print 'Neighbors:'
- for t in moose.element( '/model/chem/spine/ksolve/junction' ).neighbors['masterJunction']:
- print 'masterJunction <-', t.path
- for t in moose.wildcardFind( '/model/chem/#/ksolve' ):
- k = moose.element( t[0] )
- print k.path + ' localVoxels=', k.numLocalVoxels, ', allVoxels= ', k.numAllVoxels
- """
-
- '''
- moose.useClock( 4, '/model/chem/dend/dsolve', 'process' )
- moose.useClock( 5, '/model/chem/dend/ksolve', 'process' )
- moose.useClock( 5, '/model/chem/spine/ksolve', 'process' )
- moose.useClock( 5, '/model/chem/psd/ksolve', 'process' )
- '''
-
- makeChemPlots()
- makeElecPlots()
- moose.setClock( 0, elecDt )
- moose.setClock( 1, elecDt )
- moose.setClock( 2, elecDt )
- moose.setClock( 4, chemDt )
- moose.setClock( 5, chemDt )
- moose.setClock( 6, chemDt )
- moose.setClock( 7, plotDt )
- moose.setClock( 8, plotDt )
- moose.useClock( 0, '/model/elec/##[ISA=Compartment]', 'init' )
- moose.useClock( 1, '/model/elec/##[ISA=Compartment]', 'process' )
- moose.useClock( 1, '/model/elec/##[ISA=SpikeGen]', 'process' )
- moose.useClock( 2, '/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
- #moose.useClock( 5, '/model/chem/##[ISA=PoolBase],/model/##[ISA=ReacBase],/model/##[ISA=EnzBase]', 'process' )
- #moose.useClock( 6, '/model/chem/##[ISA=Adaptor]', 'process' )
- moose.useClock( 7, '/graphs/chem/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#', 'process' )
- moose.useClock( 5, '/model/chem/#/dsolve', 'process' )
- moose.useClock( 6, '/model/chem/#/ksolve', 'process' )
- #hsolve = moose.HSolve( '/model/elec/hsolve' )
- #moose.useClock( 1, '/model/elec/hsolve', 'process' )
- #hsolve.dt = elecDt
- #hsolve.target = '/model/elec/compt'
- #moose.reinit()
- moose.element( '/model/elec/spine_head' ).inject = 1e-9
- moose.element( '/model/chem/psd/Ca' ).concInit = 0.001
- moose.element( '/model/chem/spine/Ca' ).concInit = 0.002
- moose.element( '/model/chem/dend/DEND/Ca' ).concInit = 0.003
- moose.reinit()
- """
- print 'pre'
- eca = moose.vec( '/model/chem/psd/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'dend'
- eca = moose.vec( '/model/chem/dend/DEND/Ca' )
- #for i in ( 0, 1, 2, 30, 60, 90, 120, 144 ):
- for i in range( 13 ):
- print i, eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
-
- print 'PSD'
- eca = moose.vec( '/model/chem/psd/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'spine'
- eca = moose.vec( '/model/chem/spine/SPINE/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- """
-
- moose.start( 0.5 )
- plt.ion()
- fig = plt.figure( figsize=(8,8) )
- chem = fig.add_subplot( 211 )
- chem.set_ylim( 0, 0.004 )
- plt.ylabel( 'Conc (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/chem/#[ISA=Table]' ):
- pos = numpy.arange( 0, len(x.vector), 1 )
- line1, = chem.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- elec = fig.add_subplot( 212 )
- plt.ylabel( 'Vm (V)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- pos = numpy.arange( 0, len(x.vector), 1 )
- line1, = elec.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- fig.canvas.draw()
- eval(input())
- print('All done')
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# minimal.py ends here.
diff --git a/moose-examples/snippets/MULTI/multi1.py b/moose-examples/snippets/MULTI/multi1.py
deleted file mode 100644
index 4f60c8d7ac244755f226cf3403bffd9941513f13..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/multi1.py
+++ /dev/null
@@ -1,339 +0,0 @@
-# multi1.py ---
-# Upi Bhalla, NCBS Bangalore 2014.
-#
-# Commentary:
-#
-# This loads in a low-detail model incorporating
-# reac-diff and elec signaling in neurons. The reac-diff model
-# has just Ca and CaM in it, and there are no-cross-compartment
-# reactions though Ca diffuses everywhere. The elec model controls the
-# Ca levels in the chem compartments.
-# This version uses solvers for both chem and electrical parts.
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-import os
-os.environ['NUMPTHREADS'] = '1'
-import math
-import numpy
-import matplotlib.pyplot as plt
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- moose.setCwe( '/library' )
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "Neutral" )
- return cellId
-
-def loadChem( diffLength ):
- chem = moose.Neutral( '/model/chem' )
- neuroCompt = moose.NeuroMesh( '/model/chem/kinetics' )
- neuroCompt.separateSpines = 1
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/chem/compartment_1' )
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/chem/compartment_2' )
- #print 'Meshvolume[neuro, spine, psd] = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- modelId = moose.loadModel( 'minimal.g', '/model/chem', 'ee' )
- #modelId = moose.loadModel( 'psd_merged31d.g', '/model/chem', 'ee' )
- neuroCompt.name = 'dend'
- spineCompt.name = 'spine'
- psdCompt.name = 'psd'
-
-def makeNeuroMeshModel():
- diffLength = 10e-6 # Aim for 2 soma compartments.
- elec = loadElec()
- loadChem( diffLength )
- neuroCompt = moose.element( '/model/chem/dend' )
- neuroCompt.diffLength = diffLength
- neuroCompt.cellPortion( elec, '/model/elec/#' )
- for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if (x.diffConst > 0):
- x.diffConst = 1e-11
- for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- x.diffConst = 1e-10
-
- # Put in dend solvers
- ns = neuroCompt.numSegments
- ndc = neuroCompt.numDiffCompts
- print(('ns = ', ns, ', ndc = ', ndc))
- assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
- assert( ns == 36 ) #
- assert( ndc == 278 ) #
- nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
- nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
- nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
- nmstoich.compartment = neuroCompt
- nmstoich.ksolve = nmksolve
- nmstoich.dsolve = nmdsolve
- nmstoich.path = "/model/chem/dend/##"
- print(('done setting path, numPools = ', nmdsolve.numPools))
- assert( nmdsolve.numPools == 1 )
- assert( nmdsolve.numAllVoxels == ndc )
- assert( nmstoich.numAllPools == 1 )
- # oddly, numLocalFields does not work.
- ca = moose.element( '/model/chem/dend/DEND/Ca' )
- assert( ca.numData == ndc )
-
- # Put in spine solvers. Note that these get info from the neuroCompt
- spineCompt = moose.element( '/model/chem/spine' )
- sdc = spineCompt.mesh.num
- print(('sdc = ', sdc))
- assert( sdc == 13 )
- smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
- smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
- smstoich = moose.Stoich( '/model/chem/spine/stoich' )
- smstoich.compartment = spineCompt
- smstoich.ksolve = smksolve
- smstoich.dsolve = smdsolve
- smstoich.path = "/model/chem/spine/##"
- print(('spine num Pools = ', smstoich.numAllPools))
- assert( smstoich.numAllPools == 3 )
- assert( smdsolve.numPools == 3 )
- assert( smdsolve.numAllVoxels == sdc )
-
- # Put in PSD solvers. Note that these get info from the neuroCompt
- psdCompt = moose.element( '/model/chem/psd' )
- pdc = psdCompt.mesh.num
- assert( pdc == 13 )
- pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
- pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
- pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
- pmstoich.compartment = psdCompt
- pmstoich.ksolve = pmksolve
- pmstoich.dsolve = pmdsolve
- pmstoich.path = "/model/chem/psd/##"
- assert( pmstoich.numAllPools == 3 )
- assert( pmdsolve.numPools == 3 )
- assert( pmdsolve.numAllVoxels == pdc )
- foo = moose.element( '/model/chem/psd/Ca' )
- print(('PSD: numfoo = ', foo.numData))
- print(('PSD: numAllVoxels = ', pmksolve.numAllVoxels))
-
- # Put in junctions between the diffusion solvers
- nmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
-
- ##################################################################
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/spine/adaptCa', sdc )
- adaptCa = moose.vec( '/model/chem/spine/adaptCa' )
- chemCa = moose.vec( '/model/chem/spine/Ca' )
- assert( len( adaptCa ) == sdc )
- assert( len( chemCa ) == sdc )
- for i in range( sdc ):
- elecCa = moose.element( '/model/elec/spine_head_14_' + str(i+1) + '/NMDA_Ca_conc' )
- moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
- moose.connect( adaptCa, 'output', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 1e-4 # 520 to 0.0052 mM
-
- moose.le( '/model/chem/dend/DEND' )
- compts = neuroCompt.elecComptList
- begin = neuroCompt.startVoxelInCompt
- end = neuroCompt.endVoxelInCompt
- aCa = moose.Adaptor( '/model/chem/dend/DEND/adaptCa', len( compts))
- adaptCa = moose.vec( '/model/chem/dend/DEND/adaptCa' )
- chemCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- assert( len( chemCa ) == ndc )
- for i in zip( compts, adaptCa, begin, end ):
- name = i[0].path + '/Ca_conc'
- if ( moose.exists( name ) ):
- elecCa = moose.element( name )
- #print i[2], i[3], ' ', elecCa
- #print i[1]
- moose.connect( elecCa, 'concOut', i[1], 'input', 'Single' )
- for j in range( i[2], i[3] ):
- moose.connect( i[1], 'output', chemCa[j], 'setConc', 'Single' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 20e-6 # 10 arb units to 2 uM.
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if moose.exists( objpath ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- if obj.className == 'Neutral':
- print(("addPlot failed: object is a Neutral: ", objpath))
- return moose.element( '/' )
- else:
- #print "object was found: ", objpath, obj.className
- moose.connect( tab, 'requestOut', obj, field )
- return tab
- else:
- print(("addPlot failed: object not found: ", objpath))
- return moose.element( '/' )
-
-def makeCaPlots():
- graphs = moose.Neutral( '/graphs' )
- ca = moose.Neutral( '/graphs/ca' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'ca/somaCa' )
- addPlot( '/model/elec/lat_11_2/Ca_conc', 'getCa', 'ca/lat11Ca' )
- addPlot( '/model/elec/spine_head_14_4/NMDA_Ca_conc', 'getCa', 'ca/spine4Ca' )
- addPlot( '/model/elec/spine_head_14_12/NMDA_Ca_conc', 'getCa', 'ca/spine12Ca' )
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/spine_head_14_4', 'getVm', 'elec/spineVm' )
-
-def makeChemPlots():
- graphs = moose.Neutral( '/graphs' )
- chem = moose.Neutral( '/graphs/chem' )
- addPlot( '/model/chem/psd/Ca_CaM', 'getConc', 'chem/psdCaCam' )
- addPlot( '/model/chem/psd/Ca', 'getConc', 'chem/psdCa' )
- addPlot( '/model/chem/spine/Ca_CaM', 'getConc', 'chem/spineCaCam' )
- addPlot( '/model/chem/spine/Ca[3]', 'getConc', 'chem/spine4Ca' )
- addPlot( '/model/chem/spine/Ca[11]', 'getConc', 'chem/spine12Ca' )
- addPlot( '/model/chem/dend/DEND/Ca', 'getConc', 'chem/dendCa' )
- addPlot( '/model/chem/dend/DEND/Ca[20]', 'getConc', 'chem/dendCa20' )
-
-def makeGraphics():
- plt.ion()
- fig = plt.figure( figsize=(10,16) )
- chem = fig.add_subplot( 411 )
- chem.set_ylim( 0, 0.006 )
- plt.ylabel( 'Conc (mM)' )
- plt.xlabel( 'time (seconds)' )
- plt.legend()
-
- elec = fig.add_subplot( 412 )
- plt.ylabel( 'Vm (V)' )
- plt.xlabel( 'time (seconds)' )
- plt.legend()
-
- ca = fig.add_subplot( 413 )
- plt.ylabel( '[Ca] (mM)' )
- plt.xlabel( 'time (seconds)' )
- plt.legend()
-
- lenplot = fig.add_subplot( 414 )
- plt.ylabel( 'Ca (mM )' )
- plt.xlabel( 'Voxel#)' )
- plt.legend()
- spineCa = moose.vec( '/model/chem/spine/Ca' )
- dendCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- line1, = lenplot.plot( list(range( len( spineCa ))), spineCa.conc, label='spine' )
- line2, = lenplot.plot( list(range( len( dendCa ))), dendCa.conc, label='dend' )
-
- Ca = [ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConcBase]') ]
- line3, = lenplot.plot( list(range( len( Ca ))), Ca, label='elec' )
-
- spineCaM = moose.vec( '/model/chem/spine/Ca_CaM' )
- line4, = lenplot.plot( list(range( len( spineCaM ))), spineCaM.conc, label='spineCaM' )
- psdCaM = moose.vec( '/model/chem/psd/Ca_CaM' )
- line5, = lenplot.plot( list(range( len( psdCaM ))), psdCaM.conc, label='psdCaM' )
- lenplot.set_ylim( 0, 0.01 )
- fig.canvas.draw()
- return ( chem, elec, ca, lenplot, fig, line1, line2, line3, line4, line5 )
-
-def updateGraphics( plotlist ):
- spineCa = moose.vec( '/model/chem/spine/Ca' )
- dendCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- plotlist[5].set_ydata( spineCa.conc )
- plotlist[6].set_ydata( dendCa.conc )
-
- ca = [ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConcBase]') ]
- plotlist[7].set_ydata( ca )
- spineCaM = moose.vec( '/model/chem/spine/Ca_CaM' )
- plotlist[8].set_ydata( spineCaM.conc )
- psdCaM = moose.vec( '/model/chem/psd/Ca_CaM' )
- plotlist[9].set_ydata( psdCaM.conc )
- plotlist[4].canvas.draw()
-
-def finalizeGraphics( plotlist, cPlotDt, ePlotDt ):
- for x in moose.wildcardFind( '/graphs/chem/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
- line1, = plotlist[0].plot( pos, x.vector, label=x.name )
-
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = plotlist[1].plot( pos, x.vector, label=x.name )
-
- for x in moose.wildcardFind( '/graphs/ca/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = plotlist[2].plot( pos, x.vector, label=x.name )
- plotlist[4].canvas.draw()
- eval(input())
-
-def testNeuroMeshMultiscale():
- runtime = 0.5
- #elecDt = 0.2e-6
- elecDt = 10e-6
- chemDt = 0.0025
- ePlotDt = 0.5e-3
- cPlotDt = 0.0025
- plotName = 'nm.plot'
-
- makeNeuroMeshModel()
- print("after model is completely done")
- for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ):
- print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
-
- makeChemPlots()
- makeElecPlots()
- makeCaPlots()
- hsolve = moose.HSolve( '/model/elec/hsolve' )
- hsolve.dt = elecDt
- hsolve.target = '/model/elec/compt'
- plotlist = makeGraphics()
- moose.reinit()
- moose.element( '/model/elec/soma' ).inject = 2e-10
- moose.element( '/model/chem/psd/Ca' ).concInit = 0.001
- moose.element( '/model/chem/spine/Ca' ).concInit = 0.002
- moose.element( '/model/chem/dend/DEND/Ca' ).concInit = 0.003
- moose.reinit()
-
- numDivs = 200
- partialRuntime = runtime / numDivs
- for i in range( numDivs ):
- moose.start( partialRuntime )
- updateGraphics( plotlist )
- finalizeGraphics( plotlist, cPlotDt, ePlotDt )
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# minimal.py ends here.
diff --git a/moose-examples/snippets/MULTI/multi1_ee.py b/moose-examples/snippets/MULTI/multi1_ee.py
deleted file mode 100644
index e37a2e17ccac75a5182c42325c3bc7cc5c7a15b2..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/multi1_ee.py
+++ /dev/null
@@ -1,344 +0,0 @@
-# multi1.py ---
-# Upi Bhalla, NCBS Bangalore 2014.
-#
-# Commentary:
-#
-# This loads in a medium-detail model incorporating
-# reac-diff and elec signaling in neurons. The reac-diff model
-# has just Ca and CaM in it, and there are no-cross-compartment
-# reactions though Ca diffuses everywhere. The elec model controls the
-# Ca levels in the chem compartments.
-# This version uses solvers for both chem and electrical parts.
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-import os
-import math
-import numpy
-import matplotlib.pyplot as plt
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- moose.setCwe( '/library' )
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "Neutral" )
- return cellId
-
-def loadChem( diffLength ):
- chem = moose.Neutral( '/model/chem' )
- neuroCompt = moose.NeuroMesh( '/model/chem/kinetics' )
- neuroCompt.separateSpines = 1
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/chem/compartment_1' )
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/chem/compartment_2' )
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- modelId = moose.loadModel( 'minimal.g', '/model/chem', 'ee' )
- neuroCompt.name = 'dend'
- spineCompt.name = 'spine'
- psdCompt.name = 'psd'
-
-def makeNeuroMeshModel():
- diffLength = 10e-6 # Aim for 2 soma compartments.
- elec = loadElec()
- loadChem( diffLength )
- neuroCompt = moose.element( '/model/chem/dend' )
- neuroCompt.diffLength = diffLength
- neuroCompt.cellPortion( elec, '/model/elec/#' )
- for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if (x.diffConst > 0):
- x.diffConst = 1e-11
- for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- x.diffConst = 1e-10
-
- # Put in dend solvers
- ns = neuroCompt.numSegments
- ndc = neuroCompt.numDiffCompts
- print(('ns = ', ns, ', ndc = ', ndc))
- assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
- assert( ns == 36 ) #
- assert( ndc == 278 ) #
- nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
- nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
- nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
- nmstoich.compartment = neuroCompt
- nmstoich.ksolve = nmksolve
- nmstoich.dsolve = nmdsolve
- nmstoich.path = "/model/chem/dend/##"
- print(('done setting path, numPools = ', nmdsolve.numPools))
- assert( nmdsolve.numPools == 1 )
- assert( nmdsolve.numAllVoxels == ndc )
- assert( nmstoich.numAllPools == 1 )
- # oddly, numLocalFields does not work.
- ca = moose.element( '/model/chem/dend/DEND/Ca' )
- assert( ca.numData == ndc )
-
- # Put in spine solvers. Note that these get info from the neuroCompt
- spineCompt = moose.element( '/model/chem/spine' )
- sdc = spineCompt.mesh.num
- print(('sdc = ', sdc))
- assert( sdc == 13 )
- smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
- smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
- smstoich = moose.Stoich( '/model/chem/spine/stoich' )
- smstoich.compartment = spineCompt
- smstoich.ksolve = smksolve
- smstoich.dsolve = smdsolve
- smstoich.path = "/model/chem/spine/##"
- print(('spine num Pools = ', smstoich.numAllPools))
- assert( smstoich.numAllPools == 3 )
- assert( smdsolve.numPools == 3 )
- assert( smdsolve.numAllVoxels == sdc )
-
- # Put in PSD solvers. Note that these get info from the neuroCompt
- psdCompt = moose.element( '/model/chem/psd' )
- pdc = psdCompt.mesh.num
- assert( pdc == 13 )
- pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
- pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
- pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
- pmstoich.compartment = psdCompt
- pmstoich.ksolve = pmksolve
- pmstoich.dsolve = pmdsolve
- pmstoich.path = "/model/chem/psd/##"
- assert( pmstoich.numAllPools == 3 )
- assert( pmdsolve.numPools == 3 )
- assert( pmdsolve.numAllVoxels == pdc )
- foo = moose.element( '/model/chem/psd/Ca' )
- print(('PSD: numfoo = ', foo.numData))
- print(('PSD: numAllVoxels = ', pmksolve.numAllVoxels))
-
- # Put in junctions between the diffusion solvers
- nmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
-
- ##################################################################
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/spine/adaptCa', sdc )
- adaptCa = moose.vec( '/model/chem/spine/adaptCa' )
- chemCa = moose.vec( '/model/chem/spine/Ca' )
- assert( len( adaptCa ) == sdc )
- assert( len( chemCa ) == sdc )
- for i in range( sdc ):
- elecCa = moose.element( '/model/elec/spine_head_14_' + str(i+1) + '/NMDA_Ca_conc' )
- #print elecCa
- moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
- moose.connect( adaptCa, 'output', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 1e-4 # 520 to 0.0052 mM
- moose.le( '/model/chem/dend/DEND' )
- compts = neuroCompt.elecComptList
- begin = neuroCompt.startVoxelInCompt
- end = neuroCompt.endVoxelInCompt
- aCa = moose.Adaptor( '/model/chem/dend/DEND/adaptCa', len( compts))
- adaptCa = moose.vec( '/model/chem/dend/DEND/adaptCa' )
- chemCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- assert( len( chemCa ) == ndc )
- for i in zip( compts, adaptCa, begin, end ):
- name = i[0].path + '/Ca_conc'
- if ( moose.exists( name ) ):
- elecCa = moose.element( name )
- moose.connect( elecCa, 'concOut', i[1], 'input', 'Single' )
- for j in range( i[2], i[3] ):
- moose.connect( i[1], 'output', chemCa[j], 'setConc', 'Single' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 20e-6 # 10 arb units to 2 uM.
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if moose.exists( objpath ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- if obj.className == 'Neutral':
- print(("addPlot failed: object is a Neutral: ", objpath))
- return moose.element( '/' )
- else:
- #print "object was found: ", objpath, obj.className
- moose.connect( tab, 'requestOut', obj, field )
- return tab
- else:
- print(("addPlot failed: object not found: ", objpath))
- return moose.element( '/' )
-
-def makeCaPlots():
- graphs = moose.Neutral( '/graphs' )
- ca = moose.Neutral( '/graphs/ca' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'ca/somaCa' )
- addPlot( '/model/elec/lat_11_2/Ca_conc', 'getCa', 'ca/lat11Ca' )
- addPlot( '/model/elec/spine_head_14_4/NMDA_Ca_conc', 'getCa', 'ca/spine4Ca' )
- addPlot( '/model/elec/spine_head_14_12/NMDA_Ca_conc', 'getCa', 'ca/spine12Ca' )
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/spine_head_14_4', 'getVm', 'elec/spineVm' )
-
-def makeChemPlots():
- graphs = moose.Neutral( '/graphs' )
- chem = moose.Neutral( '/graphs/chem' )
- addPlot( '/model/chem/psd/Ca_CaM', 'getConc', 'chem/psdCaCam' )
- addPlot( '/model/chem/psd/Ca', 'getConc', 'chem/psdCa' )
- addPlot( '/model/chem/spine/Ca_CaM', 'getConc', 'chem/spineCaCam' )
- addPlot( '/model/chem/spine/Ca[3]', 'getConc', 'chem/spine4Ca' )
- addPlot( '/model/chem/spine/Ca[11]', 'getConc', 'chem/spine12Ca' )
- addPlot( '/model/chem/dend/DEND/Ca', 'getConc', 'chem/dendCa' )
- addPlot( '/model/chem/dend/DEND/Ca[20]', 'getConc', 'chem/dendCa20' )
-
-def makeGraphics( cPlotDt, ePlotDt ):
- plt.ion()
- fig = plt.figure( figsize=(10,16) )
- chem = fig.add_subplot( 411 )
- chem.set_ylim( 0, 0.006 )
- plt.ylabel( 'Conc (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/chem/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
- line1, = chem.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- elec = fig.add_subplot( 412 )
- plt.ylabel( 'Vm (V)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = elec.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- ca = fig.add_subplot( 413 )
- plt.ylabel( '[Ca] (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/ca/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = ca.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- lenplot = fig.add_subplot( 414 )
- plt.ylabel( 'Ca (mM )' )
- plt.xlabel( 'Voxel#)' )
-
- spineCa = moose.vec( '/model/chem/spine/Ca' )
- dendCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- line1, = lenplot.plot( list(range( len( spineCa ))), spineCa.conc, label='spine' )
- line2, = lenplot.plot( list(range( len( dendCa ))), dendCa.conc, label='dend' )
-
- ca = [ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConcBase]') ]
- line3, = lenplot.plot( list(range( len( ca ))), ca, label='elec' )
-
- spineCaM = moose.vec( '/model/chem/spine/Ca_CaM' )
- line4, = lenplot.plot( list(range( len( spineCaM ))), spineCaM.conc, label='spineCaM' )
- psdCaM = moose.vec( '/model/chem/psd/Ca_CaM' )
- line5, = lenplot.plot( list(range( len( psdCaM ))), psdCaM.conc, label='psdCaM' )
- plt.legend()
-
-
- fig.canvas.draw()
- eval(input())
-
- '''
- for x in moose.wildcardFind( '/graphs/##[ISA=Table]' ):
- t = numpy.arange( 0, x.vector.size, 1 )
- pylab.plot( t, x.vector, label=x.name )
- pylab.legend()
- pylab.show()
- '''
-
- print('All done')
-
-def testNeuroMeshMultiscale():
- runtime = 0.5
- elecDt = 0.2e-6
- chemDt = 0.005
- ePlotDt = 0.5e-3
- cPlotDt = 0.005
- plotName = 'nm.plot'
-
- makeNeuroMeshModel()
- print("after model is completely done")
- for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ):
- print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
-
- makeChemPlots()
- makeElecPlots()
- makeCaPlots()
- moose.setClock( 0, elecDt )
- moose.setClock( 1, elecDt )
- moose.setClock( 2, elecDt )
- moose.setClock( 4, chemDt )
- moose.setClock( 5, chemDt )
- moose.setClock( 6, chemDt )
- moose.setClock( 7, cPlotDt )
- moose.setClock( 8, ePlotDt )
- moose.useClock( 0, '/model/elec/##[ISA=Compartment]', 'init' )
- moose.useClock( 1, '/model/elec/##[ISA=Compartment]', 'process' )
- moose.useClock( 1, '/model/elec/##[ISA=SpikeGen]', 'process' )
- moose.useClock( 2, '/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
- #moose.useClock( 2, '/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
- #moose.useClock( 5, '/model/chem/##[ISA=PoolBase],/model/##[ISA=ReacBase],/model/##[ISA=EnzBase]', 'process' )
- #moose.useClock( 4, '/model/chem/##[ISA=Adaptor]', 'process' )
- moose.useClock( 4, '/model/chem/#/dsolve', 'process' )
- moose.useClock( 5, '/model/chem/#/ksolve', 'process' )
- moose.useClock( 6, '/model/chem/spine/adaptCa', 'process' )
- moose.useClock( 6, '/model/chem/dend/DEND/adaptCa', 'process' )
- moose.useClock( 7, '/graphs/chem/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#,/graphs/ca/#', 'process' )
- '''
- hsolve = moose.HSolve( '/model/elec/hsolve' )
- moose.useClock( 1, '/model/elec/hsolve', 'process' )
- hsolve.dt = elecDt
- hsolve.target = '/model/elec/compt'
- '''
- moose.reinit()
- moose.element( '/model/elec/soma' ).inject = 2e-10
- moose.element( '/model/chem/psd/Ca' ).concInit = 0.001
- moose.element( '/model/chem/spine/Ca' ).concInit = 0.002
- moose.element( '/model/chem/dend/DEND/Ca' ).concInit = 0.003
- moose.reinit()
-
- moose.start( runtime )
- makeGraphics( cPlotDt, ePlotDt )
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# minimal.py ends here.
diff --git a/moose-examples/snippets/MULTI/multi2.py b/moose-examples/snippets/MULTI/multi2.py
deleted file mode 100644
index cae9588080f90ab9fc069f13c0e09392319376bc..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/multi2.py
+++ /dev/null
@@ -1,335 +0,0 @@
-# multi2.py ---
-# Upi Bhalla, NCBS Bangalore 2014.
-#
-# Commentary:
-#
-# This loads in a medium-detail model incorporating
-# reac-diff and elec signaling in neurons. The reac-diff model is
-# psd_merged31d.g which has only Ca in the dendrites, but is quite
-# interesting in the PSD and spine head. Problem is lots of
-# cross-compartment reactions.
-# has in it, and there are no-cross-compartment
-# reactions though Ca diffuses everywhere. The elec model controls the
-# Ca levels in the chem compartments.
-# This version uses solvers for both chem and electrical parts.
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-sys.path.append('../../python')
-import os
-os.environ['NUMPTHREADS'] = '1'
-import math
-import numpy
-import matplotlib.pyplot as plt
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- moose.setCwe( '/library' )
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "Neutral" )
- return cellId
-
-def loadChem( diffLength ):
- chem = moose.Neutral( '/model/chem' )
- neuroCompt = moose.NeuroMesh( '/model/chem/kinetics' )
- neuroCompt.separateSpines = 1
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/chem/compartment_1' )
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/chem/compartment_2' )
- #print 'Meshvolume[neuro, spine, psd] = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- modelId = moose.loadModel( 'separate_compts.g', '/model/chem', 'ee' )
- #modelId = moose.loadModel( 'psd_merged31d.g', '/model/chem', 'ee' )
- neuroCompt.name = 'dend'
- spineCompt.name = 'spine'
- psdCompt.name = 'psd'
-
-def makeNeuroMeshModel():
- diffLength = 10e-6 # Aim for 2 soma compartments.
- elec = loadElec()
- loadChem( diffLength )
- neuroCompt = moose.element( '/model/chem/dend' )
- neuroCompt.diffLength = diffLength
- neuroCompt.cellPortion( elec, '/model/elec/#' )
- for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if (x.diffConst > 0):
- x.diffConst = 1e-11
- for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- x.diffConst = 1e-10
-
- # Put in dend solvers
- ns = neuroCompt.numSegments
- ndc = neuroCompt.numDiffCompts
- print(('ns = ', ns, ', ndc = ', ndc))
- assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
- assert( ns == 36 ) #
- assert( ndc == 278 ) #
- nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
- nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
- nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
- nmstoich.compartment = neuroCompt
- nmstoich.ksolve = nmksolve
- nmstoich.dsolve = nmdsolve
- nmstoich.path = "/model/chem/dend/##"
- print(('done setting path, numPools = ', nmdsolve.numPools))
- assert( nmdsolve.numPools == 1 )
- assert( nmdsolve.numAllVoxels == ndc )
- assert( nmstoich.numAllPools == 1 )
- # oddly, numLocalFields does not work.
- ca = moose.element( '/model/chem/dend/DEND/Ca' )
- assert( ca.numData == ndc )
-
- # Put in spine solvers. Note that these get info from the neuroCompt
- spineCompt = moose.element( '/model/chem/spine' )
- sdc = spineCompt.mesh.num
- print(('sdc = ', sdc))
- assert( sdc == 13 )
- smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
- smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
- smstoich = moose.Stoich( '/model/chem/spine/stoich' )
- smstoich.compartment = spineCompt
- smstoich.ksolve = smksolve
- smstoich.dsolve = smdsolve
- smstoich.path = "/model/chem/spine/##"
- print(('spine num Pools = ', smstoich.numAllPools, smdsolve.numPools))
- assert( smstoich.numAllPools == 35 )
- assert( smdsolve.numPools == 30 )
- assert( smdsolve.numAllVoxels == sdc )
-
- # Put in PSD solvers. Note that these get info from the neuroCompt
- psdCompt = moose.element( '/model/chem/psd' )
- pdc = psdCompt.mesh.num
- assert( pdc == 13 )
- pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
- pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
- pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
- pmstoich.compartment = psdCompt
- pmstoich.ksolve = pmksolve
- pmstoich.dsolve = pmdsolve
- pmstoich.path = "/model/chem/psd/##"
- print(('psd num Pools = ', pmstoich.numAllPools, pmdsolve.numPools))
- assert( pmstoich.numAllPools == 55 )
- assert( pmdsolve.numPools == 48 )
- assert( pmdsolve.numAllVoxels == pdc )
- foo = moose.element( '/model/chem/psd/Ca' )
- print(('PSD: numfoo = ', foo.numData))
- print(('PSD: numAllVoxels = ', pmksolve.numAllVoxels))
-
- # Put in junctions between the diffusion solvers
- nmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
-
- ##################################################################
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/spine/adaptCa', sdc )
- adaptCa = moose.vec( '/model/chem/spine/adaptCa' )
- chemCa = moose.vec( '/model/chem/spine/Ca' )
- #print 'aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData, "len( adaptCa ) = ", len( adaptCa )
- assert( len( adaptCa ) == sdc )
- assert( len( chemCa ) == sdc )
- for i in range( sdc ):
- elecCa = moose.element( '/model/elec/spine_head_14_' + str(i+1) + '/NMDA_Ca_conc' )
- moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
- moose.connect( adaptCa, 'output', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 5e-3 # 520 to 0.0052 mM
-
- moose.le( '/model/chem/dend/DEND' )
- compts = neuroCompt.elecComptList
- begin = neuroCompt.startVoxelInCompt
- end = neuroCompt.endVoxelInCompt
- aCa = moose.Adaptor( '/model/chem/dend/DEND/adaptCa', len( compts))
- adaptCa = moose.vec( '/model/chem/dend/DEND/adaptCa' )
- chemCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- assert( len( chemCa ) == ndc )
- for i in zip( compts, adaptCa, begin, end ):
- name = i[0].path + '/Ca_conc'
- if ( moose.exists( name ) ):
- elecCa = moose.element( name )
- moose.connect( elecCa, 'concOut', i[1], 'input', 'Single' )
- for j in range( i[2], i[3] ):
- moose.connect( i[1], 'output', chemCa[j], 'setConc', 'Single' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 20e-6 # 10 arb units to 2 uM.
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if moose.exists( objpath ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- if obj.className == 'Neutral':
- print(("addPlot failed: object is a Neutral: ", objpath))
- return moose.element( '/' )
- else:
- #print "object was found: ", objpath, obj.className
- moose.connect( tab, 'requestOut', obj, field )
- return tab
- else:
- print(("addPlot failed: object not found: ", objpath))
- return moose.element( '/' )
-
-def makeCaPlots():
- graphs = moose.Neutral( '/graphs' )
- ca = moose.Neutral( '/graphs/ca' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'ca/somaCa' )
- addPlot( '/model/elec/lat_11_2/Ca_conc', 'getCa', 'ca/lat11Ca' )
- addPlot( '/model/elec/spine_head_14_4/NMDA_Ca_conc', 'getCa', 'ca/spine4Ca' )
- addPlot( '/model/elec/spine_head_14_12/NMDA_Ca_conc', 'getCa', 'ca/spine12Ca' )
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/spine_head_14_4', 'getVm', 'elec/spineVm' )
-
-def makeChemPlots():
- graphs = moose.Neutral( '/graphs' )
- chem = moose.Neutral( '/graphs/chem' )
- addPlot( '/model/chem/psd/CaM_dash_Ca4', 'getConc', 'chem/psdCaCam' )
- addPlot( '/model/chem/psd/actCaMKII', 'getConc', 'chem/psdActCaMKII' )
- addPlot( '/model/chem/spine/CaM_dash_Ca4', 'getConc', 'chem/spineCaCam' )
- addPlot( '/model/chem/spine/CaM_dash_Ca4[12]', 'getConc', 'chem/spine12CaCam' )
- addPlot( '/model/chem/spine/actCaMKII', 'getConc', 'chem/spineActCaMKII' )
- addPlot( '/model/chem/spine/actCaMKII[11]', 'getConc', 'chem/spine12ActCaMKII' )
- addPlot( '/model/chem/psd/Ca', 'getConc', 'chem/psdCa' )
- addPlot( '/model/chem/psd/Ca[11]', 'getConc', 'chem/psd12Ca' )
- addPlot( '/model/chem/spine/Ca[3]', 'getConc', 'chem/spine4Ca' )
- addPlot( '/model/chem/spine/Ca[11]', 'getConc', 'chem/spine12Ca' )
- #addPlot( '/model/chem/dend/DEND/Ca', 'getConc', 'chem/dendCa' )
- #addPlot( '/model/chem/dend/DEND/Ca[20]', 'getConc', 'chem/dendCa20' )
-
-def makeGraphics( cPlotDt, ePlotDt ):
- plt.ion()
- fig = plt.figure( figsize=(10,16) )
- chem = fig.add_subplot( 411 )
- chem.set_ylim( 0, 0.006 )
- plt.ylabel( 'Conc (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/chem/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
- line1, = chem.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- elec = fig.add_subplot( 412 )
- plt.ylabel( 'Vm (V)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = elec.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- ca = fig.add_subplot( 413 )
- plt.ylabel( '[Ca] (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/ca/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = ca.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- lenplot = fig.add_subplot( 414 )
- plt.ylabel( 'Ca (mM )' )
- plt.xlabel( 'Voxel#)' )
-
- spineCa = moose.vec( '/model/chem/spine/Ca' )
- dendCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- line1, = lenplot.plot( list(range( len( spineCa ))), spineCa.conc, label='spine' )
- line2, = lenplot.plot( list(range( len( dendCa ))), dendCa.conc, label='dend' )
-
- ca = [ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConcBase]') ]
- line3, = lenplot.plot( list(range( len( ca ))), ca, label='elec' )
-
- spineCaM = moose.vec( '/model/chem/spine/CaM_dash_Ca4' )
- line4, = lenplot.plot( list(range( len( spineCaM ))), spineCaM.conc, label='spineCaM' )
- psdCaM = moose.vec( '/model/chem/psd/CaM_dash_Ca4' )
- line5, = lenplot.plot( list(range( len( psdCaM ))), psdCaM.conc, label='psdCaM' )
- plt.legend()
-
- fig.canvas.draw()
- eval(input())
- print('All done')
-
-def testNeuroMeshMultiscale():
- useHsolve = 0
- runtime = 0.5
- elecDt = 10e-6
- chemDt = 0.005
- ePlotDt = 0.5e-3
- cPlotDt = 0.005
- plotName = 'nm.plot'
-
- makeNeuroMeshModel()
- print("after model is completely done")
- for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ):
- print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
-
- makeChemPlots()
- makeElecPlots()
- makeCaPlots()
- for i in range( 10 ):
- moose.setClock( i, elecDt )
- for i in range( 10, 20 ):
- moose.setClock( i, chemDt )
- moose.setClock( 8, ePlotDt )
- moose.setClock( 18, cPlotDt )
- if useHsolve:
- hsolve = moose.HSolve( '/model/elec/hsolve' )
- #moose.useClock( 1, '/model/elec/hsolve', 'process' )
- hsolve.dt = elecDt
- hsolve.target = '/model/elec/compt'
- moose.reinit()
- #soma = moose.element( '/model/elec/soma' )
- moose.useClock( 18, '/graphs/chem/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#,/graphs/ca/#', 'process' )
- moose.element( '/model/elec/soma' ).inject = 2e-10
- moose.element( '/model/chem/psd/Ca' ).concInit = 0.001
- moose.element( '/model/chem/spine/Ca' ).concInit = 0.002
- moose.element( '/model/chem/dend/DEND/Ca' ).concInit = 0.003
- moose.reinit()
-
- moose.start( runtime )
- makeGraphics( cPlotDt, ePlotDt )
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# minimal.py ends here.
diff --git a/moose-examples/snippets/MULTI/multi3.py b/moose-examples/snippets/MULTI/multi3.py
deleted file mode 100644
index d6cc945f94174e9bad2cd335ea8292e090ae9ae7..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/multi3.py
+++ /dev/null
@@ -1,380 +0,0 @@
-# multi2.py ---
-# Upi Bhalla, NCBS Bangalore 2014.
-#
-# Commentary:
-#
-# This loads in a medium-detail model incorporating
-# reac-diff and elec signaling in neurons. The reac-diff model is
-# psd_merged31d.g which has only Ca in the dendrites, but is quite
-# interesting in the PSD and spine head. Problem is lots of
-# cross-compartment reactions.
-# has in it, and there are no-cross-compartment
-# reactions though Ca diffuses everywhere. The elec model controls the
-# Ca levels in the chem compartments.
-# This version uses solvers for both chem and electrical parts.
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-import os
-os.environ['NUMPTHREADS'] = '1'
-import math
-import numpy
-import matplotlib.pyplot as plt
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- moose.setCwe( '/library' )
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "Neutral" )
- return cellId
-
-def loadChem( diffLength ):
- chem = moose.Neutral( '/model/chem' )
- neuroCompt = moose.NeuroMesh( '/model/chem/kinetics' )
- neuroCompt.separateSpines = 1
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/chem/compartment_1' )
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/chem/compartment_2' )
- #print 'Meshvolume[neuro, spine, psd] = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- #modelId = moose.loadModel( 'separate_compts.g', '/model/chem', 'ee' )
- modelId = moose.loadModel( 'psd_merged31d.g', '/model/chem', 'ee' )
- neuroCompt.name = 'dend'
- spineCompt.name = 'spine'
- psdCompt.name = 'psd'
-
-def makeNeuroMeshModel():
- diffLength = 10e-6 # Aim for 2 soma compartments.
- elec = loadElec()
- loadChem( diffLength )
- neuroCompt = moose.element( '/model/chem/dend' )
- neuroCompt.diffLength = diffLength
- neuroCompt.cellPortion( elec, '/model/elec/#' )
- for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if (x.diffConst > 0):
- x.diffConst = 1e-11
- for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- x.diffConst = 1e-10
-
- # Put in dend solvers
- ns = neuroCompt.numSegments
- ndc = neuroCompt.numDiffCompts
- print(('ns = ', ns, ', ndc = ', ndc))
- assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
- assert( ns == 36 ) #
- assert( ndc == 278 ) #
- nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
- nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
- nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
- nmstoich.compartment = neuroCompt
- nmstoich.ksolve = nmksolve
- nmstoich.dsolve = nmdsolve
- nmstoich.path = "/model/chem/dend/##"
- print(('done setting path, numPools = ', nmdsolve.numPools))
- assert( nmdsolve.numPools == 1 )
- assert( nmdsolve.numAllVoxels == ndc )
- assert( nmstoich.numAllPools == 1 )
- # oddly, numLocalFields does not work.
- ca = moose.element( '/model/chem/dend/DEND/Ca' )
- assert( ca.numData == ndc )
-
- # Put in spine solvers. Note that these get info from the neuroCompt
- spineCompt = moose.element( '/model/chem/spine' )
- sdc = spineCompt.mesh.num
- print(('sdc = ', sdc))
- assert( sdc == 13 )
- smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
- smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
- smstoich = moose.Stoich( '/model/chem/spine/stoich' )
- smstoich.compartment = spineCompt
- smstoich.ksolve = smksolve
- smstoich.dsolve = smdsolve
- smstoich.path = "/model/chem/spine/##"
- print(('spine num Pools = ', smstoich.numAllPools, 'dsolve n = ', smdsolve.numPools))
- assert( smstoich.numAllPools == 36 )
- assert( smdsolve.numPools == 31 )
- assert( smdsolve.numAllVoxels == sdc )
-
- # Put in PSD solvers. Note that these get info from the neuroCompt
- psdCompt = moose.element( '/model/chem/psd' )
- pdc = psdCompt.mesh.num
- assert( pdc == 13 )
- pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
- pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
- pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
- pmstoich.compartment = psdCompt
- pmstoich.ksolve = pmksolve
- pmstoich.dsolve = pmdsolve
- pmstoich.path = "/model/chem/psd/##"
- print(('psd num Pools = ', pmstoich.numAllPools))
- assert( pmstoich.numAllPools == 56 )
- assert( pmdsolve.numPools == 49 )
- assert( pmdsolve.numAllVoxels == pdc )
- foo = moose.element( '/model/chem/psd/Ca' )
- print(('PSD: numfoo = ', foo.numData))
- print(('PSD: numAllVoxels = ', pmksolve.numAllVoxels))
-
- # Put in junctions between the diffusion solvers
- nmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
-
- # Put in cross-compartment reactions between ksolvers
- nmstoich.buildXreacs( smstoich )
- smstoich.buildXreacs( pmstoich )
-
- """
- CaNpsd = moose.vec( '/model/chem/psdMesh/PSD/PP1_PSD/CaN' )
- print 'numCaN in PSD = ', CaNpsd.nInit, ', vol = ', CaNpsd.volume
- CaNspine = moose.vec( '/model/chem/spine/SPINE/CaN_BULK/CaN' )
- print 'numCaN in spine = ', CaNspine.nInit, ', vol = ', CaNspine.volume
- """
-
- ##################################################################
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/spine/adaptCa', sdc )
- adaptCa = moose.vec( '/model/chem/spine/adaptCa' )
- chemCa = moose.vec( '/model/chem/spine/Ca' )
- #print 'aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData, "len( adaptCa ) = ", len( adaptCa )
- assert( len( adaptCa ) == sdc )
- assert( len( chemCa ) == sdc )
- for i in range( sdc ):
- elecCa = moose.element( '/model/elec/spine_head_14_' + str(i+1) + '/NMDA_Ca_conc' )
- #print elecCa
- moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
- moose.connect( adaptCa, 'output', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 5e-3 # 520 to 0.0052 mM
- #print adaptCa.outputOffset
-
-
- moose.le( '/model/chem/dend/DEND' )
-
-
- compts = neuroCompt.elecComptList
- begin = neuroCompt.startVoxelInCompt
- end = neuroCompt.endVoxelInCompt
- aCa = moose.Adaptor( '/model/chem/dend/DEND/adaptCa', len( compts))
- adaptCa = moose.vec( '/model/chem/dend/DEND/adaptCa' )
- chemCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- #print 'aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData, "len( adaptCa ) = ", len( adaptCa )
- assert( len( chemCa ) == ndc )
- for i in zip( compts, adaptCa, begin, end ):
- name = i[0].path + '/Ca_conc'
- if ( moose.exists( name ) ):
- elecCa = moose.element( name )
- #print i[2], i[3], ' ', elecCa
- #print i[1]
- moose.connect( elecCa, 'concOut', i[1], 'input', 'Single' )
- for j in range( i[2], i[3] ):
- moose.connect( i[1], 'output', chemCa[j], 'setConc', 'Single' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
- adaptCa.scale = 20e-6 # 10 arb units to 2 uM.
-
-def addPlot( objpath, field, plot ):
- #assert moose.exists( objpath )
- if moose.exists( objpath ):
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- if obj.className == 'Neutral':
- print(("addPlot failed: object is a Neutral: ", objpath))
- return moose.element( '/' )
- else:
- #print "object was found: ", objpath, obj.className
- moose.connect( tab, 'requestOut', obj, field )
- return tab
- else:
- print(("addPlot failed: object not found: ", objpath))
- return moose.element( '/' )
-
-def makeCaPlots():
- graphs = moose.Neutral( '/graphs' )
- ca = moose.Neutral( '/graphs/ca' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'ca/somaCa' )
- addPlot( '/model/elec/lat_11_2/Ca_conc', 'getCa', 'ca/lat11Ca' )
- addPlot( '/model/elec/spine_head_14_4/NMDA_Ca_conc', 'getCa', 'ca/spine4Ca' )
- addPlot( '/model/elec/spine_head_14_12/NMDA_Ca_conc', 'getCa', 'ca/spine12Ca' )
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/spine_head_14_4', 'getVm', 'elec/spineVm' )
-
-def makeChemPlots():
- graphs = moose.Neutral( '/graphs' )
- chem = moose.Neutral( '/graphs/chem' )
- addPlot( '/model/chem/psd/CaM_dash_Ca4', 'getConc', 'chem/psdCaCam' )
- addPlot( '/model/chem/psd/actCaMKII', 'getConc', 'chem/psdActCaMKII' )
- addPlot( '/model/chem/spine/CaM_dash_Ca4', 'getConc', 'chem/spineCaCam' )
- addPlot( '/model/chem/spine/CaM_dash_Ca4[12]', 'getConc', 'chem/spine12CaCam' )
- addPlot( '/model/chem/spine/actCaMKII', 'getConc', 'chem/spineActCaMKII' )
- addPlot( '/model/chem/spine/actCaMKII[11]', 'getConc', 'chem/spine12ActCaMKII' )
- addPlot( '/model/chem/psd/Ca', 'getConc', 'chem/psdCa' )
- addPlot( '/model/chem/psd/Ca[11]', 'getConc', 'chem/psd12Ca' )
- addPlot( '/model/chem/spine/Ca[3]', 'getConc', 'chem/spine4Ca' )
- addPlot( '/model/chem/spine/Ca[11]', 'getConc', 'chem/spine12Ca' )
- #addPlot( '/model/chem/dend/DEND/Ca', 'getConc', 'chem/dendCa' )
- #addPlot( '/model/chem/dend/DEND/Ca[20]', 'getConc', 'chem/dendCa20' )
-
-def makeGraphics( cPlotDt, ePlotDt ):
- plt.ion()
- fig = plt.figure( figsize=(10,16) )
- chem = fig.add_subplot( 411 )
- chem.set_ylim( 0, 0.006 )
- plt.ylabel( 'Conc (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/chem/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
- line1, = chem.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- elec = fig.add_subplot( 412 )
- plt.ylabel( 'Vm (V)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = elec.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- ca = fig.add_subplot( 413 )
- plt.ylabel( '[Ca] (mM)' )
- plt.xlabel( 'time (seconds)' )
- for x in moose.wildcardFind( '/graphs/ca/#[ISA=Table]' ):
- pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
- line1, = ca.plot( pos, x.vector, label=x.name )
- plt.legend()
-
- lenplot = fig.add_subplot( 414 )
- plt.ylabel( 'Ca (mM )' )
- plt.xlabel( 'Voxel#)' )
-
- spineCa = moose.vec( '/model/chem/spine/Ca' )
- dendCa = moose.vec( '/model/chem/dend/DEND/Ca' )
- line1, = lenplot.plot( list(range( len( spineCa ))), spineCa.conc, label='spine' )
- line2, = lenplot.plot( list(range( len( dendCa ))), dendCa.conc, label='dend' )
-
- ca = [ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConcBase]') ]
- line3, = lenplot.plot( list(range( len( ca ))), ca, label='elec' )
-
- spineCaM = moose.vec( '/model/chem/spine/CaM_dash_Ca4' )
- line4, = lenplot.plot( list(range( len( spineCaM ))), spineCaM.conc, label='spineCaM' )
- psdCaM = moose.vec( '/model/chem/psd/CaM_dash_Ca4' )
- line5, = lenplot.plot( list(range( len( psdCaM ))), psdCaM.conc, label='psdCaM' )
- plt.legend()
-
-
- fig.canvas.draw()
- eval(input())
-
- '''
- for x in moose.wildcardFind( '/graphs/##[ISA=Table]' ):
- t = numpy.arange( 0, x.vector.size, 1 )
- pylab.plot( t, x.vector, label=x.name )
- pylab.legend()
- pylab.show()
- '''
-
- print('All done')
-
-def testNeuroMeshMultiscale():
- useHsolve = 1
- runtime = 0.5
- if useHsolve:
- elecDt = 50e-6
- else:
- elecDt = 10e-6
- chemDt = 0.005
- ePlotDt = 0.5e-3
- cPlotDt = 0.005
- plotName = 'nm.plot'
- makeNeuroMeshModel()
- print("after model is completely done")
- for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ):
- print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
-
- makeChemPlots()
- makeElecPlots()
- makeCaPlots()
- moose.setClock( 0, elecDt )
- moose.setClock( 1, elecDt )
- moose.setClock( 2, elecDt )
- moose.setClock( 4, chemDt )
- moose.setClock( 5, chemDt )
- moose.setClock( 6, chemDt )
- moose.setClock( 7, cPlotDt )
- moose.setClock( 8, ePlotDt )
- if useHsolve:
- hsolve = moose.HSolve( '/model/elec/hsolve' )
- moose.useClock( 1, '/model/elec/hsolve', 'process' )
- hsolve.dt = elecDt
- hsolve.target = '/model/elec/compt'
- moose.reinit()
- else:
- moose.useClock( 0, '/model/elec/##[ISA=Compartment]', 'init' )
- moose.useClock( 1, '/model/elec/##[ISA=Compartment]', 'process' )
- moose.useClock( 2, '/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
-
- moose.useClock( 1, '/model/elec/##[ISA=SpikeGen]', 'process' )
- moose.useClock( 2, '/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
-
- moose.useClock( 4, '/model/chem/#/dsolve', 'process' )
- moose.useClock( 4, '/model/chem/#/ksolve', 'init' )
- moose.useClock( 5, '/model/chem/#/ksolve', 'process' )
- moose.useClock( 6, '/model/chem/spine/adaptCa', 'process' )
- moose.useClock( 6, '/model/chem/dend/DEND/adaptCa', 'process' )
- moose.useClock( 7, '/graphs/chem/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#,/graphs/ca/#', 'process' )
- moose.element( '/model/elec/soma' ).inject = 2e-10
- moose.element( '/model/chem/psd/Ca' ).concInit = 0.001
- moose.element( '/model/chem/spine/Ca' ).concInit = 0.002
- moose.element( '/model/chem/dend/DEND/Ca' ).concInit = 0.003
- moose.reinit()
-
- moose.start( runtime )
- makeGraphics( cPlotDt, ePlotDt )
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# minimal.py ends here.
diff --git a/moose-examples/snippets/MULTI/proto18.py b/moose-examples/snippets/MULTI/proto18.py
deleted file mode 100644
index 05ba3d549fc67b8401765b174aa5bb7ea516ded9..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/proto18.py
+++ /dev/null
@@ -1,497 +0,0 @@
-#/* FILE INFORMATION
-#** Based mostly on the traub91proto.g by Dave Beeman
-#** Main difference is addition of Glu and NMDA channels
-#** The 1991 Traub set of voltage and concentration dependent channels
-#** Implemented as tabchannels by : Dave Beeman
-#** R.D.Traub, R. K. S. Wong, R. Miles, and H. Michelson
-#** Journal of Neurophysiology, Vol. 66, p. 635 (1991)
-#**
-#** This file depends on functions and constants defined in defaults.g
-#** As it is also intended as an example of the use of the tabchannel
-#** object to implement concentration dependent channels, it has extensive
-#** comments. Note that the original units used in the paper have been
-#** converted to SI (MKS) units. Also, we define the ionic equilibrium
-#** potentials relative to the resting potential, EREST_ACT. In the
-#** paper, this was defined to be zero. Here, we use -0.060 volts, the
-#** measured value relative to the outside of the cell.
-#*/
-
-#/* November 1999 update for GENESIS 2.2: Previous versions of this file used
-# a combination of a table, tabgate, and vdep_channel to implement the
-# Ca-dependent K Channel - K(C). This new version uses the new tabchannel
-# "instant" field, introduced in GENESIS 2.2, to implement an
-# "instantaneous" gate for the multiplicative Ca-dependent factor in the
-# conductance. This allows these channels to be used with the fast
-# hsolve chanmodes > 1.
-#*/
-
-# Apr 2012 update for pymoose. Converted to equivalent MOOSE funcs.
-
-import moose
-import numpy
-import math
-
-#CONSTANTS
-EREST_ACT = -0.060 #/* hippocampal cell resting potl */
-ENA = 0.115 + EREST_ACT #// 0.055
-EK = -0.015 + EREST_ACT #// -0.075
-ECA = 0.140 + EREST_ACT #// 0.080
-SOMA_A = 3.320e-9 #// soma area in square meters
-
-#/*
-#For these channels, the maximum channel conductance (Gbar) has been
-#calculated using the CA3 soma channel conductance densities and soma
-#area. Typically, the functions which create these channels will be used
-#to create a library of prototype channels. When the cell reader creates
-#copies of these channels in various compartments, it will set the actual
-#value of Gbar by calculating it from the cell parameter file.
-#*/
-
-#//========================================================================
-#// Tabulated Ca Channel
-#//========================================================================
-
-def make_Ca():
- if moose.exists( 'Ca' ):
- return
- Ca = moose.HHChannel( 'Ca' )
- Ca.Ek = ECA
- Ca.Gbar = 40 * SOMA_A
- Ca.Gk = 0
- Ca.Xpower = 2
- Ca.Ypower = 1
- Ca.Zpower = 0
-
- xgate = moose.element( 'Ca/gateX' )
- xA = numpy.array( [ 1.6e3, 0, 1.0, -1.0 * (0.065 + EREST_ACT), -0.01389, -20e3 * (0.0511 + EREST_ACT), 20e3, -1.0, -1.0 * (0.0511 + EREST_ACT), 5.0e-3, 3000, -0.1, 0.05 ] )
-# xgate.min = -0.1
-# xgate.max = 0.05
-# xgate.divs = 3000
-#// Converting Traub's expressions for the gCa/s alpha and beta functions
-#// to SI units and entering the A, B, C, D and F parameters, we get:
-# xgate.alpha( 1.6e3, 0, 1.0, -1.0 * (0.065 + EREST_ACT), -0.01389 )
-# xgate.beta( -20e3 * (0.0511 + EREST_ACT), 20e3, -1.0, -1.0 * (0.0511 + EREST_ACT), 5.0e-3 )
- #xgate.setupAlpha( xA )
- xgate.alphaParms = xA
-
-
-# The Y gate (gCa/r) is not quite of this form. For V > EREST_ACT, alpha =
-# 5*{exp({-50*(V - EREST_ACT)})}. Otherwise, alpha = 5. Over the entire
-# range, alpha + beta = 5. To create the Y_A and Y_B tables, we use some
-# of the pieces of the setupalpha function.
- ygate = moose.element( 'Ca/gateY' )
- ygate.min = -0.1
- ygate.max = 0.05
- ygate.divs = 3000
- yA = numpy.zeros( (ygate.divs + 1), dtype=float)
- yB = numpy.zeros( (ygate.divs + 1), dtype=float)
-
-
-#Fill the Y_A table with alpha values and the Y_B table with (alpha+beta)
- dx = (ygate.max - ygate.min)/ygate.divs
- x = ygate.min
- for i in range( ygate.divs + 1 ):
- if ( x > EREST_ACT):
- yA[i] = 5.0 * math.exp( -50 * (x - EREST_ACT) )
- else:
- yA[i] = 5.0
- yB[i] = 5.0
- x += dx
- ygate.tableA = yA
- ygate.tableB = yB
-# Tell the cell reader that the current from this channel must be fed into
-# the Ca_conc pool of calcium.
- addmsg1 = moose.Mstring( '/library/Ca/addmsg1' )
- addmsg1.value = '. IkOut ../Ca_conc current'
-# in some compartments, whe have an NMDA_Ca_conc object to put the current
-# into.
- addmsg2 = moose.Mstring( '/library/Ca/addmsg2' )
- addmsg2.value = '. IkOut ../NMDA_Ca_conc current'
-# As we typically use the cell reader to create copies of these prototype
-#elements in one or more compartments, we need some way to be sure that the
-#needed messages are established. Although the cell reader has enough
-#information to create the messages which link compartments to their channels
-#and to other adjacent compartments, it most be provided with the information
-#needed to establish additional messages. This is done by placing the
-#message string in a user-defined field of one of the elements which is
-#involved in the message. The cell reader recognizes the added object names
-#"addmsg1", "addmsg2", etc. as indicating that they are to be
-#evaluated and used to set up messages. The paths are relative to the
-#element which contains the message string in its added field. Thus,
-#"../Ca_conc" refers to the sibling element Ca_conc and "."
-#refers to the Ca element itself.
-
-
-#/*************************************************************************
-#Next, we need an element to take the Calcium current calculated by the Ca
-#channel and convert it to the Ca concentration. The "Ca_concen" object
-#solves the equation dC/dt = B*I_Ca - C/tau, and sets Ca = Ca_base + C. As
-#it is easy to make mistakes in units when using this Calcium diffusion
-#equation, the units used here merit some discussion.
-
-#With Ca_base = 0, this corresponds to Traub's diffusion equation for
-#concentration, except that the sign of the current term here is positive, as
-#GENESIS uses the convention that I_Ca is the current flowing INTO the
-#compartment through the channel. In SI units, the concentration is usually
-#expressed in moles/m^3 (which equals millimoles/liter), and the units of B
-#are chosen so that B = 1/(ion_charge * Faraday * volume). Current is
-#expressed in amperes and one Faraday = 96487 coulombs. However, in this
-#case, Traub expresses the concentration in arbitrary units, current in
-#microamps and uses tau = 13.33 msec. If we use the same concentration units,
-#but express current in amperes and tau in seconds, our B constant is then
-#10^12 times the constant (called "phi") used in the paper. The actual value
-#used will be typically be determined by the cell reader from the cell
-#parameter file. However, for the prototype channel we wlll use Traub's
-#corrected value for the soma. (An error in the paper gives it as 17,402
-#rather than 17.402.) In our units, this will be 17.402e12.
-
-#*************************************************************************/
-
-
-#//========================================================================
-#// Ca conc
-#//========================================================================
-
-def make_Ca_conc():
- if moose.exists( 'Ca_conc' ):
- return
- conc = moose.CaConc( 'Ca_conc' )
- conc.tau = 0.013333 # sec
- conc.B = 17.402e12 # Curr to conc conversion for soma
- conc.Ca_base = 0.0
-
-#This Ca_concen element should receive a message from any calcium channels
-# with the current going through the channel. Here we have this specified
-# in the Ca channel, with the idea that more than one channel might
-# contribute Ca ions to this calcium pool. In the original GENESIS file
-# this was specified here in make_Ca_conc.
-
-#========================================================================
-# Tabulated Ca-dependent K AHP Channel
-#========================================================================
-
-# This is a tabchannel which gets the calcium concentration from Ca_conc
-# in order to calculate the activation of its Z gate. It is set up much
-# like the Ca channel, except that the A and B tables have values which are
-# functions of concentration, instead of voltage.
-
-def make_K_AHP():
- if moose.exists( 'K_AHP' ):
- return
-
- K_AHP = moose.HHChannel( 'K_AHP' )
- K_AHP.Ek = EK # V
- K_AHP.Gbar = 8 * SOMA_A # S
- K_AHP.Gk = 0 # S
- K_AHP.Xpower = 0
- K_AHP.Ypower = 0
- K_AHP.Zpower = 1
-
- zgate = moose.element( 'K_AHP/gateZ' )
- xmax = 500.0
- zgate.min = 0
- zgate.max = xmax
- zgate.divs = 3000
- zA = numpy.zeros( (zgate.divs + 1), dtype=float)
- zB = numpy.zeros( (zgate.divs + 1), dtype=float)
- dx = (zgate.max - zgate.min)/zgate.divs
- x = zgate.min
- for i in range( zgate.divs + 1 ):
- if (x < (xmax / 2.0 )):
- zA[i] = 0.02*x
- else:
- zA[i] = 10.0
- zB[i] = zA[i] + 1.0
- x = x + dx
-
- zgate.tableA = zA
- zgate.tableB = zB
- addmsg1 = moose.Mstring( '/library/K_AHP/addmsg1' )
- addmsg1.value = '../Ca_conc concOut . concen'
-# Use an added field to tell the cell reader to set up a message from the
-# Ca_Conc with concentration info, to the current K_AHP object.
-
-
-#//========================================================================
-#// Ca-dependent K Channel - K(C) - (vdep_channel with table and tabgate)
-#//========================================================================
-
-#The expression for the conductance of the potassium C-current channel has a
-#typical voltage and time dependent activation gate, where the time dependence
-#arises from the solution of a differential equation containing the rate
-#parameters alpha and beta. It is multiplied by a function of calcium
-#concentration that is given explicitly rather than being obtained from a
-#differential equation. Therefore, we need a way to multiply the activation
-#by a concentration dependent value which is determined from a lookup table.
-#This is accomplished by using the Z gate with the new tabchannel "instant"
-#field, introduced in GENESIS 2.2, to implement an "instantaneous" gate for
-#the multiplicative Ca-dependent factor in the conductance.
-
-def make_K_C():
- if moose.exists( 'K_C'):
- return
-
- K_C = moose.HHChannel( 'K_C' )
- K_C.Ek = EK # V
- K_C.Gbar = 100.0 * SOMA_A # S
- K_C.Gk = 0 # S
- K_C.Xpower = 1
- K_C.Zpower = 1
- K_C.instant = 4 # Flag: 0x100 means Z gate is instant.
-
- # Now make a X-table for the voltage-dependent activation parameter.
- xgate = moose.element( 'K_C/gateX' )
- xgate.min = -0.1
- xgate.max = 0.05
- xgate.divs = 3000
- xA = numpy.zeros( (xgate.divs + 1), dtype=float)
- xB = numpy.zeros( (xgate.divs + 1), dtype=float)
- dx = (xgate.max - xgate.min)/xgate.divs
- x = xgate.min
- for i in range( xgate.divs + 1 ):
- alpha = 0.0
- beta = 0.0
- if (x < EREST_ACT + 0.05):
- alpha = math.exp( 53.872 * (x - EREST_ACT) - 0.66835 ) / 0.018975
- beta = 2000* (math.exp ( (EREST_ACT + 0.0065 - x)/0.027)) - alpha
- else:
- alpha = 2000 * math.exp( ( EREST_ACT + 0.0065 - x)/0.027 )
- beta = 0.0
- xA[i] = alpha
- xB[i] = alpha + beta
- x = x + dx
- xgate.tableA = xA
- xgate.tableB = xB
-
-# Create a table for the function of concentration, allowing a
-# concentration range of 0 to 1000, with 50 divisions. This is done
-# using the Z gate, which can receive a CONCEN message. By using
-# the "instant" flag, the A and B tables are evaluated as lookup tables,
-# rather than being used in a differential equation.
- zgate = moose.element( 'K_C/gateZ' )
- zgate.min = 0.0
- xmax = 500.0
- zgate.max = xmax
- zgate.divs = 3000
- zA = numpy.zeros( (zgate.divs + 1), dtype=float)
- zB = numpy.zeros( (zgate.divs + 1), dtype=float)
- dx = ( zgate.max - zgate.min)/ zgate.divs
- x = zgate.min
- for i in range( xgate.divs + 1 ):
- if ( x < ( xmax / 4.0 ) ):
- zA[i] = x * 4.0 / xmax
- else:
- zA[i] = 1.0
- zB[i] = 1.0
- x += dx
- zgate.tableA = zA
- zgate.tableB = zB
-
-# Now we need to provide for messages that link to external elements.
-# The message that sends the Ca concentration to the Z gate tables is stored
-# in an added field of the channel, so that it may be found by the cell
-# reader.
- addmsg1 = moose.Mstring( '/library/K_C/addmsg1' )
- addmsg1.value = '../Ca_conc concOut . concen'
-
-
-# The remaining channels are straightforward tabchannel implementations
-
-#/========================================================================
-#/ Tabchannel Na Hippocampal cell channel
-#/========================================================================
-def make_Na():
- if moose.exists( 'Na' ):
- return
- Na = moose.HHChannel( 'Na' )
- Na.Ek = ENA # V
- Na.Gbar = 300 * SOMA_A # S
- Na.Gk = 0 # S
- Na.Xpower = 2
- Na.Ypower = 1
- Na.Zpower = 0
-
- xgate = moose.element( 'Na/gateX' )
- xA = numpy.array( [ 320e3 * (0.0131 + EREST_ACT),
- -320e3, -1.0, -1.0 * (0.0131 + EREST_ACT), -0.004,
- -280e3 * (0.0401 + EREST_ACT), 280e3, -1.0,
- -1.0 * (0.0401 + EREST_ACT), 5.0e-3,
- 3000, -0.1, 0.05 ] )
- xgate.alphaParms = xA
-
-
- #xgate.alpha( 320e3 * (0.0131 + EREST_ACT), -320e3, -1.0, -1.0 * (0.0131 + EREST_ACT), -0.004 )
- #xgate.beta( -280e3 * (0.0401 + EREST_ACT), 280e3, -1.0, -1.0 * (0.0401 + EREST_ACT), 5.0e-3 )
-
- ygate = moose.element( 'Na/gateY' )
- yA = numpy.array( [ 128.0, 0.0, 0.0, -1.0 * (0.017 + EREST_ACT), 0.018,
- 4.0e3, 0.0, 1.0, -1.0 * (0.040 + EREST_ACT), -5.0e-3,
- 3000, -0.1, 0.05 ] )
- ygate.alphaParms = yA
-
- #ygate.alpha( 128.0, 0.0, 0.0, -1.0 * (0.017 + EREST_ACT), 0.018 )
- #ygate.beta( 4.0e3, 0.0, 1.0, -1.0 * (0.040 + EREST_ACT), -5.0e-3 )
-
-#========================================================================
-# Tabchannel K(DR) Hippocampal cell channel
-#========================================================================
-def make_K_DR():
- if moose.exists( 'K_DR' ):
- return
- K_DR = moose.HHChannel( 'K_DR' )
- K_DR.Ek = EK # V
- K_DR.Gbar = 150 * SOMA_A # S
- K_DR.Gk = 0 # S
- K_DR.Xpower = 1
- K_DR.Ypower = 0
- K_DR.Zpower = 0
-
- xgate = moose.element( 'K_DR/gateX' )
- xA = numpy.array( [ 16e3 * (0.0351 + EREST_ACT),
- -16e3, -1.0, -1.0 * (0.0351 + EREST_ACT), -0.005,
- 250, 0.0, 0.0, -1.0 * (0.02 + EREST_ACT), 0.04,
- 3000, -0.1, 0.05 ] )
- xgate.alphaParms = xA
- #xgate.alpha( 16e3 * (0.0351 + EREST_ACT), -16e3, -1.0, -1.0 * (0.0351 + EREST_ACT), -0.005 )
- #xgate.beta( 250, 0.0, 0.0, -1.0 * (0.02 + EREST_ACT), 0.04 )
-
-#========================================================================
-# Tabchannel K(A) Hippocampal cell channel
-#========================================================================
-def make_K_A():
- if moose.exists( 'K_A' ):
- return
- K_A = moose.HHChannel( 'K_A' )
- K_A.Ek = EK # V
- K_A.Gbar = 50 * SOMA_A # S
- K_A.Gk = 0 # S
- K_A.Xpower = 1
- K_A.Ypower = 1
- K_A.Zpower = 0
-
- xgate = moose.element( 'K_A/gateX' )
- xA = numpy.array( [ 20e3 * (0.0131 + EREST_ACT),
- -20e3, -1.0, -1.0 * (0.0131 + EREST_ACT), -0.01,
- -17.5e3 * (0.0401 + EREST_ACT),
- 17.5e3, -1.0, -1.0 * (0.0401 + EREST_ACT), 0.01,
- 3000, -0.1, 0.05 ] )
- xgate.alphaParms = xA
- # xgate.alpha( 20e3 * (0.0131 + EREST_ACT), -20e3, -1.0, -1.0 * (0.0131 + EREST_ACT), -0.01 )
- # xgate.beta( -17.5e3 * (0.0401 + EREST_ACT), 17.5e3, -1.0, -1.0 * (0.0401 + EREST_ACT), 0.01 )
-
- ygate = moose.element( 'K_A/gateY' )
- yA = numpy.array( [ 1.6, 0.0, 0.0, 0.013 - EREST_ACT, 0.018,
- 50.0, 0.0, 1.0, -1.0 * (0.0101 + EREST_ACT), -0.005,
- 3000, -0.1, 0.05 ] )
- ygate.alphaParms = yA
- # ygate.alpha( 1.6, 0.0, 0.0, 0.013 - EREST_ACT, 0.018 )
- # ygate.beta( 50.0, 0.0, 1.0, -1.0 * (0.0101 + EREST_ACT), -0.005 )
-#========================================================================
-# SynChan: Glu receptor
-#========================================================================
-
-def make_glu():
- if moose.exists( 'glu' ):
- return
- glu = moose.SynChan( 'glu' )
- glu.Ek = 0.0
- glu.tau1 = 2.0e-3
- glu.tau2 = 9.0e-3
- glu.Gbar = 40 * SOMA_A
-
-#========================================================================
-# SynChan: NMDA receptor
-#========================================================================
-
-def make_NMDA():
- if moose.exists( 'NMDA' ):
- return
- NMDA = moose.SynChan( 'NMDA' )
- NMDA.Ek = 0.0
- NMDA.tau1 = 20.0e-3
- NMDA.tau2 = 20.0e-3
- NMDA.Gbar = 5 * SOMA_A
-
- block = moose.MgBlock( '/library/NMDA/block' )
- block.CMg = 1.2 # [Mg] in mM
- block.Zk = 2
- block.KMg_A = 1.0/0.28
- block.KMg_B = 1.0/62
-
- moose.connect( NMDA, 'channelOut', block, 'origChannel', 'OneToOne' )
- addmsg1 = moose.Mstring( '/library/NMDA/addmsg1' )
- addmsg1.value = '.. channel ./block channel'
- #Here we want to also tell the cell reader to _remove_ the original
- #Gk, Ek term going from the channel to the compartment, as this is
- # now handled by the MgBlock.
- #addmsg2 = moose.Mstring( 'NMDA/addmsg2'
- #addmsg2.value = 'DropMsg .. channel'
- addmsg3 = moose.Mstring( '/library/NMDA/addmsg3' )
- addmsg3.value = '.. VmOut . Vm'
-
-
-#addfield NMDA addmsg1
-#setfield NMDA addmsg1 ".. ./block VOLTAGE Vm"
-#addfield NMDA addmsg2
-#setfield NMDA addmsg2 "./block .. CHANNEL Gk Ek"
-
-#========================================================================
-# The Ca_NMDA channel is a subset of the NMDA channel that carries Ca.
-# It is identical to above, except that the Ek for Ca is much higher:
-# 0.08 V from the consts at the top of this file.
-# This is about the reversal potl for 1 uM Ca_in, 2 mM out.
-# Also we do not want this channel to contribute to the current,
-# which is already accounted for in the main channel. So there is
-# no CHANNEL message to the parent compartment.
-# I would like to have used the Nernst to do the Ca potential, and
-# Synchans now take Ek messages but I haven't yet used this.
-#========================================================================
-
-def make_Ca_NMDA():
- if moose.exists( 'Ca_NMDA' ):
- return
- Ca_NMDA = moose.SynChan( 'Ca_NMDA' )
- Ca_NMDA.Ek = ECA
- Ca_NMDA.tau1 = 20.0e-3
- Ca_NMDA.tau2 = 20.0e-3
- Ca_NMDA.Gbar = 5 * SOMA_A
-
- block = moose.MgBlock( '/library/Ca_NMDA/block' )
- block.CMg = 1.2 # [Mg] in mM
- block.Zk = 2
- block.KMg_A = 1.0/0.28
- block.KMg_B = 1.0/62
-
- moose.connect( Ca_NMDA, 'channelOut', block, 'origChannel', 'OneToOne' )
- addmsg1 = moose.Mstring( '/library/Ca_NMDA/addmsg1' )
- addmsg1.value = '.. VmOut ./block Vm'
- addmsg2 = moose.Mstring( '/library/Ca_NMDA/addmsg2' )
- addmsg2.value = './block IkOut ../NMDA_Ca_conc current'
- # The original model has the Ca current also coming here.
-
-#========================================================================
-# Ca pool for influx through Ca_NMDA
-#========================================================================
-def make_NMDA_Ca_conc():
- if moose.exists( 'NMDA_Ca_conc' ):
- return
- NMDA_Ca_conc = moose.CaConc( 'NMDA_Ca_conc' )
- NMDA_Ca_conc.tau = 0.004 # sec. Faster in spine than dend
- NMDA_Ca_conc.B = 17.402e12 # overridden by cellreader.
- NMDA_Ca_conc.Ca_base = 0.0
-
-# This pool used to set up Ca info coming to it. Now we insist that the
-# originating channel should specify the deferred message.
-
-#=====================================================================
-# SPIKE DETECTOR
-#=====================================================================
-
-#//addmsg axon/spike axon BUFFER name
-def make_axon():
- if moose.exists( 'axon' ):
- return
- axon = moose.SpikeGen( 'axon' )
- axon.threshold = -40e-3 # V
- axon.abs_refract = 10e-3 # sec
-
diff --git a/moose-examples/snippets/MULTI/psd_merged30.g b/moose-examples/snippets/MULTI/psd_merged30.g
deleted file mode 100644
index c896b1c5f13a5fe0fd5be8339a0384a0501afa63..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/psd_merged30.g
+++ /dev/null
@@ -1,1452 +0,0 @@
-//genesis
-// kkit Version 11 flat dumpfile
-
-// Saved on Fri Jul 19 17:23:18 2013
-
-include kkit {argv 1}
-
-FASTDT = 0.0001
-SIMDT = 0.001
-CONTROLDT = 10
-PLOTDT = 10
-MAXTIME = 2000
-TRANSIENT_TIME = 10
-VARIABLE_DT_FLAG = 1
-DEFAULT_VOL = 1e-20
-VERSION = 11.0
-setfield /file/modpath value /home2/bhalla/scripts/modules
-kparms
-
-//genesis
-
-initdump -version 3 -ignoreorphans 1
-simobjdump doqcsinfo filename accessname accesstype transcriber developer \
- citation species tissue cellcompartment methodology sources \
- model_implementation model_validation x y z
-simobjdump table input output alloced step_mode stepsize x y z
-simobjdump xtree path script namemode sizescale
-simobjdump xcoredraw xmin xmax ymin ymax
-simobjdump xtext editable
-simobjdump xgraph xmin xmax ymin ymax overlay
-simobjdump xplot pixflags script fg ysquish do_slope wy
-simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
- link savename file version md5sum mod_save_flag x y z
-simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
- z
-simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
- geomname xtree_fg_req xtree_textfg_req x y z
-simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
-simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
- keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
-simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
- trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
-simobjdump xtab input output alloced step_mode stepsize notes editfunc \
- xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
-simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
- xtree_textfg_req x y z
-simobjdump transport input output alloced step_mode stepsize dt delay clock \
- kf xtree_fg_req xtree_textfg_req x y z
-simobjdump proto x y z
-simobjdump text str
-simundump geometry /kinetics/geometry 0 1e-20 3 sphere "" white black 0 0 0
-simundump geometry /kinetics/geometry[1] 0 9e-20 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[3] 0 1e-18 3 sphere "" white black 0 0 \
- 0
-simundump text /kinetics/notes 0 ""
-call /kinetics/notes LOAD \
-""
-simundump text /kinetics/geometry/notes 0 ""
-call /kinetics/geometry/notes LOAD \
-""
-simundump text /kinetics/geometry[1]/notes 0 ""
-call /kinetics/geometry[1]/notes LOAD \
-""
-simundump text /kinetics/geometry[2]/notes 0 ""
-call /kinetics/geometry[2]/notes LOAD \
-""
-simundump group /kinetics/PSD 0 20 black x 0 0 "" PSD defaultfile.g 0 0 0 27 \
- 12 0
-simundump text /kinetics/PSD/notes 0 ""
-call /kinetics/PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/tot_PSD_R 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry blue 0 -4 7 0
-simundump text /kinetics/PSD/tot_PSD_R/notes 0 ""
-call /kinetics/PSD/tot_PSD_R/notes LOAD \
-""
-simundump kpool /kinetics/PSD/actCaMKII 0 0 2 2 12 12 0 0 6 0 \
- /kinetics/geometry 12 20 70 33 0
-simundump text /kinetics/PSD/actCaMKII/notes 0 ""
-call /kinetics/PSD/actCaMKII/notes LOAD \
-""
-simundump kenz /kinetics/PSD/actCaMKII/CaMKII_1 0 0 0 0 0 6 0.033332 8 2 0 0 \
- "" red 35 "" -6 3 0
-simundump text /kinetics/PSD/actCaMKII/CaMKII_1/notes 0 ""
-call /kinetics/PSD/actCaMKII/CaMKII_1/notes LOAD \
-""
-simundump kenz /kinetics/PSD/actCaMKII/CaMKII_2 0 0 0 0 0 6 0.033332 8 2 0 0 \
- "" red 35 "" -2 3 0
-simundump text /kinetics/PSD/actCaMKII/CaMKII_2/notes 0 ""
-call /kinetics/PSD/actCaMKII/CaMKII_2/notes LOAD \
-""
-simundump group /kinetics/PSD/PP1_PSD 1 yellow 20 x 0 0 "" PP1_PSD \
- /home2/bhalla/scripts/modules/PP1_PSD_0.g 0 \
- 62a600ae10e53f567e47decb4f2b6488 0 12 27 0
-simundump text /kinetics/PSD/PP1_PSD/notes 0 ""
-call /kinetics/PSD/PP1_PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-active 1 0 4 4 24 24 0 0 6 0 \
- /kinetics/geometry cyan yellow 44 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/notes 0 \
- "Cohen et al Meth Enz 159 390-408 is main source of info\nconc = 1.8 uM"
-call /kinetics/PSD/PP1_PSD/PP1-active/notes LOAD \
-"Cohen et al Meth Enz 159 390-408 is main source of info" \
-"conc = 1.8 uM"
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/PP1_2 0 0 0 0 0 6 0.0010416 \
- 0.2 0.05 0 0 "" red blue "" -2 -4 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/PP1_2/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/PP1_2/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/PP1_1 0 0 0 0 0 6 0.0010416 \
- 0.2 0.05 0 0 "" red blue "" -6 -4 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/PP1_1/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/PP1_1/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 61 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 71 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 78 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c 0 0 0 0 0 54.001 \
- 0.020833 0.5 0.125 0 0 "" red cyan "" 88 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 83 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/I1 1 0 4 4 24 24 0 0 6 0 \
- /kinetics/geometry orange yellow 35.35 21.88 0
-simundump text /kinetics/PSD/PP1_PSD/I1/notes 0 \
- "I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet\ninhibitor (Foulkes et al Eur J Biochem 132 309-313 9183).\nWe treat it as non-compet, so it just turns the enz off\nwithout interacting with the binding site.\nCohen et al ann rev bioch refer to results where conc is \n1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM,\nwe need >= 1.8 uM.\n\n"
-call /kinetics/PSD/PP1_PSD/I1/notes LOAD \
-"I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet" \
-"inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183)." \
-"We treat it as non-compet, so it just turns the enz off" \
-"without interacting with the binding site." \
-"Cohen et al ann rev bioch refer to results where conc is " \
-"1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM," \
-"we need >= 1.8 uM." \
-"" \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-I1 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry brown yellow 36 29 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-I1/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-I1/notes LOAD \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 1 1 0 "" white yellow 33 \
- 26 0
-simundump text /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes 0 \
- "Let us assume that the equil in this case is very far over to the\nright. This is probably safe.\n"
-call /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes LOAD \
-"Let us assume that the equil in this case is very far over to the" \
-"right. This is probably safe." \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/Inact-PP1 1 83.33 0.1 "" white yellow \
- 17 26 0
-simundump text /kinetics/PSD/PP1_PSD/Inact-PP1/notes 0 \
- "K inhib = 1nM from Cohen Ann Rev Bioch 1989, \n4 nM from Foukes et al \nAssume 2 nM. kf /kb = 8.333e-4"
-call /kinetics/PSD/PP1_PSD/Inact-PP1/notes LOAD \
-"K inhib = 1nM from Cohen Ann Rev Bioch 1989, " \
-"4 nM from Foukes et al " \
-"Assume 2 nM. kf /kb = 8.333e-4"
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-I1_p 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry brown yellow 22 29 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-I1_p/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-I1_p/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/I1_p 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry orange yellow 21 22 0
-simundump text /kinetics/PSD/PP1_PSD/I1_p/notes 0 \
- "Dephosph is mainly by PP2B"
-call /kinetics/PSD/PP1_PSD/I1_p/notes LOAD \
-"Dephosph is mainly by PP2B"
-simundump kpool /kinetics/PSD/PP1_PSD/CaN 0 1e-12 1 1 6 6 0 0 6 0 \
- /kinetics/geometry 1 yellow -1 33 0
-simundump text /kinetics/PSD/PP1_PSD/CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/CaN/notes LOAD \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/CaM-Bind-CaN 0 7.6667 0.002 "" white \
- yellow 21 40 0
-simundump text /kinetics/PSD/PP1_PSD/CaM-Bind-CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/CaM-Bind-CaN/notes LOAD \
-""
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- /kinetics/geometry[2] blue yellow 12 33 0
-simundump text /kinetics/PSD/PP1_PSD/Ca2_CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/Ca2_CaN/notes LOAD \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/Ca_bind_CaN 0 0.11111 1 "" white yellow \
- 7 40 0
-simundump text /kinetics/PSD/PP1_PSD/Ca_bind_CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/Ca_bind_CaN/notes LOAD \
-""
-simundump kreac /kinetics/PSD/move_to_PSD 0 0.1 3 "" white 0 -8 -5 0
-simundump text /kinetics/PSD/move_to_PSD/notes 0 ""
-call /kinetics/PSD/move_to_PSD/notes LOAD \
-""
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- -8 1 0
-simundump text /kinetics/PSD/R_S2/notes 0 ""
-call /kinetics/PSD/R_S2/notes LOAD \
-""
-simundump kpool /kinetics/PSD/R_SpS 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry \
- blue 0 -4 1 0
-simundump text /kinetics/PSD/R_SpS/notes 0 ""
-call /kinetics/PSD/R_SpS/notes LOAD \
-""
-simundump kpool /kinetics/PSD/R_SpSp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry \
- 28 0 0 1 0
-simundump text /kinetics/PSD/R_SpSp/notes 0 ""
-call /kinetics/PSD/R_SpSp/notes LOAD \
-""
-simundump kpool /kinetics/PSD/basal_phosphatase 0 0 1 1 6 6 0 0 6 0 \
- /kinetics/geometry 61 0 -4 -2 0
-simundump text /kinetics/PSD/basal_phosphatase/notes 0 \
- "There isn't any clear info for this. I had originally called \nit PP2A, but that causes odd interactions with other pathways.\n"
-call /kinetics/PSD/basal_phosphatase/notes LOAD \
-"There isn't any clear info for this. I had originally called " \
-"it PP2A, but that causes odd interactions with other pathways." \
-""
-simundump kenz /kinetics/PSD/basal_phosphatase/P1 0 0 0 0 0 60 0.46295 \
- 0.44443 0.11111 0 0 "" red 61 "" -6 -1 0
-simundump text /kinetics/PSD/basal_phosphatase/P1/notes 0 ""
-call /kinetics/PSD/basal_phosphatase/P1/notes LOAD \
-""
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-simundump text /kinetics/PSD/basal_phosphatase/P2/notes 0 ""
-call /kinetics/PSD/basal_phosphatase/P2/notes LOAD \
-""
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-simundump text /kinetics/PSD/PKA-active/notes 0 ""
-call /kinetics/PSD/PKA-active/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PKA-active/PKA-phosph-I1 0 0 0 0 0 54.001 \
- 0.11111 36 9 0 0 "" red 27 "" 27 19 0
-simundump text /kinetics/PSD/PKA-active/PKA-phosph-I1/notes 0 ""
-call /kinetics/PSD/PKA-active/PKA-phosph-I1/notes LOAD \
-""
-simundump group /kinetics/PSD/CaMKII_PSD 0 33 20 x 0 0 "" CaMKII_PSD \
- defaultfile.g 0 0 0 39 32 0
-simundump text /kinetics/PSD/CaMKII_PSD/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/NMDAR 0 0 40 40 240 240 0 0 6 0 \
- /kinetics/geometry blue 33 67 8 0
-simundump text /kinetics/PSD/CaMKII_PSD/NMDAR/notes 0 \
- "The stochiometry is a bit off here. Each NMDAR actually\nbinds to a holoenzyme, about 12 CaMKII subunits. But\nour CaMKII calculations are in terms of individual\nsubunits. So as a hack, we put in much more NMDAR than\nis actually there.\n\nDec 2011: Reconsidered this, now only 120 NMDARs.\n\nJune 02 2012. Consider these as anchor points for a dodecamer.\nThere are far more effected CaMKII bindin...."
-call /kinetics/PSD/CaMKII_PSD/NMDAR/notes LOAD \
-"The stochiometry is a bit off here. Each NMDAR actually" \
-"binds to a holoenzyme, about 12 CaMKII subunits. But" \
-"our CaMKII calculations are in terms of individual" \
-"subunits. So as a hack, we put in much more NMDAR than" \
-"is actually there." \
-"" \
-"Dec 2011: Reconsidered this, now only 120 NMDARs." \
-"" \
-"June 02 2012. Consider these as anchor points for a dodecamer." \
-"There are far more effected CaMKII binding sites then, than" \
-"individual molecules of NMDAR. Raised limit to 40."
-simundump kpool /kinetics/PSD/CaMKII_PSD/tot-auto 0 0 2 1 6 12 0 0 6 0 \
- /kinetics/geometry 29 33 74 36 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/notes LOAD \
-""
-simundump kenz /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph 0 0 0 0 0 7.732 \
- 0.0033333 8 2 0 0 "" red 29 "" 72 23 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph/notes LOAD \
-""
-simundump kenz /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 0 0 0 0 0 7.732 \
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/tot_CaMKII 0 0 2 2 12 12 0 0 6 0 \
- /kinetics/geometry 23 33 84 36 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot_CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot_CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/286P 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 59 33 52 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/286P/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/286P/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 47 33 61 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/notes LOAD \
-""
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- 0 7.732 0.0052083 8 2 0 0 "" red 47 "" 72 20 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph/notes 0 \
- ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph/notes LOAD \
-""
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- 54.001 0.015625 24 6 0 0 "" red 47 "" 78 20 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305/notes LOAD \
-""
-simundump kenz /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 0 0 0 0 0 \
- 7.732 0.0013021 2 0.5 0 0 "" red 47 "" 60 20 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/basal_CaMKII 0 0 1 1 6 6 0 0 6 0 \
- /kinetics/geometry blue 33 81 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/basal_CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/basal_CaMKII/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM 0 10.945 \
- 0.0022 "" white 33 54 28 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes 0 \
- "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?"
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-simundump kreac /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM 0 10.945 2.2 "" \
- white 33 65 28 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM 0 0 0 0 0 0 0 0 6 \
- 0 /kinetics/geometry 47 33 56 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-CaM 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 50 33 63 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr286 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 57 33 69 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 62 33 75 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr305 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 30 33 88 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr305/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 0 33 81 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/transloc_1 0 0.0001 0 "" white 33 63 \
- 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/transloc_1/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/transloc_1/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/back_1 0 0.04 6.6667e-06 "" white 33 \
- 75 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/back_1/notes 0 \
- "Rates set by the translocation experiments of \nShen and Meyer, Science 1999."
-call /kinetics/PSD/CaMKII_PSD/back_1/notes LOAD \
-"Rates set by the translocation experiments of " \
-"Shen and Meyer, Science 1999."
-simundump kreac /kinetics/PSD/CaMKII_PSD/transloc_2 0 0.0001 0 "" white 33 56 \
- 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/transloc_2/notes 0 \
- "Same as for transloc_1\n\n\n"
-call /kinetics/PSD/CaMKII_PSD/transloc_2/notes LOAD \
-"Same as for transloc_1" \
-"" \
-"" \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/back_2 0 0.04 6.6667e-06 "" white 33 \
- 89 13 0
-simundump text /kinetics/PSD/CaMKII_PSD/back_2/notes 0 "Same as for back_1\n"
-call /kinetics/PSD/CaMKII_PSD/back_2/notes LOAD \
-"Same as for back_1" \
-""
-simundump kpool /kinetics/PSD/PP2A 1 0 1 1 6 6 0 0 6 0 /kinetics/geometry red \
- 20 45 17 0
-simundump text /kinetics/PSD/PP2A/notes 0 ""
-call /kinetics/PSD/PP2A/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p 1 0.0012791 0.0012791 \
- 0.06907 0.06907 54.001 0.0013289 0.92593 0.22222 0 0 "" red red "" 29 27 0
-simundump text /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes 0 \
- "k1 changed from 3.3e-6 to 6.6e-6\n"
-call /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes LOAD \
-"k1 changed from 3.3e-6 to 6.6e-6" \
-""
-simundump kenz /kinetics/PSD/PP2A/PP2A-dephosph-I1 1 2.2155e-07 2.2155e-07 \
- 1.1964e-05 1.1964e-05 54.001 0.0013289 0.92593 0.22222 0 0 "" red red "" 27 \
- 20 0
-simundump text /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes 0 \
- "PP2A does most of the dephosph of I1 at basal Ca levels. See\nthe review by Cohen in Ann Rev Biochem 1989.\nFor now, lets halve Km. k1 was 3.3e-6, now 6.6e-6\n"
-call /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes LOAD \
-"PP2A does most of the dephosph of I1 at basal Ca levels. See" \
-"the review by Cohen in Ann Rev Biochem 1989." \
-"For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6" \
-""
-simundump group /kinetics/PSD/CaM 1 blue 20 x 0 0 "" defaultfile \
- defaultfile.g 0 fbb0ff81553508bc01f3dd51428742fb 0 31 37 0
-simundump text /kinetics/PSD/CaM/notes 0 ""
-call /kinetics/PSD/CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaM/CaM 1 1e-12 20 20 120 120 0 0 6 0 \
- /kinetics/geometry pink blue 35 39 0
-simundump text /kinetics/PSD/CaM/CaM/notes 0 \
- "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n"
-call /kinetics/PSD/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-Ca3-bind-Ca 1 0.077501 10 "" white blue \
- 49 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes 0 \
- "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-simundump kpool /kinetics/PSD/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry hotpink blue 47 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca3/notes 0 ""
-call /kinetics/PSD/CaM/CaM-Ca3/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-bind-Ca 1 1.4141 8.4853 "" white blue \
- 37 36 0
-simundump text /kinetics/PSD/CaM/CaM-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/PSD/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/PSD/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry pink blue 43 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca2/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kreac /kinetics/PSD/CaM/CaM-Ca2-bind-Ca 1 0.60001 10 "" white blue \
- 45 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes 0 \
- "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n"
-call /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-Ca-bind-Ca 1 1.4141 8.4853 "" white \
- blue 41 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/PSD/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry pink blue 39 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kpool /kinetics/PSD/CaM/Ca 1 1e-12 0.08 0.08 0.48 0.48 0 0 6 0 \
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-call /kinetics/PSD/CaM/Ca/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaM/CaM-Ca4/notes 0 ""
-call /kinetics/PSD/CaM/CaM-Ca4/notes LOAD \
-""
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-call /kinetics/PSD/CaM_CaN/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p/notes 0 ""
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-""
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-""
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-""
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-simundump text /kinetics/DEND/Ca/notes 0 ""
-call /kinetics/DEND/Ca/notes LOAD \
-""
-simundump text /kinetics/geometry[3]/notes 0 ""
-call /kinetics/geometry[3]/notes LOAD \
-""
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-""
-simundump kpool /kinetics/SPINE/iR 0 0 4.4444 4.4444 240 240 0 0 54 0 \
- /kinetics/geometry 0 yellow -8 -10 0
-simundump text /kinetics/SPINE/iR/notes 0 "Same as Fus3\n"
-call /kinetics/SPINE/iR/notes LOAD \
-"Same as Fus3" \
-""
-simundump group /kinetics/SPINE/CaM 1 blue 5 x 0 0 "" defaultfile \
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-""
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-simundump text /kinetics/SPINE/CaM/CaM/notes 0 \
- "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n"
-call /kinetics/SPINE/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca 1 0.0086112 10 "" white \
- blue 51 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes 0 \
- "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 54 0 \
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-simundump text /kinetics/SPINE/CaM/CaM-Ca3/notes 0 ""
-call /kinetics/SPINE/CaM/CaM-Ca3/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-bind-Ca 1 0.15712 8.4853 "" white \
- blue 39 1 0
-simundump text /kinetics/SPINE/CaM/CaM-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/SPINE/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 54 0 \
- /kinetics/geometry pink blue 45 4 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca2/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca 1 0.066668 10 "" white \
- blue 47 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes 0 \
- "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n"
-call /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca-bind-Ca 1 0.15712 8.4853 "" white \
- blue 43 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 54 0 \
- /kinetics/geometry pink blue 41 4 0
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- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kpool /kinetics/SPINE/CaM/Ca 1 1e-12 0.08 0.08 4.32 4.32 0 0 54 0 \
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-call /kinetics/SPINE/CaM/Ca/notes LOAD \
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-""
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-call /kinetics/SPINE/CaMKII_BULK/tot_CaMKII/notes LOAD \
-""
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- /kinetics/geometry 59 33 54 -2 0
-simundump text /kinetics/SPINE/CaMKII_BULK/286P/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/286P/notes LOAD \
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-""
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- ""
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- ""
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-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes 0 \
- ""
-call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes LOAD \
-""
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- 0 /kinetics/geometry blue 33 83 -2 0
-simundump text /kinetics/SPINE/CaMKII_BULK/basal_CaMKII/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/basal_CaMKII/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes 0 \
- "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?"
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
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-""
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-""
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-call /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM/notes LOAD \
-""
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-""
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-""
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-""
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-call /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p/notes LOAD \
-""
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- "Strack et al JBC 1997 show that PP2A is the primary\nphosphatase acting on CaMKII in the bulk."
-call /kinetics/SPINE/PP2A/notes LOAD \
-"Strack et al JBC 1997 show that PP2A is the primary" \
-"phosphatase acting on CaMKII in the bulk."
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-call /kinetics/SPINE/PP2A/Deph-thr305a/notes LOAD \
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-"From Quintana et al 2005"
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-""
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-"23 Dec 2011" \
-"CaMKII_merged16.g" \
-"Added Ca-binding step to the CaN activation pathway." \
-"Based on CaMKII_merged15.g" \
-"" \
-"CaMKII_merged16a.g" \
-"Halved the Kb for CaN-bind-CaM" \
-"" \
-"CaMKII_merged17.g" \
-" Used more rates from Saucerman and Bers BPJ 2008" \
-"" \
-"CaMKII_merged17a.g" \
-"Fix to init conc of PP1-active in PSD: from 2 to 4." \
-"" \
-"CaMKII_merged17b.g" \
-"Raised PP2A CoInit from 0.1111 uM to 1 uM, to avoid sub-molecular" \
-"levels in PSD. Scaled kcats down to match." \
-"" \
-"CaMKII_merged20.g" \
-"First pass at a version with a reasonable basal PKA and a less" \
-"saturating effect on PP1-active of CaMKII." \
-"" \
-"CaMKII_merged20c.g: This version turns on but does not go off" \
-"afterwards. " \
-"" \
-"CaMKII_merged20d.g: 10x higher Km and kcat for PP1 on CaMKII." \
-"" \
-"CaMKII_merged20e.g: Km = 5 and kcat =0.5" \
-"" \
-"02 June 2012. CaMKII_merged20g.g: NMDAR = 40, effective # of" \
-"sites given that CaMKII is a dodecamer." \
-"" \
-"CaMKII_merged20h.g: Lowered Kb for CaM-Bind-CaN from 0.006 to " \
-"0.002/sec." \
-"" \
-"CaMKII_merged20i.g: Set PKA-active in both compts to be 0.02 uM." \
-"" \
-"CaMKII_merged20j.g: Faster CaN diffusion, by 6x. Now matches" \
-"CaM with 6:54." \
-"" \
-"CaMKII_merged20k.g: Halved CaMKII affinity for NMDAR." \
-"" \
-"CaMKII_merged21.g: Removed bulk PP1. Use PP2A to dephosphorylate" \
-"CaMKII in bulk." \
-"" \
-"19 July 2013. psd_merged30.g: Variant for signeur loading." \
-""
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-addmsg /kinetics/PSD/CaMKII_PSD/back_1 /kinetics/SPINE/CaMKII_BULK/CaMKII REAC B A
-addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 REAC sA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 MM_PRD pA
-addmsg /kinetics/PSD/CaMKII_PSD/back_2 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 REAC B A
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA
-addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p REAC sA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p REAC sA B
-addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaM_CaN REAC B A
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/PP2A/Deph-thr286 /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286b /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286 ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/PP2A/Deph-thr286 SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286b ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/PP2A/Deph-thr286b SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr305 ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/PP2A/Deph-thr305 SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286c ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/PP2A/Deph-thr286c SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr305a ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 /kinetics/SPINE/PP2A/Deph-thr305a SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaN_BULK/CaN REAC A B
-addmsg /kinetics/SPINE/CaM/CaM-Ca4 /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaM_CaN /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN PRODUCT n
-addmsg /kinetics/SPINE/CaN_BULK/Ca2_CaN /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/CaN /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca2_CaN /kinetics/SPINE/CaN_BULK/Ca_bind_CaN PRODUCT n
-addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaN_BULK/Ca2_CaN REAC B A
-addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaN_BULK/Ca2_CaN REAC A B
-addmsg /kinetics/PSD/tot_PSD_R /graphs/conc1/tot_PSD_R.Co PLOT Co *tot_PSD_R.Co *blue
-addmsg /kinetics/PSD/R_S2 /graphs/conc1/R.Co PLOT Co *R.Co *4
-addmsg /kinetics/PSD/CaM/Ca /graphs/conc1/Ca.Co PLOT Co *Ca.Co *red
-addmsg /kinetics/PSD/PP1_PSD/PP1-active /graphs/conc1/PP1-active.Co PLOT Co *PP1-active.Co *cyan
-addmsg /kinetics/PSD/CaM_CaN /graphs/conc1/CaM_CaN.Co PLOT Co *CaM_CaN.Co *1
-addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII /graphs/conc1/tot-CaM-CaMKII.Co PLOT Co *tot-CaM-CaMKII.Co *47
-addmsg /kinetics/PSD/CaMKII_PSD/tot-auto /graphs/conc1/tot-auto.Co PLOT Co *tot-auto.Co *29
-addmsg /kinetics/PSD/CaM/CaM-Ca4 /graphs/conc1/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue
-addmsg /kinetics/SPINE/iR /graphs/conc2/iR.Co PLOT Co *iR.Co *0
-addmsg /kinetics/PSD/R_SpSp /graphs/conc2/Rpp.Co PLOT Co *Rpp.Co *28
-addmsg /kinetics/SPINE/CaM/Ca /graphs/conc2/Ca.Co PLOT Co *Ca.Co *red
-addmsg /kinetics/SPINE/CaM_CaN /graphs/conc2/CaM_CaN.Co PLOT Co *CaM_CaN.Co *1
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII /graphs/conc2/tot-CaM-CaMKII.Co PLOT Co *tot-CaM-CaMKII.Co *47
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /graphs/conc2/tot-auto.Co PLOT Co *tot-auto.Co *29
-addmsg /kinetics/SPINE/CaM/CaM-Ca4 /graphs/conc2/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue
-enddump
-// End of dump
-
-call /kinetics/PSD/PP1_PSD/PP1-active/notes LOAD \
-"Cohen et al Meth Enz 159 390-408 is main source of info" \
-"conc = 1.8 uM"
-call /kinetics/PSD/PP1_PSD/I1/notes LOAD \
-"I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet" \
-"inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183)." \
-"We treat it as non-compet, so it just turns the enz off" \
-"without interacting with the binding site." \
-"Cohen et al ann rev bioch refer to results where conc is " \
-"1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM," \
-"we need >= 1.8 uM." \
-"" \
-""
-call /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes LOAD \
-"Let us assume that the equil in this case is very far over to the" \
-"right. This is probably safe." \
-""
-call /kinetics/PSD/PP1_PSD/Inact-PP1/notes LOAD \
-"K inhib = 1nM from Cohen Ann Rev Bioch 1989, " \
-"4 nM from Foukes et al " \
-"Assume 2 nM. kf /kb = 8.333e-4"
-call /kinetics/PSD/PP1_PSD/I1_p/notes LOAD \
-"Dephosph is mainly by PP2B"
-call /kinetics/PSD/basal_phosphatase/notes LOAD \
-"There isn't any clear info for this. I had originally called " \
-"it PP2A, but that causes odd interactions with other pathways." \
-""
-call /kinetics/PSD/CaMKII_PSD/NMDAR/notes LOAD \
-"The stochiometry is a bit off here. Each NMDAR actually" \
-"binds to a holoenzyme, about 12 CaMKII subunits. But" \
-"our CaMKII calculations are in terms of individual" \
-"subunits. So as a hack, we put in much more NMDAR than" \
-"is actually there." \
-"" \
-"Dec 2011: Reconsidered this, now only 120 NMDARs." \
-"" \
-"June 02 2012. Consider these as anchor points for a dodecamer." \
-"There are far more effected CaMKII binding sites then, than" \
-"individual molecules of NMDAR. Raised limit to 40."
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-call /kinetics/PSD/CaMKII_PSD/back_1/notes LOAD \
-"Rates set by the translocation experiments of " \
-"Shen and Meyer, Science 1999."
-call /kinetics/PSD/CaMKII_PSD/transloc_2/notes LOAD \
-"Same as for transloc_1" \
-"" \
-"" \
-""
-call /kinetics/PSD/CaMKII_PSD/back_2/notes LOAD \
-"Same as for back_1" \
-""
-call /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes LOAD \
-"k1 changed from 3.3e-6 to 6.6e-6" \
-""
-call /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes LOAD \
-"PP2A does most of the dephosph of I1 at basal Ca levels. See" \
-"the review by Cohen in Ann Rev Biochem 1989." \
-"For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6" \
-""
-call /kinetics/PSD/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-call /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/PSD/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/PSD/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-call /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/PSD/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/iR/notes LOAD \
-"Same as Fus3" \
-""
-call /kinetics/SPINE/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-call /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/SPINE/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-call /kinetics/SPINE/PP2A/notes LOAD \
-"Strack et al JBC 1997 show that PP2A is the primary" \
-"phosphatase acting on CaMKII in the bulk."
-call /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN/notes LOAD \
-"From Quintana et al 2005"
-complete_loading
diff --git a/moose-examples/snippets/MULTI/psd_merged30b.g b/moose-examples/snippets/MULTI/psd_merged30b.g
deleted file mode 100644
index 73e00c22854585e43a771728b1cb7f67212e34fc..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/psd_merged30b.g
+++ /dev/null
@@ -1,1452 +0,0 @@
-//genesis
-// kkit Version 11 flat dumpfile
-
-// Saved on Mon Aug 12 22:34:03 2013
-
-include kkit {argv 1}
-
-FASTDT = 0.0001
-SIMDT = 0.001
-CONTROLDT = 10
-PLOTDT = 10
-MAXTIME = 2000
-TRANSIENT_TIME = 10
-VARIABLE_DT_FLAG = 1
-DEFAULT_VOL = 1e-20
-VERSION = 11.0
-setfield /file/modpath value /home2/bhalla/scripts/modules
-kparms
-
-//genesis
-
-initdump -version 3 -ignoreorphans 1
-simobjdump doqcsinfo filename accessname accesstype transcriber developer \
- citation species tissue cellcompartment methodology sources \
- model_implementation model_validation x y z
-simobjdump table input output alloced step_mode stepsize x y z
-simobjdump xtree path script namemode sizescale
-simobjdump xcoredraw xmin xmax ymin ymax
-simobjdump xtext editable
-simobjdump xgraph xmin xmax ymin ymax overlay
-simobjdump xplot pixflags script fg ysquish do_slope wy
-simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
- link savename file version md5sum mod_save_flag x y z
-simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
- z
-simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
- geomname xtree_fg_req xtree_textfg_req x y z
-simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
-simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
- keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
-simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
- trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
-simobjdump xtab input output alloced step_mode stepsize notes editfunc \
- xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
-simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
- xtree_textfg_req x y z
-simobjdump transport input output alloced step_mode stepsize dt delay clock \
- kf xtree_fg_req xtree_textfg_req x y z
-simobjdump proto x y z
-simobjdump text str
-simundump geometry /kinetics/geometry 0 1e-20 3 sphere "" white black 0 0 0
-simundump geometry /kinetics/geometry[1] 0 9e-20 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[3] 0 1e-18 3 sphere "" white black 0 0 \
- 0
-simundump text /kinetics/notes 0 ""
-call /kinetics/notes LOAD \
-""
-simundump text /kinetics/geometry/notes 0 ""
-call /kinetics/geometry/notes LOAD \
-""
-simundump text /kinetics/geometry[1]/notes 0 ""
-call /kinetics/geometry[1]/notes LOAD \
-""
-simundump text /kinetics/geometry[2]/notes 0 ""
-call /kinetics/geometry[2]/notes LOAD \
-""
-simundump text /kinetics/geometry[3]/notes 0 ""
-call /kinetics/geometry[3]/notes LOAD \
-""
-simundump group /kinetics/PSD 0 20 black x 0 0 "" PSD defaultfile.g 0 0 0 27 \
- 12 0
-simundump text /kinetics/PSD/notes 0 ""
-call /kinetics/PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/tot_PSD_R 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry blue 0 -4 7 0
-simundump text /kinetics/PSD/tot_PSD_R/notes 0 ""
-call /kinetics/PSD/tot_PSD_R/notes LOAD \
-""
-simundump kpool /kinetics/PSD/actCaMKII 0 0 2 2 12 12 0 0 6 0 \
- /kinetics/geometry 12 20 70 33 0
-simundump text /kinetics/PSD/actCaMKII/notes 0 ""
-call /kinetics/PSD/actCaMKII/notes LOAD \
-""
-simundump kenz /kinetics/PSD/actCaMKII/CaMKII_1 0 0 0 0 0 6 0.033332 8 2 0 0 \
- "" red 35 "" -6 3 0
-simundump text /kinetics/PSD/actCaMKII/CaMKII_1/notes 0 ""
-call /kinetics/PSD/actCaMKII/CaMKII_1/notes LOAD \
-""
-simundump kenz /kinetics/PSD/actCaMKII/CaMKII_2 0 0 0 0 0 6 0.033332 8 2 0 0 \
- "" red 35 "" -2 3 0
-simundump text /kinetics/PSD/actCaMKII/CaMKII_2/notes 0 ""
-call /kinetics/PSD/actCaMKII/CaMKII_2/notes LOAD \
-""
-simundump group /kinetics/PSD/PP1_PSD 1 yellow 20 x 0 0 "" PP1_PSD \
- /home2/bhalla/scripts/modules/PP1_PSD_0.g 0 \
- 62a600ae10e53f567e47decb4f2b6488 0 12 27 0
-simundump text /kinetics/PSD/PP1_PSD/notes 0 ""
-call /kinetics/PSD/PP1_PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-active 1 0 4 4 24 24 0 0 6 0 \
- /kinetics/geometry cyan yellow 44 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/notes 0 \
- "Cohen et al Meth Enz 159 390-408 is main source of info\nconc = 1.8 uM"
-call /kinetics/PSD/PP1_PSD/PP1-active/notes LOAD \
-"Cohen et al Meth Enz 159 390-408 is main source of info" \
-"conc = 1.8 uM"
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/PP1_2 0 0 0 0 0 6 0.0010416 \
- 0.2 0.05 0 0 "" red blue "" -2 -4 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/PP1_2/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/PP1_2/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/PP1_1 0 0 0 0 0 6 0.0010416 \
- 0.2 0.05 0 0 "" red blue "" -6 -4 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/PP1_1/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/PP1_1/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 61 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 71 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 78 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c 0 0 0 0 0 54.001 \
- 0.020833 0.5 0.125 0 0 "" red cyan "" 88 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 83 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/I1 1 0 4 4 24 24 0 0 6 0 \
- /kinetics/geometry orange yellow 35.35 21.88 0
-simundump text /kinetics/PSD/PP1_PSD/I1/notes 0 \
- "I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet\ninhibitor (Foulkes et al Eur J Biochem 132 309-313 9183).\nWe treat it as non-compet, so it just turns the enz off\nwithout interacting with the binding site.\nCohen et al ann rev bioch refer to results where conc is \n1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM,\nwe need >= 1.8 uM.\n\n"
-call /kinetics/PSD/PP1_PSD/I1/notes LOAD \
-"I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet" \
-"inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183)." \
-"We treat it as non-compet, so it just turns the enz off" \
-"without interacting with the binding site." \
-"Cohen et al ann rev bioch refer to results where conc is " \
-"1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM," \
-"we need >= 1.8 uM." \
-"" \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-I1 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry brown yellow 36 29 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-I1/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-I1/notes LOAD \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 1 1 0 "" white yellow 33 \
- 26 0
-simundump text /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes 0 \
- "Let us assume that the equil in this case is very far over to the\nright. This is probably safe.\n"
-call /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes LOAD \
-"Let us assume that the equil in this case is very far over to the" \
-"right. This is probably safe." \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/Inact-PP1 1 83.33 0.1 "" white yellow \
- 17 26 0
-simundump text /kinetics/PSD/PP1_PSD/Inact-PP1/notes 0 \
- "K inhib = 1nM from Cohen Ann Rev Bioch 1989, \n4 nM from Foukes et al \nAssume 2 nM. kf /kb = 8.333e-4"
-call /kinetics/PSD/PP1_PSD/Inact-PP1/notes LOAD \
-"K inhib = 1nM from Cohen Ann Rev Bioch 1989, " \
-"4 nM from Foukes et al " \
-"Assume 2 nM. kf /kb = 8.333e-4"
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-I1_p 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry brown yellow 22 29 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-I1_p/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-I1_p/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/I1_p 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry orange yellow 21 22 0
-simundump text /kinetics/PSD/PP1_PSD/I1_p/notes 0 \
- "Dephosph is mainly by PP2B"
-call /kinetics/PSD/PP1_PSD/I1_p/notes LOAD \
-"Dephosph is mainly by PP2B"
-simundump kpool /kinetics/PSD/PP1_PSD/CaN 0 1e-12 1 1 6 6 0 0 6 0 \
- /kinetics/geometry 1 yellow -1 33 0
-simundump text /kinetics/PSD/PP1_PSD/CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/CaN/notes LOAD \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/CaM-Bind-CaN 0 7.6667 0.002 "" white \
- yellow 21 40 0
-simundump text /kinetics/PSD/PP1_PSD/CaM-Bind-CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/CaM-Bind-CaN/notes LOAD \
-""
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- /kinetics/geometry[2] blue yellow 12 33 0
-simundump text /kinetics/PSD/PP1_PSD/Ca2_CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/Ca2_CaN/notes LOAD \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/Ca_bind_CaN 0 0.11111 1 "" white yellow \
- 7 40 0
-simundump text /kinetics/PSD/PP1_PSD/Ca_bind_CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/Ca_bind_CaN/notes LOAD \
-""
-simundump kreac /kinetics/PSD/move_to_PSD 0 0.1 3 "" white 0 -8 -5 0
-simundump text /kinetics/PSD/move_to_PSD/notes 0 ""
-call /kinetics/PSD/move_to_PSD/notes LOAD \
-""
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- -8 1 0
-simundump text /kinetics/PSD/R_S2/notes 0 ""
-call /kinetics/PSD/R_S2/notes LOAD \
-""
-simundump kpool /kinetics/PSD/R_SpS 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry \
- blue 0 -4 1 0
-simundump text /kinetics/PSD/R_SpS/notes 0 ""
-call /kinetics/PSD/R_SpS/notes LOAD \
-""
-simundump kpool /kinetics/PSD/R_SpSp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry \
- 28 0 0 1 0
-simundump text /kinetics/PSD/R_SpSp/notes 0 ""
-call /kinetics/PSD/R_SpSp/notes LOAD \
-""
-simundump kpool /kinetics/PSD/basal_phosphatase 0 0 1 1 6 6 0 0 6 0 \
- /kinetics/geometry 61 0 -4 -2 0
-simundump text /kinetics/PSD/basal_phosphatase/notes 0 \
- "There isn't any clear info for this. I had originally called \nit PP2A, but that causes odd interactions with other pathways.\n"
-call /kinetics/PSD/basal_phosphatase/notes LOAD \
-"There isn't any clear info for this. I had originally called " \
-"it PP2A, but that causes odd interactions with other pathways." \
-""
-simundump kenz /kinetics/PSD/basal_phosphatase/P1 0 0 0 0 0 60 0.46295 \
- 0.44443 0.11111 0 0 "" red 61 "" -6 -1 0
-simundump text /kinetics/PSD/basal_phosphatase/P1/notes 0 ""
-call /kinetics/PSD/basal_phosphatase/P1/notes LOAD \
-""
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-simundump text /kinetics/PSD/basal_phosphatase/P2/notes 0 ""
-call /kinetics/PSD/basal_phosphatase/P2/notes LOAD \
-""
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-simundump text /kinetics/PSD/PKA-active/notes 0 ""
-call /kinetics/PSD/PKA-active/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PKA-active/PKA-phosph-I1 0 0 0 0 0 54.001 \
- 0.11111 36 9 0 0 "" red 27 "" 27 19 0
-simundump text /kinetics/PSD/PKA-active/PKA-phosph-I1/notes 0 ""
-call /kinetics/PSD/PKA-active/PKA-phosph-I1/notes LOAD \
-""
-simundump group /kinetics/PSD/CaMKII_PSD 0 33 20 x 0 0 "" CaMKII_PSD \
- defaultfile.g 0 0 0 39 32 0
-simundump text /kinetics/PSD/CaMKII_PSD/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/NMDAR 0 0 40 40 240 240 0 0 6 0 \
- /kinetics/geometry blue 33 67 8 0
-simundump text /kinetics/PSD/CaMKII_PSD/NMDAR/notes 0 \
- "The stochiometry is a bit off here. Each NMDAR actually\nbinds to a holoenzyme, about 12 CaMKII subunits. But\nour CaMKII calculations are in terms of individual\nsubunits. So as a hack, we put in much more NMDAR than\nis actually there.\n\nDec 2011: Reconsidered this, now only 120 NMDARs.\n\nJune 02 2012. Consider these as anchor points for a dodecamer.\nThere are far more effected CaMKII bindin...."
-call /kinetics/PSD/CaMKII_PSD/NMDAR/notes LOAD \
-"The stochiometry is a bit off here. Each NMDAR actually" \
-"binds to a holoenzyme, about 12 CaMKII subunits. But" \
-"our CaMKII calculations are in terms of individual" \
-"subunits. So as a hack, we put in much more NMDAR than" \
-"is actually there." \
-"" \
-"Dec 2011: Reconsidered this, now only 120 NMDARs." \
-"" \
-"June 02 2012. Consider these as anchor points for a dodecamer." \
-"There are far more effected CaMKII binding sites then, than" \
-"individual molecules of NMDAR. Raised limit to 40."
-simundump kpool /kinetics/PSD/CaMKII_PSD/tot-auto 0 0 2 1 6 12 0 0 6 0 \
- /kinetics/geometry 29 33 74 36 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/notes LOAD \
-""
-simundump kenz /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph 0 0 0 0 0 7.732 \
- 0.0033333 8 2 0 0 "" red 29 "" 72 23 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph/notes LOAD \
-""
-simundump kenz /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 0 0 0 0 0 7.732 \
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/tot_CaMKII 0 0 2 2 12 12 0 0 6 0 \
- /kinetics/geometry 23 33 84 36 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot_CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot_CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/286P 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 59 33 52 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/286P/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/286P/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 47 33 61 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/notes LOAD \
-""
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- 0 7.732 0.0052083 8 2 0 0 "" red 47 "" 72 20 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph/notes 0 \
- ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph/notes LOAD \
-""
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- 54.001 0.015625 24 6 0 0 "" red 47 "" 78 20 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305/notes LOAD \
-""
-simundump kenz /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 0 0 0 0 0 \
- 7.732 0.0013021 2 0.5 0 0 "" red 47 "" 60 20 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/basal_CaMKII 0 0 1 1 6 6 0 0 6 0 \
- /kinetics/geometry blue 33 81 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/basal_CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/basal_CaMKII/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM 0 10.945 \
- 0.0022 "" white 33 54 28 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes 0 \
- "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?"
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-simundump kreac /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM 0 10.945 2.2 "" \
- white 33 65 28 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM 0 0 0 0 0 0 0 0 6 \
- 0 /kinetics/geometry 47 33 56 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-CaM 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 50 33 63 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr286 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 57 33 69 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 62 33 75 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr305 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 30 33 88 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr305/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 0 33 81 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/transloc_1 0 0.0001 0 "" white 33 63 \
- 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/transloc_1/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/transloc_1/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/back_1 0 0.04 6.6667e-06 "" white 33 \
- 75 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/back_1/notes 0 \
- "Rates set by the translocation experiments of \nShen and Meyer, Science 1999."
-call /kinetics/PSD/CaMKII_PSD/back_1/notes LOAD \
-"Rates set by the translocation experiments of " \
-"Shen and Meyer, Science 1999."
-simundump kreac /kinetics/PSD/CaMKII_PSD/transloc_2 0 0.0001 0 "" white 33 56 \
- 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/transloc_2/notes 0 \
- "Same as for transloc_1\n\n\n"
-call /kinetics/PSD/CaMKII_PSD/transloc_2/notes LOAD \
-"Same as for transloc_1" \
-"" \
-"" \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/back_2 0 0.04 6.6667e-06 "" white 33 \
- 89 13 0
-simundump text /kinetics/PSD/CaMKII_PSD/back_2/notes 0 "Same as for back_1\n"
-call /kinetics/PSD/CaMKII_PSD/back_2/notes LOAD \
-"Same as for back_1" \
-""
-simundump kpool /kinetics/PSD/PP2A 1 0 1 1 6 6 0 0 6 0 /kinetics/geometry red \
- 20 45 17 0
-simundump text /kinetics/PSD/PP2A/notes 0 ""
-call /kinetics/PSD/PP2A/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p 1 0.0012791 0.0012791 \
- 0.06907 0.06907 54.001 0.0013289 0.92593 0.22222 0 0 "" red red "" 29 27 0
-simundump text /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes 0 \
- "k1 changed from 3.3e-6 to 6.6e-6\n"
-call /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes LOAD \
-"k1 changed from 3.3e-6 to 6.6e-6" \
-""
-simundump kenz /kinetics/PSD/PP2A/PP2A-dephosph-I1 1 2.2155e-07 2.2155e-07 \
- 1.1964e-05 1.1964e-05 54.001 0.0013289 0.92593 0.22222 0 0 "" red red "" 27 \
- 20 0
-simundump text /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes 0 \
- "PP2A does most of the dephosph of I1 at basal Ca levels. See\nthe review by Cohen in Ann Rev Biochem 1989.\nFor now, lets halve Km. k1 was 3.3e-6, now 6.6e-6\n"
-call /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes LOAD \
-"PP2A does most of the dephosph of I1 at basal Ca levels. See" \
-"the review by Cohen in Ann Rev Biochem 1989." \
-"For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6" \
-""
-simundump group /kinetics/PSD/CaM 1 blue 20 x 0 0 "" defaultfile \
- defaultfile.g 0 fbb0ff81553508bc01f3dd51428742fb 0 31 37 0
-simundump text /kinetics/PSD/CaM/notes 0 ""
-call /kinetics/PSD/CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaM/CaM 1 1e-12 20 20 120 120 0 0 6 0 \
- /kinetics/geometry pink blue 35 39 0
-simundump text /kinetics/PSD/CaM/CaM/notes 0 \
- "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n"
-call /kinetics/PSD/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-Ca3-bind-Ca 1 0.077501 10 "" white blue \
- 49 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes 0 \
- "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-simundump kpool /kinetics/PSD/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry hotpink blue 47 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca3/notes 0 ""
-call /kinetics/PSD/CaM/CaM-Ca3/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-bind-Ca 1 1.4141 8.4853 "" white blue \
- 37 36 0
-simundump text /kinetics/PSD/CaM/CaM-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/PSD/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/PSD/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry pink blue 43 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca2/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kreac /kinetics/PSD/CaM/CaM-Ca2-bind-Ca 1 0.60001 10 "" white blue \
- 45 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes 0 \
- "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n"
-call /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-Ca-bind-Ca 1 1.4141 8.4853 "" white \
- blue 41 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/PSD/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry pink blue 39 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kpool /kinetics/PSD/CaM/Ca 1 1e-11 0.08 0.08 0.48 0.48 0 0 6 0 \
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-call /kinetics/PSD/CaM/Ca/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaM/CaM-Ca4/notes 0 ""
-call /kinetics/PSD/CaM/CaM-Ca4/notes LOAD \
-""
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-call /kinetics/PSD/CaM_CaN/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p/notes 0 ""
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-""
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-""
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-""
-simundump kpool /kinetics/DEND/Ca 0 1e-11 0.08 0.08 48 48 0 0 600 0 \
- /kinetics/geometry[3] 62 13 13 -27 0
-simundump text /kinetics/DEND/Ca/notes 0 ""
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-""
-simundump group /kinetics/SPINE 0 5 black x 0 0 "" SPINE defaultfile.g 0 0 0 \
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-call /kinetics/SPINE/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/iR 0 0 4.4444 4.4444 240 240 0 0 54 0 \
- /kinetics/geometry 0 yellow -8 -10 0
-simundump text /kinetics/SPINE/iR/notes 0 "Same as Fus3\n"
-call /kinetics/SPINE/iR/notes LOAD \
-"Same as Fus3" \
-""
-simundump group /kinetics/SPINE/CaM 1 blue 5 x 0 0 "" defaultfile \
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-""
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-simundump text /kinetics/SPINE/CaM/CaM/notes 0 \
- "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n"
-call /kinetics/SPINE/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca 1 0.0086112 10 "" white \
- blue 51 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes 0 \
- "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 54 0 \
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-simundump text /kinetics/SPINE/CaM/CaM-Ca3/notes 0 ""
-call /kinetics/SPINE/CaM/CaM-Ca3/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-bind-Ca 1 0.15712 8.4853 "" white \
- blue 39 1 0
-simundump text /kinetics/SPINE/CaM/CaM-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/SPINE/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 54 0 \
- /kinetics/geometry pink blue 45 4 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca2/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca 1 0.066668 10 "" white \
- blue 47 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes 0 \
- "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n"
-call /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca-bind-Ca 1 0.15712 8.4853 "" white \
- blue 43 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 54 0 \
- /kinetics/geometry pink blue 41 4 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kpool /kinetics/SPINE/CaM/Ca 1 1e-11 0.08 0.08 4.32 4.32 0 0 54 0 \
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-simundump text /kinetics/SPINE/CaM/Ca/notes 0 ""
-call /kinetics/SPINE/CaM/Ca/notes LOAD \
-""
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-call /kinetics/SPINE/CaM/CaM-Ca4/notes LOAD \
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-call /kinetics/SPINE/CaMKII_BULK/tot-auto/notes LOAD \
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-call /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph/notes LOAD \
-""
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-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/tot_CaMKII/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/tot_CaMKII/notes LOAD \
-""
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- /kinetics/geometry 59 33 54 -2 0
-simundump text /kinetics/SPINE/CaMKII_BULK/286P/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/286P/notes LOAD \
-""
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-call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/notes LOAD \
-""
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- ""
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-""
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- ""
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-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes 0 \
- ""
-call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes LOAD \
-""
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- 0 /kinetics/geometry blue 33 83 -2 0
-simundump text /kinetics/SPINE/CaMKII_BULK/basal_CaMKII/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/basal_CaMKII/notes LOAD \
-""
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- 0.0022 "" white 33 56 -7 0
-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes 0 \
- "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?"
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
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-""
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-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM/notes LOAD \
-""
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-call /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM/notes LOAD \
-""
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-""
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-""
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-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p/notes LOAD \
-""
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-""
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-""
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-simundump text /kinetics/SPINE/PP2A/notes 0 \
- "Strack et al JBC 1997 show that PP2A is the primary\nphosphatase acting on CaMKII in the bulk."
-call /kinetics/SPINE/PP2A/notes LOAD \
-"Strack et al JBC 1997 show that PP2A is the primary" \
-"phosphatase acting on CaMKII in the bulk."
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-simundump text /kinetics/SPINE/PP2A/Deph-thr305a/notes 0 ""
-call /kinetics/SPINE/PP2A/Deph-thr305a/notes LOAD \
-""
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-call /kinetics/SPINE/CaN_BULK/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaN_BULK/CaN/notes 0 ""
-call /kinetics/SPINE/CaN_BULK/CaN/notes LOAD \
-""
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- white yellow 23 5 0
-simundump text /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN/notes 0 \
- "From Quintana et al 2005"
-call /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN/notes LOAD \
-"From Quintana et al 2005"
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-""
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-""
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-xtextload /file/notes \
-"23 Dec 2011" \
-"CaMKII_merged16.g" \
-"Added Ca-binding step to the CaN activation pathway." \
-"Based on CaMKII_merged15.g" \
-"" \
-"CaMKII_merged16a.g" \
-"Halved the Kb for CaN-bind-CaM" \
-"" \
-"CaMKII_merged17.g" \
-" Used more rates from Saucerman and Bers BPJ 2008" \
-"" \
-"CaMKII_merged17a.g" \
-"Fix to init conc of PP1-active in PSD: from 2 to 4." \
-"" \
-"CaMKII_merged17b.g" \
-"Raised PP2A CoInit from 0.1111 uM to 1 uM, to avoid sub-molecular" \
-"levels in PSD. Scaled kcats down to match." \
-"" \
-"CaMKII_merged20.g" \
-"First pass at a version with a reasonable basal PKA and a less" \
-"saturating effect on PP1-active of CaMKII." \
-"" \
-"CaMKII_merged20c.g: This version turns on but does not go off" \
-"afterwards. " \
-"" \
-"CaMKII_merged20d.g: 10x higher Km and kcat for PP1 on CaMKII." \
-"" \
-"CaMKII_merged20e.g: Km = 5 and kcat =0.5" \
-"" \
-"02 June 2012. CaMKII_merged20g.g: NMDAR = 40, effective # of" \
-"sites given that CaMKII is a dodecamer." \
-"" \
-"CaMKII_merged20h.g: Lowered Kb for CaM-Bind-CaN from 0.006 to " \
-"0.002/sec." \
-"" \
-"CaMKII_merged20i.g: Set PKA-active in both compts to be 0.02 uM." \
-"" \
-"CaMKII_merged20j.g: Faster CaN diffusion, by 6x. Now matches" \
-"CaM with 6:54." \
-"" \
-"CaMKII_merged20k.g: Halved CaMKII affinity for NMDAR." \
-"" \
-"CaMKII_merged21.g: Removed bulk PP1. Use PP2A to dephosphorylate" \
-"CaMKII in bulk." \
-"" \
-"19 July 2013. psd_merged30.g: Variant for signeur loading." \
-""
-addmsg /kinetics/PSD/R_S2 /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit
-addmsg /kinetics/PSD/R_SpS /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit
-addmsg /kinetics/PSD/R_SpSp /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit
-addmsg /kinetics/PSD/actCaMKII/CaMKII_1 /kinetics/PSD/actCaMKII REAC eA B
-addmsg /kinetics/PSD/actCaMKII/CaMKII_2 /kinetics/PSD/actCaMKII REAC eA B
-addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM /kinetics/PSD/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-CaM /kinetics/PSD/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/PSD/CaMKII_PSD/tot-auto /kinetics/PSD/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/PSD/actCaMKII /kinetics/PSD/actCaMKII/CaMKII_1 ENZYME n
-addmsg /kinetics/PSD/R_S2 /kinetics/PSD/actCaMKII/CaMKII_1 SUBSTRATE n
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-addmsg /kinetics/PSD/PP1_PSD/PP1-active/PP1_2 /kinetics/PSD/PP1_PSD/PP1-active REAC eA B
-addmsg /kinetics/PSD/PP1_PSD/PP1-active/PP1_1 /kinetics/PSD/PP1_PSD/PP1-active REAC eA B
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-addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a /kinetics/PSD/PP1_PSD/PP1-active REAC eA B
-addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c /kinetics/PSD/PP1_PSD/PP1-active REAC eA B
-addmsg /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 /kinetics/PSD/PP1_PSD/PP1-active REAC B A
-addmsg /kinetics/PSD/PP1_PSD/Inact-PP1 /kinetics/PSD/PP1_PSD/PP1-active REAC A B
-addmsg /kinetics/PSD/PP1_PSD/PP1-active /kinetics/PSD/PP1_PSD/PP1-active/PP1_2 ENZYME n
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-addmsg /kinetics/PSD/CaM_CaN/dephosph_inhib1 /kinetics/PSD/PP1_PSD/I1 MM_PRD pA
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-addmsg /kinetics/PSD/PP1_PSD/Inact-PP1 /kinetics/PSD/PP1_PSD/PP1-I1_p REAC B A
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-addmsg /kinetics/PSD/PP1_PSD/PP1-active/PP1_1 /kinetics/PSD/R_S2 MM_PRD pA
-addmsg /kinetics/PSD/move_to_PSD /kinetics/PSD/R_S2 REAC B A
-addmsg /kinetics/PSD/actCaMKII/CaMKII_1 /kinetics/PSD/R_S2 REAC sA B
-addmsg /kinetics/PSD/basal_phosphatase/P2 /kinetics/PSD/R_SpS MM_PRD pA
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-addmsg /kinetics/PSD/basal_phosphatase/P1 /kinetics/PSD/basal_phosphatase REAC eA B
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-addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286 /kinetics/PSD/CaMKII_PSD/tot-auto SUMTOTAL n nInit
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-addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305 /kinetics/PSD/CaMKII_PSD/tot-auto REAC eA B
-addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 /kinetics/PSD/CaMKII_PSD/tot-auto REAC eA B
-addmsg /kinetics/PSD/CaMKII_PSD/basal_CaMKII /kinetics/PSD/CaMKII_PSD/tot-auto SUMTOTAL n nInit
-addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph /kinetics/PSD/CaMKII_PSD/tot-auto REAC eA B
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-addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM /kinetics/PSD/CaMKII_PSD/286P SUMTOTAL n nInit
-addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286 /kinetics/PSD/CaMKII_PSD/286P SUMTOTAL n nInit
-addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII SUMTOTAL n nInit
-addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-CaM /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII SUMTOTAL n nInit
-addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305 /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII REAC eA B
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-addmsg /kinetics/PSD/CaMKII_PSD/transloc_2 /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM REAC B A
-addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM REAC B A
-addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM MM_PRD pA
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-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 MM_PRD pA
-addmsg /kinetics/PSD/CaMKII_PSD/back_2 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 REAC B A
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA
-addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p REAC sA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p REAC sA B
-addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaM_CaN REAC B A
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/PP2A/Deph-thr286 /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286b /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286 ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/PP2A/Deph-thr286 SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286b ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/PP2A/Deph-thr286b SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr305 ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/PP2A/Deph-thr305 SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286c ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/PP2A/Deph-thr286c SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr305a ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 /kinetics/SPINE/PP2A/Deph-thr305a SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaN_BULK/CaN REAC A B
-addmsg /kinetics/SPINE/CaM/CaM-Ca4 /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaM_CaN /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN PRODUCT n
-addmsg /kinetics/SPINE/CaN_BULK/Ca2_CaN /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/CaN /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca2_CaN /kinetics/SPINE/CaN_BULK/Ca_bind_CaN PRODUCT n
-addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaN_BULK/Ca2_CaN REAC B A
-addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaN_BULK/Ca2_CaN REAC A B
-addmsg /kinetics/PSD/tot_PSD_R /graphs/conc1/tot_PSD_R.Co PLOT Co *tot_PSD_R.Co *blue
-addmsg /kinetics/PSD/R_S2 /graphs/conc1/R.Co PLOT Co *R.Co *4
-addmsg /kinetics/PSD/CaM/Ca /graphs/conc1/Ca.Co PLOT Co *Ca.Co *red
-addmsg /kinetics/PSD/PP1_PSD/PP1-active /graphs/conc1/PP1-active.Co PLOT Co *PP1-active.Co *cyan
-addmsg /kinetics/PSD/CaM_CaN /graphs/conc1/CaM_CaN.Co PLOT Co *CaM_CaN.Co *1
-addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII /graphs/conc1/tot-CaM-CaMKII.Co PLOT Co *tot-CaM-CaMKII.Co *47
-addmsg /kinetics/PSD/CaMKII_PSD/tot-auto /graphs/conc1/tot-auto.Co PLOT Co *tot-auto.Co *29
-addmsg /kinetics/PSD/CaM/CaM-Ca4 /graphs/conc1/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue
-addmsg /kinetics/SPINE/iR /graphs/conc2/iR.Co PLOT Co *iR.Co *0
-addmsg /kinetics/PSD/R_SpSp /graphs/conc2/Rpp.Co PLOT Co *Rpp.Co *28
-addmsg /kinetics/SPINE/CaM/Ca /graphs/conc2/Ca.Co PLOT Co *Ca.Co *red
-addmsg /kinetics/SPINE/CaM_CaN /graphs/conc2/CaM_CaN.Co PLOT Co *CaM_CaN.Co *1
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII /graphs/conc2/tot-CaM-CaMKII.Co PLOT Co *tot-CaM-CaMKII.Co *47
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /graphs/conc2/tot-auto.Co PLOT Co *tot-auto.Co *29
-addmsg /kinetics/SPINE/CaM/CaM-Ca4 /graphs/conc2/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue
-enddump
-// End of dump
-
-call /kinetics/PSD/PP1_PSD/PP1-active/notes LOAD \
-"Cohen et al Meth Enz 159 390-408 is main source of info" \
-"conc = 1.8 uM"
-call /kinetics/PSD/PP1_PSD/I1/notes LOAD \
-"I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet" \
-"inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183)." \
-"We treat it as non-compet, so it just turns the enz off" \
-"without interacting with the binding site." \
-"Cohen et al ann rev bioch refer to results where conc is " \
-"1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM," \
-"we need >= 1.8 uM." \
-"" \
-""
-call /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes LOAD \
-"Let us assume that the equil in this case is very far over to the" \
-"right. This is probably safe." \
-""
-call /kinetics/PSD/PP1_PSD/Inact-PP1/notes LOAD \
-"K inhib = 1nM from Cohen Ann Rev Bioch 1989, " \
-"4 nM from Foukes et al " \
-"Assume 2 nM. kf /kb = 8.333e-4"
-call /kinetics/PSD/PP1_PSD/I1_p/notes LOAD \
-"Dephosph is mainly by PP2B"
-call /kinetics/PSD/basal_phosphatase/notes LOAD \
-"There isn't any clear info for this. I had originally called " \
-"it PP2A, but that causes odd interactions with other pathways." \
-""
-call /kinetics/PSD/CaMKII_PSD/NMDAR/notes LOAD \
-"The stochiometry is a bit off here. Each NMDAR actually" \
-"binds to a holoenzyme, about 12 CaMKII subunits. But" \
-"our CaMKII calculations are in terms of individual" \
-"subunits. So as a hack, we put in much more NMDAR than" \
-"is actually there." \
-"" \
-"Dec 2011: Reconsidered this, now only 120 NMDARs." \
-"" \
-"June 02 2012. Consider these as anchor points for a dodecamer." \
-"There are far more effected CaMKII binding sites then, than" \
-"individual molecules of NMDAR. Raised limit to 40."
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-call /kinetics/PSD/CaMKII_PSD/back_1/notes LOAD \
-"Rates set by the translocation experiments of " \
-"Shen and Meyer, Science 1999."
-call /kinetics/PSD/CaMKII_PSD/transloc_2/notes LOAD \
-"Same as for transloc_1" \
-"" \
-"" \
-""
-call /kinetics/PSD/CaMKII_PSD/back_2/notes LOAD \
-"Same as for back_1" \
-""
-call /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes LOAD \
-"k1 changed from 3.3e-6 to 6.6e-6" \
-""
-call /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes LOAD \
-"PP2A does most of the dephosph of I1 at basal Ca levels. See" \
-"the review by Cohen in Ann Rev Biochem 1989." \
-"For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6" \
-""
-call /kinetics/PSD/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-call /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/PSD/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/PSD/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-call /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/PSD/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/iR/notes LOAD \
-"Same as Fus3" \
-""
-call /kinetics/SPINE/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-call /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/SPINE/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-call /kinetics/SPINE/PP2A/notes LOAD \
-"Strack et al JBC 1997 show that PP2A is the primary" \
-"phosphatase acting on CaMKII in the bulk."
-call /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN/notes LOAD \
-"From Quintana et al 2005"
-complete_loading
diff --git a/moose-examples/snippets/MULTI/psd_merged31d.g b/moose-examples/snippets/MULTI/psd_merged31d.g
deleted file mode 100644
index e677d13f37cddb1c1883837d04aa9177517058e1..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/psd_merged31d.g
+++ /dev/null
@@ -1,1488 +0,0 @@
-//genesis
-// kkit Version 11 flat dumpfile
-
-// Saved on Mon Sep 23 22:48:38 2013
-
-include kkit {argv 1}
-
-FASTDT = 0.0001
-SIMDT = 0.001
-CONTROLDT = 10
-PLOTDT = 10
-MAXTIME = 2000
-TRANSIENT_TIME = 10
-VARIABLE_DT_FLAG = 1
-DEFAULT_VOL = 1e-20
-VERSION = 11.0
-setfield /file/modpath value /home2/bhalla/scripts/modules
-kparms
-
-//genesis
-
-initdump -version 3 -ignoreorphans 1
-simobjdump doqcsinfo filename accessname accesstype transcriber developer \
- citation species tissue cellcompartment methodology sources \
- model_implementation model_validation x y z
-simobjdump table input output alloced step_mode stepsize x y z
-simobjdump xtree path script namemode sizescale
-simobjdump xcoredraw xmin xmax ymin ymax
-simobjdump xtext editable
-simobjdump xgraph xmin xmax ymin ymax overlay
-simobjdump xplot pixflags script fg ysquish do_slope wy
-simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
- link savename file version md5sum mod_save_flag x y z
-simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
- z
-simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
- geomname xtree_fg_req xtree_textfg_req x y z
-simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
-simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
- keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
-simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
- trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
-simobjdump xtab input output alloced step_mode stepsize notes editfunc \
- xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
-simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
- xtree_textfg_req x y z
-simobjdump transport input output alloced step_mode stepsize dt delay clock \
- kf xtree_fg_req xtree_textfg_req x y z
-simobjdump proto x y z
-simobjdump text str
-simundump geometry /kinetics/geometry 0 1e-20 3 sphere "" white black 0 0 0
-simundump geometry /kinetics/geometry[1] 0 9e-20 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[3] 0 1e-18 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[4] 0 1e-20 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[5] 0 9e-20 3 sphere "" white black 0 0 \
- 0
-simundump text /kinetics/notes 0 ""
-call /kinetics/notes LOAD \
-""
-simundump text /kinetics/geometry/notes 0 ""
-call /kinetics/geometry/notes LOAD \
-""
-simundump text /kinetics/geometry[1]/notes 0 ""
-call /kinetics/geometry[1]/notes LOAD \
-""
-simundump text /kinetics/geometry[2]/notes 0 ""
-call /kinetics/geometry[2]/notes LOAD \
-""
-simundump text /kinetics/geometry[3]/notes 0 ""
-call /kinetics/geometry[3]/notes LOAD \
-""
-simundump text /kinetics/geometry[4]/notes 0 ""
-call /kinetics/geometry[4]/notes LOAD \
-""
-simundump text /kinetics/geometry[5]/notes 0 ""
-call /kinetics/geometry[5]/notes LOAD \
-""
-simundump group /kinetics/PSD 0 20 black x 0 0 "" PSD defaultfile.g 0 0 0 27 \
- 12 0
-simundump text /kinetics/PSD/notes 0 ""
-call /kinetics/PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/tot_PSD_R 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry blue 0 -4 7 0
-simundump text /kinetics/PSD/tot_PSD_R/notes 0 ""
-call /kinetics/PSD/tot_PSD_R/notes LOAD \
-""
-simundump kpool /kinetics/PSD/actCaMKII 0 0 2 2 12 12 0 0 6 0 \
- /kinetics/geometry 12 20 70 33 0
-simundump text /kinetics/PSD/actCaMKII/notes 0 ""
-call /kinetics/PSD/actCaMKII/notes LOAD \
-""
-simundump kenz /kinetics/PSD/actCaMKII/CaMKII_1 0 0 0 0 0 6 0.033332 8 2 0 0 \
- "" red 35 "" -6 3 0
-simundump text /kinetics/PSD/actCaMKII/CaMKII_1/notes 0 ""
-call /kinetics/PSD/actCaMKII/CaMKII_1/notes LOAD \
-""
-simundump kenz /kinetics/PSD/actCaMKII/CaMKII_2 0 0 0 0 0 6 0.033332 8 2 0 0 \
- "" red 35 "" -2 3 0
-simundump text /kinetics/PSD/actCaMKII/CaMKII_2/notes 0 ""
-call /kinetics/PSD/actCaMKII/CaMKII_2/notes LOAD \
-""
-simundump group /kinetics/PSD/PP1_PSD 1 yellow 20 x 0 0 "" PP1_PSD \
- /home2/bhalla/scripts/modules/PP1_PSD_0.g 0 \
- 62a600ae10e53f567e47decb4f2b6488 0 12 27 0
-simundump text /kinetics/PSD/PP1_PSD/notes 0 ""
-call /kinetics/PSD/PP1_PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-active 1 0 4 4 24 24 0 0 6 0 \
- /kinetics/geometry cyan yellow 44 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/notes 0 \
- "Cohen et al Meth Enz 159 390-408 is main source of info\nconc = 1.8 uM"
-call /kinetics/PSD/PP1_PSD/PP1-active/notes LOAD \
-"Cohen et al Meth Enz 159 390-408 is main source of info" \
-"conc = 1.8 uM"
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/PP1_2 0 0 0 0 0 6 0.0010416 \
- 0.2 0.05 0 0 "" red blue "" -2 -4 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/PP1_2/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/PP1_2/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/PP1_1 0 0 0 0 0 6 0.0010416 \
- 0.2 0.05 0 0 "" red blue "" -6 -4 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/PP1_1/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/PP1_1/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 61 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 71 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305 0 0 0 0 0 54.001 \
- 0.083333 2 0.5 0 0 "" red cyan "" 78 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c 0 0 0 0 0 54.001 \
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-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c/notes LOAD \
-""
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- 0.083333 2 0.5 0 0 "" red cyan "" 83 25 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/I1 1 0 4 4 24 24 0 0 6 0 \
- /kinetics/geometry orange yellow 35.35 21.88 0
-simundump text /kinetics/PSD/PP1_PSD/I1/notes 0 \
- "I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet\ninhibitor (Foulkes et al Eur J Biochem 132 309-313 9183).\nWe treat it as non-compet, so it just turns the enz off\nwithout interacting with the binding site.\nCohen et al ann rev bioch refer to results where conc is \n1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM,\nwe need >= 1.8 uM.\n\n"
-call /kinetics/PSD/PP1_PSD/I1/notes LOAD \
-"I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet" \
-"inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183)." \
-"We treat it as non-compet, so it just turns the enz off" \
-"without interacting with the binding site." \
-"Cohen et al ann rev bioch refer to results where conc is " \
-"1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM," \
-"we need >= 1.8 uM." \
-"" \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-I1 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry brown yellow 36 29 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-I1/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-I1/notes LOAD \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 1 1 0 "" white yellow 33 \
- 26 0
-simundump text /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes 0 \
- "Let us assume that the equil in this case is very far over to the\nright. This is probably safe.\n"
-call /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes LOAD \
-"Let us assume that the equil in this case is very far over to the" \
-"right. This is probably safe." \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/Inact-PP1 1 83.33 0.1 "" white yellow \
- 17 26 0
-simundump text /kinetics/PSD/PP1_PSD/Inact-PP1/notes 0 \
- "K inhib = 1nM from Cohen Ann Rev Bioch 1989, \n4 nM from Foukes et al \nAssume 2 nM. kf /kb = 8.333e-4"
-call /kinetics/PSD/PP1_PSD/Inact-PP1/notes LOAD \
-"K inhib = 1nM from Cohen Ann Rev Bioch 1989, " \
-"4 nM from Foukes et al " \
-"Assume 2 nM. kf /kb = 8.333e-4"
-simundump kpool /kinetics/PSD/PP1_PSD/PP1-I1_p 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry brown yellow 22 29 0
-simundump text /kinetics/PSD/PP1_PSD/PP1-I1_p/notes 0 ""
-call /kinetics/PSD/PP1_PSD/PP1-I1_p/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP1_PSD/I1_p 1 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry orange yellow 21 22 0
-simundump text /kinetics/PSD/PP1_PSD/I1_p/notes 0 \
- "Dephosph is mainly by PP2B"
-call /kinetics/PSD/PP1_PSD/I1_p/notes LOAD \
-"Dephosph is mainly by PP2B"
-simundump kpool /kinetics/PSD/PP1_PSD/CaN 0 1e-12 1 1 6 6 0 0 6 0 \
- /kinetics/geometry 1 yellow -1 33 0
-simundump text /kinetics/PSD/PP1_PSD/CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/CaN/notes LOAD \
-""
-simundump kreac /kinetics/PSD/PP1_PSD/CaM-Bind-CaN 0 7.6667 0.002 "" white \
- yellow 21 40 0
-simundump text /kinetics/PSD/PP1_PSD/CaM-Bind-CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/CaM-Bind-CaN/notes LOAD \
-""
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- /kinetics/geometry[2] blue yellow 12 33 0
-simundump text /kinetics/PSD/PP1_PSD/Ca2_CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/Ca2_CaN/notes LOAD \
-""
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- 7 40 0
-simundump text /kinetics/PSD/PP1_PSD/Ca_bind_CaN/notes 0 ""
-call /kinetics/PSD/PP1_PSD/Ca_bind_CaN/notes LOAD \
-""
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-simundump text /kinetics/PSD/move_to_PSD/notes 0 ""
-call /kinetics/PSD/move_to_PSD/notes LOAD \
-""
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- -8 1 0
-simundump text /kinetics/PSD/R_S2/notes 0 ""
-call /kinetics/PSD/R_S2/notes LOAD \
-""
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- blue 0 -4 1 0
-simundump text /kinetics/PSD/R_SpS/notes 0 ""
-call /kinetics/PSD/R_SpS/notes LOAD \
-""
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- 28 0 0 1 0
-simundump text /kinetics/PSD/R_SpSp/notes 0 ""
-call /kinetics/PSD/R_SpSp/notes LOAD \
-""
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- /kinetics/geometry 61 0 -4 -2 0
-simundump text /kinetics/PSD/basal_phosphatase/notes 0 \
- "There isn't any clear info for this. I had originally called \nit PP2A, but that causes odd interactions with other pathways.\n"
-call /kinetics/PSD/basal_phosphatase/notes LOAD \
-"There isn't any clear info for this. I had originally called " \
-"it PP2A, but that causes odd interactions with other pathways." \
-""
-simundump kenz /kinetics/PSD/basal_phosphatase/P1 0 0 0 0 0 60 0.46295 \
- 0.44443 0.11111 0 0 "" red 61 "" -6 -1 0
-simundump text /kinetics/PSD/basal_phosphatase/P1/notes 0 ""
-call /kinetics/PSD/basal_phosphatase/P1/notes LOAD \
-""
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-simundump text /kinetics/PSD/basal_phosphatase/P2/notes 0 ""
-call /kinetics/PSD/basal_phosphatase/P2/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PKA-active 1 0 0.02 0.02 0.12 0.12 0 0 6 0 \
- /kinetics/geometry yellow 20 14 17 0
-simundump text /kinetics/PSD/PKA-active/notes 0 ""
-call /kinetics/PSD/PKA-active/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PKA-active/PKA-phosph-I1 0 0 0 0 0 54.001 \
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-simundump text /kinetics/PSD/PKA-active/PKA-phosph-I1/notes 0 ""
-call /kinetics/PSD/PKA-active/PKA-phosph-I1/notes LOAD \
-""
-simundump group /kinetics/PSD/CaMKII_PSD 0 27 20 x 0 0 "" CaMKII_PSD \
- defaultfile.g 0 0 0 39 32 0
-simundump text /kinetics/PSD/CaMKII_PSD/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph/notes LOAD \
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/tot_CaMKII 0 0 2 2 12 12 0 0 6 0 \
- /kinetics/geometry 23 27 84 36 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot_CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot_CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/286P 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 59 27 52 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/286P/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/286P/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 47 27 61 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/notes LOAD \
-""
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- 0 7.732 0.0052083 8 2 0 0 "" red 47 "" 72 20 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph/notes 0 \
- ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305/notes LOAD \
-""
-simundump kenz /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 0 0 0 0 0 \
- 7.732 0.0013021 2 0.5 0 0 "" red 47 "" 60 20 0
-simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/basal_CaMKII 0 0 1 1 6 6 0 0 6 0 \
- /kinetics/geometry blue 27 81 33 0
-simundump text /kinetics/PSD/CaMKII_PSD/basal_CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/basal_CaMKII/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM 0 10.945 \
- 0.0022 "" white 27 54 28 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes 0 \
- "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?"
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-simundump kreac /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM 0 10.945 2.2 "" \
- white 27 65 28 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM/notes LOAD \
-""
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- 0 /kinetics/geometry 47 27 56 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-CaM 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 50 27 63 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-CaM/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-CaM/notes LOAD \
-""
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- /kinetics/geometry 57 27 69 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 62 27 75 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr305 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 30 27 88 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr305/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr305/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 0 27 81 22 0
-simundump text /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/transloc_1 0 1 1e-06 "" white 27 63 \
- 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/transloc_1/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/transloc_1/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/back_1 0 0.04 6.6667e-06 "" white 27 \
- 75 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/back_1/notes 0 \
- "Rates set by the translocation experiments of \nShen and Meyer, Science 1999."
-call /kinetics/PSD/CaMKII_PSD/back_1/notes LOAD \
-"Rates set by the translocation experiments of " \
-"Shen and Meyer, Science 1999."
-simundump kreac /kinetics/PSD/CaMKII_PSD/transloc_2 0 0.0001 1e-06 "" white \
- 27 56 12 0
-simundump text /kinetics/PSD/CaMKII_PSD/transloc_2/notes 0 \
- "Same as for transloc_1\n\n\n"
-call /kinetics/PSD/CaMKII_PSD/transloc_2/notes LOAD \
-"Same as for transloc_1" \
-"" \
-"" \
-""
-simundump kreac /kinetics/PSD/CaMKII_PSD/back_2 0 0.04 6.6667e-06 "" white 27 \
- 89 13 0
-simundump text /kinetics/PSD/CaMKII_PSD/back_2/notes 0 "Same as for back_1\n"
-call /kinetics/PSD/CaMKII_PSD/back_2/notes LOAD \
-"Same as for back_1" \
-""
-simundump kpool /kinetics/PSD/CaMKII_PSD/bar 0 0 0.66667 0.66667 4 4 0 0 6 0 \
- /kinetics/geometry[4] blue 27 50 18 0
-simundump text /kinetics/PSD/CaMKII_PSD/bar/notes 0 ""
-call /kinetics/PSD/CaMKII_PSD/bar/notes LOAD \
-""
-simundump kpool /kinetics/PSD/PP2A 1 0 1 1 6 6 0 0 6 0 /kinetics/geometry red \
- 20 45 17 0
-simundump text /kinetics/PSD/PP2A/notes 0 ""
-call /kinetics/PSD/PP2A/notes LOAD \
-""
-simundump kenz /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p 1 0.0012791 0.0012791 \
- 0.06907 0.06907 54.001 0.0013289 0.92593 0.22222 0 0 "" red red "" 29 27 0
-simundump text /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes 0 \
- "k1 changed from 3.3e-6 to 6.6e-6\n"
-call /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes LOAD \
-"k1 changed from 3.3e-6 to 6.6e-6" \
-""
-simundump kenz /kinetics/PSD/PP2A/PP2A-dephosph-I1 1 2.2155e-07 2.2155e-07 \
- 1.1964e-05 1.1964e-05 54.001 0.0013289 0.92593 0.22222 0 0 "" red red "" 27 \
- 20 0
-simundump text /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes 0 \
- "PP2A does most of the dephosph of I1 at basal Ca levels. See\nthe review by Cohen in Ann Rev Biochem 1989.\nFor now, lets halve Km. k1 was 3.3e-6, now 6.6e-6\n"
-call /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes LOAD \
-"PP2A does most of the dephosph of I1 at basal Ca levels. See" \
-"the review by Cohen in Ann Rev Biochem 1989." \
-"For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6" \
-""
-simundump group /kinetics/PSD/CaM 1 blue 20 x 0 0 "" defaultfile \
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-simundump text /kinetics/PSD/CaM/notes 0 ""
-call /kinetics/PSD/CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaM/CaM 1 1e-12 20 20 120 120 0 0 6 0 \
- /kinetics/geometry pink blue 35 39 0
-simundump text /kinetics/PSD/CaM/CaM/notes 0 \
- "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n"
-call /kinetics/PSD/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-Ca3-bind-Ca 1 0.077501 10 "" white blue \
- 49 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes 0 \
- "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-simundump kpool /kinetics/PSD/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry hotpink blue 47 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca3/notes 0 ""
-call /kinetics/PSD/CaM/CaM-Ca3/notes LOAD \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-bind-Ca 1 1.4141 8.4853 "" white blue \
- 37 36 0
-simundump text /kinetics/PSD/CaM/CaM-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/PSD/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/PSD/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry pink blue 43 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca2/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kreac /kinetics/PSD/CaM/CaM-Ca2-bind-Ca 1 0.60001 10 "" white blue \
- 45 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes 0 \
- "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n"
-call /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-simundump kreac /kinetics/PSD/CaM/CaM-Ca-bind-Ca 1 1.4141 8.4853 "" white \
- blue 41 36 0
-simundump text /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/PSD/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry pink blue 39 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kpool /kinetics/PSD/CaM/Ca 1 1e-11 0.08 0.08 0.48 0.48 0 0 6 4 \
- /kinetics/geometry red blue 43 33 0
-simundump text /kinetics/PSD/CaM/Ca/notes 0 ""
-call /kinetics/PSD/CaM/Ca/notes LOAD \
-""
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- /kinetics/geometry blue blue 52 39 0
-simundump text /kinetics/PSD/CaM/CaM-Ca4/notes 0 ""
-call /kinetics/PSD/CaM/CaM-Ca4/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaM_CaN 1 1e-12 0 0 0 0 0 0 6 0 \
- /kinetics/geometry 1 20 30 33 0
-simundump text /kinetics/PSD/CaM_CaN/notes 0 ""
-call /kinetics/PSD/CaM_CaN/notes LOAD \
-""
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- 0.0063334 1.36 0.34 0 0 "" white 1 "" 29 30 0
-simundump text /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p/notes 0 ""
-call /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p/notes LOAD \
-""
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-simundump text /kinetics/PSD/CaM_CaN/dephosph_inhib1/notes 0 ""
-call /kinetics/PSD/CaM_CaN/dephosph_inhib1/notes LOAD \
-""
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- -30 0
-simundump text /kinetics/DEND/notes 0 ""
-call /kinetics/DEND/notes LOAD \
-""
-simundump kpool /kinetics/DEND/Ca 0 1e-11 0.08 0.08 48 48 0 0 600 0 \
- /kinetics/geometry[3] 62 13 13 -27 0
-simundump text /kinetics/DEND/Ca/notes 0 ""
-call /kinetics/DEND/Ca/notes LOAD \
-""
-simundump group /kinetics/SPINE 0 5 black x 0 0 "" SPINE defaultfile.g 0 0 0 \
- 29 -23 0
-simundump text /kinetics/SPINE/notes 0 ""
-call /kinetics/SPINE/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/iR 0 0 4.4444 4.4444 240 240 0 0 54 0 \
- /kinetics/geometry 0 yellow -8 -10 0
-simundump text /kinetics/SPINE/iR/notes 0 "Same as Fus3\n"
-call /kinetics/SPINE/iR/notes LOAD \
-"Same as Fus3" \
-""
-simundump group /kinetics/SPINE/CaM 1 blue 5 x 0 0 "" defaultfile \
- defaultfile.g 0 fbb0ff81553508bc01f3dd51428742fb 0 33 2 0
-simundump text /kinetics/SPINE/CaM/notes 0 ""
-call /kinetics/SPINE/CaM/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaM/CaM 1 1e-12 20 20 1080 1080 0 0 54 0 \
- /kinetics/geometry pink blue 37 4 0
-simundump text /kinetics/SPINE/CaM/CaM/notes 0 \
- "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n"
-call /kinetics/SPINE/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca 1 0.0086112 10 "" white \
- blue 51 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes 0 \
- "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 54 0 \
- /kinetics/geometry hotpink blue 49 4 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca3/notes 0 ""
-call /kinetics/SPINE/CaM/CaM-Ca3/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-bind-Ca 1 0.15712 8.4853 "" white \
- blue 39 1 0
-simundump text /kinetics/SPINE/CaM/CaM-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/SPINE/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 54 0 \
- /kinetics/geometry pink blue 45 4 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca2/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca 1 0.066668 10 "" white \
- blue 47 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes 0 \
- "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n"
-call /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-simundump kreac /kinetics/SPINE/CaM/CaM-Ca-bind-Ca 1 0.15712 8.4853 "" white \
- blue 43 1 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes 0 \
- "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...."
-call /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 54 0 \
- /kinetics/geometry pink blue 41 4 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca/notes 0 \
- "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-simundump kpool /kinetics/SPINE/CaM/Ca 1 1e-11 0.08 0.08 4.32 4.32 0 0 54 0 \
- /kinetics/geometry red blue 45 -2 0
-simundump text /kinetics/SPINE/CaM/Ca/notes 0 ""
-call /kinetics/SPINE/CaM/Ca/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaM/CaM-Ca4 1 1e-12 0 0 0 0 0 0 54 0 \
- /kinetics/geometry blue blue 54 4 0
-simundump text /kinetics/SPINE/CaM/CaM-Ca4/notes 0 ""
-call /kinetics/SPINE/CaM/CaM-Ca4/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/notes LOAD \
-""
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- /kinetics/geometry 29 33 76 1 0
-simundump text /kinetics/SPINE/CaMKII_BULK/tot-auto/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/tot-auto/notes LOAD \
-""
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-call /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph/notes LOAD \
-""
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-call /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaMKII_BULK/tot_CaMKII 0 0 2 22 1188 108 0 0 \
- 54 0 /kinetics/geometry 23 33 86 1 0
-simundump text /kinetics/SPINE/CaMKII_BULK/tot_CaMKII/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/tot_CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaMKII_BULK/286P 0 0 0 0 0 0 0 0 54 0 \
- /kinetics/geometry 59 33 54 -2 0
-simundump text /kinetics/SPINE/CaMKII_BULK/286P/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/286P/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII 0 0 0 0 0 0 0 0 54 \
- 0 /kinetics/geometry 47 33 63 -2 0
-simundump text /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/notes LOAD \
-""
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- 0 0 0 69.588 0.0005787 8 2 0 0 "" red 47 "" 74 -15 0
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- ""
-call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph/notes LOAD \
-""
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- ""
-call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305/notes LOAD \
-""
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- 0 69.588 0.00014468 2 0.5 0 0 "" red 47 "" 62 -15 0
-simundump text /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes 0 \
- ""
-call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaMKII_BULK/basal_CaMKII 0 0 1 1 54 54 0 0 54 \
- 0 /kinetics/geometry blue 33 83 -2 0
-simundump text /kinetics/SPINE/CaMKII_BULK/basal_CaMKII/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/basal_CaMKII/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM 0 1.2161 \
- 0.0022 "" white 33 56 -7 0
-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes 0 \
- "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?"
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
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- white 33 67 -7 0
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-call /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM/notes LOAD \
-""
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- 54 0 /kinetics/geometry 47 33 58 -13 0
-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/CaMKII/notes LOAD \
-""
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- 0 /kinetics/geometry 30 33 90 -13 0
-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305/notes LOAD \
-""
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- /kinetics/geometry 0 33 83 -13 0
-simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaMKII_BULK/NMDAR 0 0 4.4444 4.4444 240 240 0 \
- 0 54 0 /kinetics/geometry blue 33 67 8 0
-simundump text /kinetics/SPINE/CaMKII_BULK/NMDAR/notes 0 \
- "The stochiometry is a bit off here. Each NMDAR actually\nbinds to a holoenzyme, about 12 CaMKII subunits. But\nour CaMKII calculations are in terms of individual\nsubunits. So as a hack, we put in much more NMDAR than\nis actually there.\n\nDec 2011: Reconsidered this, now only 120 NMDARs.\n\nJune 02 2012. Consider these as anchor points for a dodecamer.\nThere are far more effected CaMKII bindin...."
-call /kinetics/SPINE/CaMKII_BULK/NMDAR/notes LOAD \
-"The stochiometry is a bit off here. Each NMDAR actually" \
-"binds to a holoenzyme, about 12 CaMKII subunits. But" \
-"our CaMKII calculations are in terms of individual" \
-"subunits. So as a hack, we put in much more NMDAR than" \
-"is actually there." \
-"" \
-"Dec 2011: Reconsidered this, now only 120 NMDARs." \
-"" \
-"June 02 2012. Consider these as anchor points for a dodecamer." \
-"There are far more effected CaMKII binding sites then, than" \
-"individual molecules of NMDAR. Raised limit to 40."
-simundump kpool /kinetics/SPINE/CaMKII_BULK/foo 0 0 0.18519 0.18519 10 10 0 0 \
- 54 0 /kinetics/geometry[5] blue 33 43 9 0
-simundump text /kinetics/SPINE/CaMKII_BULK/foo/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/foo/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaMKII_BULK/tr0/notes 0 ""
-call /kinetics/SPINE/CaMKII_BULK/tr0/notes LOAD \
-""
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-simundump text /kinetics/SPINE/CaM_CaN/notes 0 ""
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-""
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-simundump text /kinetics/SPINE/actCaMKII/notes 0 ""
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-""
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- /kinetics/geometry 62 5 46 -10 0
-simundump text /kinetics/SPINE/PP2A/notes 0 \
- "Strack et al JBC 1997 show that PP2A is the primary\nphosphatase acting on CaMKII in the bulk."
-call /kinetics/SPINE/PP2A/notes LOAD \
-"Strack et al JBC 1997 show that PP2A is the primary" \
-"phosphatase acting on CaMKII in the bulk."
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-""
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-"23 Dec 2011" \
-"CaMKII_merged16.g" \
-"Added Ca-binding step to the CaN activation pathway." \
-"Based on CaMKII_merged15.g" \
-"" \
-"CaMKII_merged16a.g" \
-"Halved the Kb for CaN-bind-CaM" \
-"" \
-"CaMKII_merged17.g" \
-" Used more rates from Saucerman and Bers BPJ 2008" \
-"" \
-"CaMKII_merged17a.g" \
-"Fix to init conc of PP1-active in PSD: from 2 to 4." \
-"" \
-"CaMKII_merged17b.g" \
-"Raised PP2A CoInit from 0.1111 uM to 1 uM, to avoid sub-molecular" \
-"levels in PSD. Scaled kcats down to match." \
-"" \
-"CaMKII_merged20.g" \
-"First pass at a version with a reasonable basal PKA and a less" \
-"saturating effect on PP1-active of CaMKII." \
-"" \
-"CaMKII_merged20c.g: This version turns on but does not go off" \
-"afterwards. " \
-"" \
-"CaMKII_merged20d.g: 10x higher Km and kcat for PP1 on CaMKII." \
-"" \
-"CaMKII_merged20e.g: Km = 5 and kcat =0.5" \
-"" \
-"02 June 2012. CaMKII_merged20g.g: NMDAR = 40, effective # of" \
-"sites given that CaMKII is a dodecamer." \
-"" \
-"CaMKII_merged20h.g: Lowered Kb for CaM-Bind-CaN from 0.006 to " \
-"0.002/sec." \
-"" \
-"CaMKII_merged20i.g: Set PKA-active in both compts to be 0.02 uM." \
-"" \
-"CaMKII_merged20j.g: Faster CaN diffusion, by 6x. Now matches" \
-"CaM with 6:54." \
-"" \
-"CaMKII_merged20k.g: Halved CaMKII affinity for NMDAR." \
-"" \
-"CaMKII_merged21.g: Removed bulk PP1. Use PP2A to dephosphorylate" \
-"CaMKII in bulk." \
-"" \
-"19 July 2013. psd_merged30.g: Variant for signeur loading." \
-"" \
-"23 Sep 2013. psd_merged31.g: moved NMDAR to spine bulk, to check" \
-"possible bug in handling of cross-compartment reactions." \
-"23 Sep 2013. psd_merged31b.g: added dummy reaction tr0 to check" \
-"what happens with a simple cross-compt reaction." \
-"23 Sep 2013. psd_merged31c.g: moved tr0 to the CaMKII_PSD to see" \
-"if this fixes the problem." \
-"psd_merged31d.g: Tried eliminating NMDAR as substrate." \
-""
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-addmsg /kinetics/PSD/actCaMKII/CaMKII_1 /kinetics/PSD/actCaMKII REAC eA B
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-addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 MM_PRD pA
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 MM_PRD pA
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM /kinetics/SPINE/CaMKII_BULK/CaMKII REAC A B
-addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/CaMKII_BULK/CaMKII MM_PRD pA
-addmsg /kinetics/SPINE/PP2A/Deph-thr286b /kinetics/SPINE/CaMKII_BULK/CaMKII MM_PRD pA
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph /kinetics/SPINE/CaMKII_BULK/CaMKII REAC sA B
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph /kinetics/SPINE/CaMKII_BULK/CaMKII REAC sA B
-addmsg /kinetics/PSD/CaMKII_PSD/back_1 /kinetics/SPINE/CaMKII_BULK/CaMKII REAC B A
-addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 REAC sA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 MM_PRD pA
-addmsg /kinetics/PSD/CaMKII_PSD/back_2 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 REAC B A
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA
-addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p REAC sA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p REAC sA B
-addmsg /kinetics/PSD/CaMKII_PSD/transloc_2 /kinetics/SPINE/CaMKII_BULK/NMDAR REAC A B
-addmsg /kinetics/PSD/CaMKII_PSD/transloc_1 /kinetics/SPINE/CaMKII_BULK/NMDAR REAC A B
-addmsg /kinetics/PSD/CaMKII_PSD/back_1 /kinetics/SPINE/CaMKII_BULK/NMDAR REAC B A
-addmsg /kinetics/PSD/CaMKII_PSD/back_2 /kinetics/SPINE/CaMKII_BULK/NMDAR REAC B A
-addmsg /kinetics/SPINE/CaMKII_BULK/tr0 /kinetics/SPINE/CaMKII_BULK/foo REAC A B
-addmsg /kinetics/SPINE/CaMKII_BULK/foo /kinetics/SPINE/CaMKII_BULK/tr0 SUBSTRATE n
-addmsg /kinetics/PSD/CaMKII_PSD/bar /kinetics/SPINE/CaMKII_BULK/tr0 PRODUCT n
-addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaM_CaN REAC B A
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /kinetics/SPINE/actCaMKII SUMTOTAL n nInit
-addmsg /kinetics/SPINE/PP2A/Deph-thr286 /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286b /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/PP2A REAC eA B
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286 ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/PP2A/Deph-thr286 SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286b ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/PP2A/Deph-thr286b SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr305 ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/PP2A/Deph-thr305 SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286c ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/PP2A/Deph-thr286c SUBSTRATE n
-addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr305a ENZYME n
-addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 /kinetics/SPINE/PP2A/Deph-thr305a SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaN_BULK/CaN REAC A B
-addmsg /kinetics/SPINE/CaM/CaM-Ca4 /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaM_CaN /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN PRODUCT n
-addmsg /kinetics/SPINE/CaN_BULK/Ca2_CaN /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/CaN /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca2_CaN /kinetics/SPINE/CaN_BULK/Ca_bind_CaN PRODUCT n
-addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n
-addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaN_BULK/Ca2_CaN REAC B A
-addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaN_BULK/Ca2_CaN REAC A B
-addmsg /kinetics/PSD/tot_PSD_R /graphs/conc1/tot_PSD_R.Co PLOT Co *tot_PSD_R.Co *blue
-addmsg /kinetics/PSD/R_S2 /graphs/conc1/R.Co PLOT Co *R.Co *4
-addmsg /kinetics/PSD/CaM/Ca /graphs/conc1/Ca.Co PLOT Co *Ca.Co *red
-addmsg /kinetics/PSD/PP1_PSD/PP1-active /graphs/conc1/PP1-active.Co PLOT Co *PP1-active.Co *cyan
-addmsg /kinetics/PSD/CaM_CaN /graphs/conc1/CaM_CaN.Co PLOT Co *CaM_CaN.Co *1
-addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII /graphs/conc1/tot-CaM-CaMKII.Co PLOT Co *tot-CaM-CaMKII.Co *47
-addmsg /kinetics/PSD/CaMKII_PSD/tot-auto /graphs/conc1/tot-auto.Co PLOT Co *tot-auto.Co *29
-addmsg /kinetics/PSD/CaM/CaM-Ca4 /graphs/conc1/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue
-addmsg /kinetics/SPINE/iR /graphs/conc2/iR.Co PLOT Co *iR.Co *0
-addmsg /kinetics/PSD/R_SpSp /graphs/conc2/Rpp.Co PLOT Co *Rpp.Co *28
-addmsg /kinetics/SPINE/CaM/Ca /graphs/conc2/Ca.Co PLOT Co *Ca.Co *red
-addmsg /kinetics/SPINE/CaM_CaN /graphs/conc2/CaM_CaN.Co PLOT Co *CaM_CaN.Co *1
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII /graphs/conc2/tot-CaM-CaMKII.Co PLOT Co *tot-CaM-CaMKII.Co *47
-addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /graphs/conc2/tot-auto.Co PLOT Co *tot-auto.Co *29
-addmsg /kinetics/SPINE/CaM/CaM-Ca4 /graphs/conc2/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue
-enddump
-// End of dump
-
-call /kinetics/PSD/PP1_PSD/PP1-active/notes LOAD \
-"Cohen et al Meth Enz 159 390-408 is main source of info" \
-"conc = 1.8 uM"
-call /kinetics/PSD/PP1_PSD/I1/notes LOAD \
-"I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet" \
-"inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183)." \
-"We treat it as non-compet, so it just turns the enz off" \
-"without interacting with the binding site." \
-"Cohen et al ann rev bioch refer to results where conc is " \
-"1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM," \
-"we need >= 1.8 uM." \
-"" \
-""
-call /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes LOAD \
-"Let us assume that the equil in this case is very far over to the" \
-"right. This is probably safe." \
-""
-call /kinetics/PSD/PP1_PSD/Inact-PP1/notes LOAD \
-"K inhib = 1nM from Cohen Ann Rev Bioch 1989, " \
-"4 nM from Foukes et al " \
-"Assume 2 nM. kf /kb = 8.333e-4"
-call /kinetics/PSD/PP1_PSD/I1_p/notes LOAD \
-"Dephosph is mainly by PP2B"
-call /kinetics/PSD/basal_phosphatase/notes LOAD \
-"There isn't any clear info for this. I had originally called " \
-"it PP2A, but that causes odd interactions with other pathways." \
-""
-call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-call /kinetics/PSD/CaMKII_PSD/back_1/notes LOAD \
-"Rates set by the translocation experiments of " \
-"Shen and Meyer, Science 1999."
-call /kinetics/PSD/CaMKII_PSD/transloc_2/notes LOAD \
-"Same as for transloc_1" \
-"" \
-"" \
-""
-call /kinetics/PSD/CaMKII_PSD/back_2/notes LOAD \
-"Same as for back_1" \
-""
-call /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes LOAD \
-"k1 changed from 3.3e-6 to 6.6e-6" \
-""
-call /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes LOAD \
-"PP2A does most of the dephosph of I1 at basal Ca levels. See" \
-"the review by Cohen in Ann Rev Biochem 1989." \
-"For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6" \
-""
-call /kinetics/PSD/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-call /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/PSD/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/PSD/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-call /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/PSD/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/iR/notes LOAD \
-"Same as Fus3" \
-""
-call /kinetics/SPINE/CaM/CaM/notes LOAD \
-"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \
-"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \
-"it is comparable to CaMK levels. " \
-""
-call /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes LOAD \
-"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
-"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
-call /kinetics/SPINE/CaM/CaM-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca2/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes LOAD \
-"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
-"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes LOAD \
-"Lets use the fast rate consts here. Since the rates are so different, I am not" \
-"sure whether the order is relevant. These correspond to the TR2C fragment." \
-"We use the Martin et al rates here, plus the Drabicowski binding consts." \
-"All are scaled by 3X to cell temp." \
-"kf = 2e-10 kb = 72" \
-"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \
-"If kb=72, kf = 2e-10 (Exactly the same !)" \
-"" \
-"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \
-"two steps, each binding 1 Ca. This improves numerical" \
-"stability and is conceptually better too." \
-"" \
-"Overall rates are the same, so each kf and kb is the " \
-"square root of the earlier ones. So" \
-"kf = 1.125e-4, kb = 8.4853" \
-""
-call /kinetics/SPINE/CaM/CaM-Ca/notes LOAD \
-"This is the intermediate where the TR2 end (the high-affinity end) has" \
-"bound the Ca but the TR1 end has not."
-call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \
-"Same values as for the main compartment" \
-"Can the main compartment pool of Ca/CaM be used?"
-call /kinetics/SPINE/CaMKII_BULK/NMDAR/notes LOAD \
-"The stochiometry is a bit off here. Each NMDAR actually" \
-"binds to a holoenzyme, about 12 CaMKII subunits. But" \
-"our CaMKII calculations are in terms of individual" \
-"subunits. So as a hack, we put in much more NMDAR than" \
-"is actually there." \
-"" \
-"Dec 2011: Reconsidered this, now only 120 NMDARs." \
-"" \
-"June 02 2012. Consider these as anchor points for a dodecamer." \
-"There are far more effected CaMKII binding sites then, than" \
-"individual molecules of NMDAR. Raised limit to 40."
-call /kinetics/SPINE/PP2A/notes LOAD \
-"Strack et al JBC 1997 show that PP2A is the primary" \
-"phosphatase acting on CaMKII in the bulk."
-call /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN/notes LOAD \
-"From Quintana et al 2005"
-complete_loading
diff --git a/moose-examples/snippets/MULTI/runcell18.py b/moose-examples/snippets/MULTI/runcell18.py
deleted file mode 100644
index cbe5037c594bb37eca4086c9fcd286e24e89f723..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/runcell18.py
+++ /dev/null
@@ -1,71 +0,0 @@
-# First pass at loading and running a cell model
-import os
-os.environ['NUMPTHREADS'] = '1'
-
-import moose
-import proto18
-
-def dumpPlots( fname ):
- if ( os.path.exists( fname ) ):
- os.remove( fname )
- tab.xplot( fname, 'soma.Vm' )
- catab.xplot( fname, 'soma.Ca' )
-
-library = moose.Neutral( '/library' )
-moose.setCwe( '/library' )
-proto18.make_Ca()
-proto18.make_Ca_conc()
-proto18.make_K_AHP()
-proto18.make_K_C()
-proto18.make_Na()
-proto18.make_K_DR()
-proto18.make_K_A()
-proto18.make_glu()
-proto18.make_NMDA()
-proto18.make_Ca_NMDA()
-proto18.make_NMDA_Ca_conc()
-proto18.make_axon()
-
-cellId = moose.loadModel( 'ca1_asym.p', '/cell', "hsolve" )
-moose.le( cellId )
-moose.le( '/cell/lat_14_1' )
-#le( '/cell' )
-graphs = moose.Neutral( '/graphs' )
-tab = moose.Table( '/graphs/soma' )
-catab = moose.Table( '/graphs/ca' )
-soma = moose.element( '/cell/soma' )
-soma.inject = 2e-10
-moose.connect( tab, 'requestOut', soma, 'getVm' )
-capool = moose.element( '/cell/soma/Ca_conc' )
-moose.connect( catab, 'requestOut', capool, 'getCa' )
-print((1))
-dt = 50e-6
-moose.setClock( 0, dt )
-moose.setClock( 1, dt )
-moose.setClock( 2, dt )
-moose.setClock( 3, 2e-4 )
-moose.useClock( 0, '/cell/##[ISA=Compartment]', 'init' )
-moose.useClock( 1, '/cell/##[ISA=Compartment]', 'process' )
-moose.useClock( 2, '/cell/##[ISA!=Compartment]', 'process' )
-moose.useClock( 3, '/graphs/soma,/graphs/ca', 'process' )
-
-print((2))
-moose.reinit()
-print((3))
-moose.start( 0.1 )
-dumpPlots( '50usec.plot' )
-print((4))
-moose.reinit()
-hsolve = moose.HSolve( '/cell/hsolve' )
-moose.useClock( 1, '/cell/hsolve', 'process' )
-hsolve.dt = dt
-hsolve.target = '/cell/soma'
-moose.reinit()
-moose.reinit()
-print((5))
-moose.start( 0.1 )
-print((6))
-
-dumpPlots( 'h50usec.plot' )
-
-print((7))
diff --git a/moose-examples/snippets/MULTI/x_compt.g b/moose-examples/snippets/MULTI/x_compt.g
deleted file mode 100644
index 627aadbf25d8023ce4fac5432bc0943552985438..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/x_compt.g
+++ /dev/null
@@ -1,222 +0,0 @@
-//genesis
-// kkit Version 11 flat dumpfile
-
-// Saved on Thu Sep 26 22:28:32 2013
-
-include kkit {argv 1}
-
-FASTDT = 0.0001
-SIMDT = 0.01
-CONTROLDT = 5
-PLOTDT = 1
-MAXTIME = 100
-TRANSIENT_TIME = 2
-VARIABLE_DT_FLAG = 0
-DEFAULT_VOL = 1e-20
-VERSION = 11.0
-setfield /file/modpath value /home2/bhalla/scripts/modules
-kparms
-
-//genesis
-
-initdump -version 3 -ignoreorphans 1
-simobjdump doqcsinfo filename accessname accesstype transcriber developer \
- citation species tissue cellcompartment methodology sources \
- model_implementation model_validation x y z
-simobjdump table input output alloced step_mode stepsize x y z
-simobjdump xtree path script namemode sizescale
-simobjdump xcoredraw xmin xmax ymin ymax
-simobjdump xtext editable
-simobjdump xgraph xmin xmax ymin ymax overlay
-simobjdump xplot pixflags script fg ysquish do_slope wy
-simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
- link savename file version md5sum mod_save_flag x y z
-simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
- z
-simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
- geomname xtree_fg_req xtree_textfg_req x y z
-simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
-simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
- keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
-simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
- trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
-simobjdump xtab input output alloced step_mode stepsize notes editfunc \
- xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
-simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
- xtree_textfg_req x y z
-simobjdump transport input output alloced step_mode stepsize dt delay clock \
- kf xtree_fg_req xtree_textfg_req x y z
-simobjdump proto x y z
-simobjdump text str
-simundump geometry /kinetics/geometry 0 1e-18 3 sphere "" white black 2 -6 0
-simundump geometry /kinetics/geometry[1] 0 1e-19 3 sphere "" white black 0 -8 \
- 0
-simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black -3 \
- -6 0
-simundump geometry /kinetics/geometry[3] 0 1e-19 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[4] 0 1e-20 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[5] 0 1e-19 3 sphere "" white black 0 0 \
- 0
-simundump geometry /kinetics/geometry[6] 0 1e-20 3 sphere "" white black 0 0 \
- 0
-simundump text /kinetics/notes 0 ""
-call /kinetics/notes LOAD \
-""
-simundump text /kinetics/geometry/notes 0 ""
-call /kinetics/geometry/notes LOAD \
-""
-simundump text /kinetics/geometry[1]/notes 0 ""
-call /kinetics/geometry[1]/notes LOAD \
-""
-simundump text /kinetics/geometry[2]/notes 0 ""
-call /kinetics/geometry[2]/notes LOAD \
-""
-simundump text /kinetics/geometry[3]/notes 0 ""
-call /kinetics/geometry[3]/notes LOAD \
-""
-simundump text /kinetics/geometry[4]/notes 0 ""
-call /kinetics/geometry[4]/notes LOAD \
-""
-simundump text /kinetics/geometry[5]/notes 0 ""
-call /kinetics/geometry[5]/notes LOAD \
-""
-simundump text /kinetics/geometry[6]/notes 0 ""
-call /kinetics/geometry[6]/notes LOAD \
-""
-simundump group /kinetics/DEND 0 yellow black x 0 0 "" DEND defaultfile.g 0 0 \
- 0 -3 -3 0
-simundump text /kinetics/DEND/notes 0 ""
-call /kinetics/DEND/notes LOAD \
-""
-simundump kpool /kinetics/DEND/Ca 0 1e-10 0.08 0.08 48 48 0 0 600 0 \
- /kinetics/geometry blue yellow -4 4 0
-simundump text /kinetics/DEND/Ca/notes 0 ""
-call /kinetics/DEND/Ca/notes LOAD \
-""
-simundump group /kinetics/SPINE 0 28 black x 0 1 "" SPINE defaultfile.g 0 0 0 \
- 0 -6 0
-simundump text /kinetics/SPINE/notes 0 ""
-call /kinetics/SPINE/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/Ca 0 1e-10 0.08 0.08 4.8 4.8 0 0 60 0 \
- /kinetics/geometry[1] blue 28 -2 4 0
-simundump text /kinetics/SPINE/Ca/notes 0 ""
-call /kinetics/SPINE/Ca/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaM 0 1e-11 5 5 300 300 0 0 60 0 \
- /kinetics/geometry[1] 55 28 -2 2 0
-simundump text /kinetics/SPINE/CaM/notes 0 ""
-call /kinetics/SPINE/CaM/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/Ca_CaM 0 1e-11 0 0 0 0 0 0 60 0 \
- /kinetics/geometry[1] blue 28 1 -1 0
-simundump text /kinetics/SPINE/Ca_CaM/notes 0 ""
-call /kinetics/SPINE/Ca_CaM/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/kreac 0 0.1 0.1 "" white 28 -1 0 0
-simundump text /kinetics/SPINE/kreac/notes 0 ""
-call /kinetics/SPINE/kreac/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/CaMKII 0 0 8.3333 8.3333 500 500 0 0 60 0 \
- /kinetics/geometry[3] 7 28 -1 -3 0
-simundump text /kinetics/SPINE/CaMKII/notes 0 ""
-call /kinetics/SPINE/CaMKII/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/CaM_bind_CaMKII 0 0.0016667 0.01 "" white 28 \
- 1 -4 0
-simundump text /kinetics/SPINE/CaM_bind_CaMKII/notes 0 ""
-call /kinetics/SPINE/CaM_bind_CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/foo 0 0 0.16667 0.16667 10 10 0 0 60 0 \
- /kinetics/geometry[5] blue 28 -2 -9 0
-simundump text /kinetics/SPINE/foo/notes 0 ""
-call /kinetics/SPINE/foo/notes LOAD \
-""
-simundump kpool /kinetics/SPINE/bar 0 0 0.33333 0 0 20 0 0 60 0 \
- /kinetics/geometry[5] blue 28 -2 -11 0
-simundump text /kinetics/SPINE/bar/notes 0 ""
-call /kinetics/SPINE/bar/notes LOAD \
-""
-simundump kreac /kinetics/SPINE/r2 0 0.1 0.1 "" white 28 0 -10 0
-simundump text /kinetics/SPINE/r2/notes 0 ""
-call /kinetics/SPINE/r2/notes LOAD \
-""
-simundump group /kinetics/PSD 0 0 black x 0 0 "" PSD defaultfile.g 0 0 0 3 -3 \
- 0
-simundump text /kinetics/PSD/notes 0 ""
-call /kinetics/PSD/notes LOAD \
-""
-simundump kpool /kinetics/PSD/Ca 0 1e-10 0.08 0.08 0.48 0.48 0 0 6 0 \
- /kinetics/geometry[2] blue 0 1 4 0
-simundump text /kinetics/PSD/Ca/notes 0 ""
-call /kinetics/PSD/Ca/notes LOAD \
-""
-simundump kpool /kinetics/PSD/CaM 0 1e-11 5 5 30 30 0 0 6 0 \
- /kinetics/geometry[2] 53 0 1 2 0
-simundump text /kinetics/PSD/CaM/notes 0 ""
-call /kinetics/PSD/CaM/notes LOAD \
-""
-simundump kpool /kinetics/PSD/Ca_CaM 0 1e-11 0 0 0 0 0 0 6 0 \
- /kinetics/geometry[2] blue 0 4 -1 0
-simundump text /kinetics/PSD/Ca_CaM/notes 0 ""
-call /kinetics/PSD/Ca_CaM/notes LOAD \
-""
-simundump kreac /kinetics/PSD/kreac 0 0.1 0.1 "" white 0 2 0 0
-simundump text /kinetics/PSD/kreac/notes 0 ""
-call /kinetics/PSD/kreac/notes LOAD \
-""
-simundump kpool /kinetics/PSD/Ca_CaM_CaMKII 0 0 0 0 0 0 0 0 6 0 \
- /kinetics/geometry[4] blue 0 4 -5 0
-simundump text /kinetics/PSD/Ca_CaM_CaMKII/notes 0 ""
-call /kinetics/PSD/Ca_CaM_CaMKII/notes LOAD \
-""
-simundump kpool /kinetics/PSD/zod 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[6] \
- blue 0 3 -11 0
-simundump text /kinetics/PSD/zod/notes 0 ""
-call /kinetics/PSD/zod/notes LOAD \
-""
-simundump xgraph /graphs/conc1 0 0 100 0 1 0
-simundump xgraph /graphs/conc2 0 0 100 0 1 0
-simundump xgraph /moregraphs/conc3 0 0 100 0 1 0
-simundump xgraph /moregraphs/conc4 0 0 100 0 1 0
-simundump xcoredraw /edit/draw 0 -6 6 -13 6
-simundump xtree /edit/draw/tree 0 \
- /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \
- "edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>" auto 0.6
-simundump xtext /file/notes 0 1
-xtextload /file/notes \
-"23 sep 2013. Variant of minimal.g. Added a cross-compartment" \
-"reaction taking CaMKII to PSD upon binding of CaM." \
-"23 Sep 2013. x_compt2.g Added a dummy reaction to show that" \
-"x-compt reacts work even with bigger reacs." \
-""
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/Ca REAC A B
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/CaM REAC A B
-addmsg /kinetics/SPINE/kreac /kinetics/SPINE/Ca_CaM REAC B A
-addmsg /kinetics/SPINE/CaM_bind_CaMKII /kinetics/SPINE/Ca_CaM REAC A B
-addmsg /kinetics/SPINE/Ca /kinetics/SPINE/kreac SUBSTRATE n
-addmsg /kinetics/SPINE/CaM /kinetics/SPINE/kreac SUBSTRATE n
-addmsg /kinetics/SPINE/Ca_CaM /kinetics/SPINE/kreac PRODUCT n
-addmsg /kinetics/SPINE/CaM_bind_CaMKII /kinetics/SPINE/CaMKII REAC A B
-addmsg /kinetics/SPINE/Ca_CaM /kinetics/SPINE/CaM_bind_CaMKII SUBSTRATE n
-addmsg /kinetics/SPINE/CaMKII /kinetics/SPINE/CaM_bind_CaMKII SUBSTRATE n
-addmsg /kinetics/PSD/Ca_CaM_CaMKII /kinetics/SPINE/CaM_bind_CaMKII PRODUCT n
-addmsg /kinetics/SPINE/r2 /kinetics/SPINE/foo REAC A B
-addmsg /kinetics/SPINE/r2 /kinetics/SPINE/bar REAC A B
-addmsg /kinetics/SPINE/foo /kinetics/SPINE/r2 SUBSTRATE n
-addmsg /kinetics/SPINE/bar /kinetics/SPINE/r2 SUBSTRATE n
-addmsg /kinetics/PSD/zod /kinetics/SPINE/r2 PRODUCT n
-addmsg /kinetics/PSD/kreac /kinetics/PSD/Ca REAC A B
-addmsg /kinetics/PSD/kreac /kinetics/PSD/CaM REAC A B
-addmsg /kinetics/PSD/kreac /kinetics/PSD/Ca_CaM REAC B A
-addmsg /kinetics/PSD/Ca /kinetics/PSD/kreac SUBSTRATE n
-addmsg /kinetics/PSD/CaM /kinetics/PSD/kreac SUBSTRATE n
-addmsg /kinetics/PSD/Ca_CaM /kinetics/PSD/kreac PRODUCT n
-addmsg /kinetics/SPINE/CaM_bind_CaMKII /kinetics/PSD/Ca_CaM_CaMKII REAC B A
-addmsg /kinetics/SPINE/r2 /kinetics/PSD/zod REAC B A
-enddump
-// End of dump
-
-complete_loading
diff --git a/moose-examples/snippets/MULTI/x_compt.py b/moose-examples/snippets/MULTI/x_compt.py
deleted file mode 100644
index 62c20560e896179a52787a05c2fbdba6b7ffccdc..0000000000000000000000000000000000000000
--- a/moose-examples/snippets/MULTI/x_compt.py
+++ /dev/null
@@ -1,376 +0,0 @@
-# __DEPRECATED__ __BROKEN__
-# x_compt.py ---
-# Upi Bhalla, NCBS Bangalore 2013.
-#
-# Commentary:
-#
-# Testing system for loading in arbitrary multiscale models based on
-# model definition files.
-# This version examines cross-compartment reactions. It is based on
-# minimal.py. It uses a minimal model with Ca in all 3 compartments,
-# and a binding reaction of Ca to CaM (just one step) in SPINE and PSD.
-# Incoming Ca from synaptic events comes to the PSD.
-# The CaMKII binds CaM in the spine, and the product goes reversibly
-# to the PSD. Just to be sure, another reaction involving foo, bar and zod
-# is also set up to go to and from the PSD.
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-
-# Code:
-
-import sys
-sys.path.append('../../python')
-import os
-os.environ['NUMPTHREADS'] = '1'
-import math
-
-import moose
-import proto18
-
-EREST_ACT = -70e-3
-
-def loadElec():
- library = moose.Neutral( '/library' )
- moose.setCwe( '/library' )
- proto18.make_Ca()
- proto18.make_Ca_conc()
- proto18.make_K_AHP()
- proto18.make_K_C()
- proto18.make_Na()
- proto18.make_K_DR()
- proto18.make_K_A()
- proto18.make_glu()
- proto18.make_NMDA()
- proto18.make_Ca_NMDA()
- proto18.make_NMDA_Ca_conc()
- proto18.make_axon()
- model = moose.Neutral( '/model' )
- cellId = moose.loadModel( 'ca1_asym.p', '/model/elec', "hsolve" )
- return cellId
-
-def addPlot( objpath, field, plot ):
- assert moose.exists( objpath )
- tab = moose.Table( '/graphs/' + plot )
- obj = moose.element( objpath )
- moose.connect( tab, 'requestOut', obj, field )
- return tab
-
-
-def dumpPlots( fname ):
- if ( os.path.exists( fname ) ):
- os.remove( fname )
- for x in moose.wildcardFind( '/graphs/#[ISA=Table]' ):
- moose.element( x[0] ).xplot( fname, x[0].name )
- for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
- moose.element( x[0] ).xplot( fname, x[0].name + '_e' )
-
-def moveCompt( path, oldParent, newParent ):
- meshEntries = moose.element( newParent.path + '/mesh' )
- # Set up vol messaging from new compts to all their child objects.
- for x in moose.wildcardFind( path + '/##[ISA=PoolBase]' ):
- moose.connect( meshEntries, 'mesh', x, 'mesh', 'OneToOne' )
- orig = moose.element( path )
- moose.move( orig, newParent )
- moose.delete( moose.vec( oldParent.path ) )
- chem = moose.element( '/model/chem' )
- moose.move( newParent, chem )
-
-def loadChem( neuroCompt, spineCompt, psdCompt ):
- # We need the compartments to come in with a volume of 1 to match the
- # original CubeMesh.
- assert( neuroCompt.volume == 1.0 )
- assert( spineCompt.volume == 1.0 )
- assert( psdCompt.volume == 1.0 )
- assert( neuroCompt.mesh.num == 1 )
- #print 'volume = ', neuroCompt.mesh[0].volume
- #assert( neuroCompt.mesh[0].volume == 1.0 )
- #an unfortunate mismatch
- # So we'll have to resize the volumes of the current compartments to the
- # new ones.
-
- modelId = moose.loadModel( 'x_compt.g', '/model', 'ee' )
- chem = moose.element( '/model/model' )
- chem.name = 'chem'
- oldN = moose.element( '/model/chem/compartment_1' )
- oldS = moose.element( '/model/chem/compartment_2' )
- oldP = moose.element( '/model/chem/kinetics' )
- oldN.volume = neuroCompt.mesh[0].volume
- oldS.volume = spineCompt.mesh[0].volume
- oldP.volume = psdCompt.mesh[0].volume
- moveCompt( '/model/chem/kinetics/DEND', oldN, neuroCompt )
- moveCompt( '/model/chem/kinetics/SPINE', oldS, spineCompt )
- moveCompt( '/model/chem/kinetics/PSD', oldP, psdCompt )
-
-def makeNeuroMeshModel():
- diffLength = 20e-6 # But we only want diffusion over part of the model.
- numSyn = 13
- elec = loadElec()
- synInput = moose.SpikeGen( '/model/elec/synInput' )
- synInput.threshold = -1.0
- synInput.edgeTriggered = 0
- synInput.Vm( 0 )
- synInput.refractT = 47e-3
-
- for i in range( numSyn ):
- name = '/model/elec/spine_head_14_' + str( i + 1 )
- r = moose.element( name + '/glu' )
- r.synapse.num = 1
- syn = moose.element( r.path + '/synapse' )
- moose.connect( synInput, 'spikeOut', syn, 'addSpike', 'Single' )
- syn.weight = 0.2 * i * ( numSyn - 1 - i )
- syn.delay = i * 1.0e-3
-
- neuroCompt = moose.NeuroMesh( '/model/neuroMesh' )
- #print 'neuroMeshvolume = ', neuroCompt.mesh[0].volume
- neuroCompt.separateSpines = 1
- neuroCompt.diffLength = diffLength
- neuroCompt.geometryPolicy = 'cylinder'
- spineCompt = moose.SpineMesh( '/model/spineMesh' )
- #print 'spineMeshvolume = ', spineCompt.mesh[0].volume
- moose.connect( neuroCompt, 'spineListOut', spineCompt, 'spineList', 'OneToOne' )
- psdCompt = moose.PsdMesh( '/model/psdMesh' )
- #print 'psdMeshvolume = ', psdCompt.mesh[0].volume
- moose.connect( neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne' )
- loadChem( neuroCompt, spineCompt, psdCompt )
- #for x in moose.wildcardFind( '/model/chem/##/Ca' ):
- # x.diffConst = 1e-11
-
- # Put in the solvers, see how they fare.
- nmksolve = moose.GslStoich( '/model/chem/neuroMesh/ksolve' )
- nmksolve.path = '/model/chem/neuroMesh/##'
- nmksolve.compartment = moose.element( '/model/chem/neuroMesh' )
- nmksolve.method = 'rk5'
- nm = moose.element( '/model/chem/neuroMesh/mesh' )
- moose.connect( nm, 'remesh', nmksolve, 'remesh' )
- #print "neuron: nv=", nmksolve.numLocalVoxels, ", nav=", nmksolve.numAllVoxels, nmksolve.numVarPools, nmksolve.numAllPools
-
- #print 'setting up smksolve'
- smksolve = moose.GslStoich( '/model/chem/spineMesh/ksolve' )
- smksolve.path = '/model/chem/spineMesh/##'
- smksolve.compartment = moose.element( '/model/chem/spineMesh' )
- smksolve.method = 'rk5'
- sm = moose.element( '/model/chem/spineMesh/mesh' )
- moose.connect( sm, 'remesh', smksolve, 'remesh' )
- #print "spine: nv=", smksolve.numLocalVoxels, ", nav=", smksolve.numAllVoxels, smksolve.numVarPools, smksolve.numAllPools
- #
- #print 'setting up pmksolve'
- pmksolve = moose.GslStoich( '/model/chem/psdMesh/ksolve' )
- pmksolve.path = '/model/chem/psdMesh/##'
- pmksolve.compartment = moose.element( '/model/chem/psdMesh' )
- pmksolve.method = 'rk5'
- pm = moose.element( '/model/chem/psdMesh/mesh' )
- moose.connect( pm, 'remesh', pmksolve, 'remesh' )
- #print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools
- #
- #print 'neuroMeshvolume = ', neuroCompt.mesh[0].volume
-
- #print 'Assigning the cell model'
- # Now to set up the model.
- #neuroCompt.cell = elec
- neuroCompt.cellPortion( elec, '/model/elec/lat_14_#,/model/elec/spine_neck#,/model/elec/spine_head#' )
- ns = neuroCompt.numSegments
- #assert( ns == 11 ) # dend, 5x (shaft+head)
- ndc = neuroCompt.numDiffCompts
- assert( ndc == 13 )
- ndc = neuroCompt.mesh.num
- assert( ndc == 13 )
-
- sdc = spineCompt.mesh.num
- assert( sdc == 13 )
- pdc = psdCompt.mesh.num
- assert( pdc == 13 )
- #print 'mesh nums ( neuro, spine, psd ) = ', ndc, sdc, pdc, ', numSeg = ', ns
-
- mesh = moose.vec( '/model/chem/neuroMesh/mesh' )
- #for i in range( ndc ):
- # print 's[', i, '] = ', mesh[i].volume
- mesh2 = moose.vec( '/model/chem/spineMesh/mesh' )
-# for i in range( sdc ):
-# print 's[', i, '] = ', mesh2[i].volume
- #print 'numPSD = ', moose.element( '/model/chem/psdMesh/mesh' ).localNumField
- mesh = moose.vec( '/model/chem/psdMesh/mesh' )
- #print 'psd mesh.volume = ', mesh.volume
- #for i in range( pdc ):
- # print 's[', i, '] = ', mesh[i].volume
- #
- # We need to use the spine solver as the master for the purposes of
- # these calculations. This will handle the diffusion calculations
- # between head and dendrite, and between head and PSD.
- smksolve.addJunction( nmksolve )
- #print "spine: nv=", smksolve.numLocalVoxels, ", nav=", smksolve.numAllVoxels, smksolve.numVarPools, smksolve.numAllPools
- smksolve.addJunction( pmksolve )
- #print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools
-
- # oddly, numLocalFields does not work.
- #moose.le( '/model/chem/neuroMesh' )
- ca = moose.element( '/model/chem/neuroMesh/DEND/Ca' )
- assert( ca.lastDimension == ndc )
- """
- CaNpsd = moose.vec( '/model/chem/psdMesh/PSD/PP1_PSD/CaN' )
- print 'numCaN in PSD = ', CaNpsd.nInit, ', vol = ', CaNpsd.volume
- CaNspine = moose.vec( '/model/chem/spineMesh/SPINE/CaN_BULK/CaN' )
- print 'numCaN in spine = ', CaNspine.nInit, ', vol = ', CaNspine.volume
- """
-
- # set up adaptors
- aCa = moose.Adaptor( '/model/chem/psdMesh/adaptCa', pdc )
- adaptCa = moose.vec( '/model/chem/psdMesh/adaptCa' )
- chemCa = moose.vec( '/model/chem/psdMesh/PSD/Ca' )
- assert( len( adaptCa ) == pdc )
- assert( len( chemCa ) == pdc )
- for i in range( pdc ):
- path = '/model/elec/spine_head_14_' + str( i + 1 ) + '/NMDA_Ca_conc'
- elecCa = moose.element( path )
- moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
- moose.connect( adaptCa, 'outputSrc', chemCa, 'setConc', 'OneToOne' )
- adaptCa.inputOffset = 0.0 #
- adaptCa.outputOffset = 0.000 # 100 nM offset in chem.
- adaptCa.scale = 1e-5 # 520 to 0.0052 mM
- #print adaptCa.outputOffset
- #print adaptCa.scale
-
-def makeElecPlots():
- graphs = moose.Neutral( '/graphs' )
- elec = moose.Neutral( '/graphs/elec' )
- addPlot( '/model/elec/soma', 'getVm', 'elec/somaVm' )
- addPlot( '/model/elec/soma/Ca_conc', 'getCa', 'elec/somaCa' )
- addPlot( '/model/elec/basal_3', 'getVm', 'elec/basal3Vm' )
- addPlot( '/model/elec/apical_14', 'getVm', 'elec/apical_14Vm' )
- addPlot( '/model/elec/apical_14/Ca_conc', 'getCa', 'elec/apical_14Ca' )
- addPlot( '/model/elec/spine_head_14_7', 'getVm', 'elec/spine_7Vm' )
- addPlot( '/model/elec/spine_head_14_7/NMDA_Ca_conc', 'getCa', 'elec/spine_7Ca' )
- addPlot( '/model/elec/spine_head_14_13/NMDA_Ca_conc', 'getCa', 'elec/spine_13Ca' )
-
-def makeChemPlots():
- graphs = moose.Neutral( '/graphs' )
- addPlot( '/model/chem/psdMesh/PSD/Ca[0]', 'getConc', 'pCa0' )
- addPlot( '/model/chem/psdMesh/PSD/Ca[6]', 'getConc', 'pCa6' )
- addPlot( '/model/chem/psdMesh/PSD/Ca[12]', 'getConc', 'pCa12' )
-
- addPlot( '/model/chem/spineMesh/SPINE/Ca[0]', 'getConc', 'sCa0' )
- addPlot( '/model/chem/spineMesh/SPINE/Ca[6]', 'getConc', 'sCa6' )
- addPlot( '/model/chem/spineMesh/SPINE/Ca[12]', 'getConc', 'sCa12' )
-
- addPlot( '/model/chem/neuroMesh/DEND/Ca[0]', 'getConc', 'dend0Ca' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca[60]', 'getConc', 'dend60Ca' )
- addPlot( '/model/chem/neuroMesh/DEND/Ca[144]', 'getConc', 'dend144Ca' )
-
- addPlot( '/model/chem/psdMesh/PSD/CaM[0]', 'getConc', 'pCaM0' )
- addPlot( '/model/chem/psdMesh/PSD/CaM[6]', 'getConc', 'pCaM6' )
- addPlot( '/model/chem/psdMesh/PSD/CaM[12]', 'getConc', 'pCaM12' )
-
- addPlot( '/model/chem/spineMesh/SPINE/CaM[0]', 'getConc', 'sCaM0' )
- addPlot( '/model/chem/spineMesh/SPINE/CaM[6]', 'getConc', 'sCaM6' )
- addPlot( '/model/chem/spineMesh/SPINE/CaM[12]', 'getConc', 'sCaM12' )
-
- addPlot( '/model/chem/spineMesh/SPINE/CaMKII[6]', 'getConc', 'sCaMKII6' )
-
- addPlot( '/model/chem/psdMesh/PSD/Ca_CaM[0]', 'getConc', 'pCaCaM0' )
- addPlot( '/model/chem/psdMesh/PSD/Ca_CaM[6]', 'getConc', 'pCaCaM6' )
- addPlot( '/model/chem/psdMesh/PSD/Ca_CaM[12]', 'getConc', 'pCaCaM12' )
-
- addPlot( '/model/chem/spineMesh/SPINE/Ca_CaM[0]', 'getConc', 'sCaCaM0' )
- addPlot( '/model/chem/spineMesh/SPINE/Ca_CaM[6]', 'getConc', 'sCaCaM6' )
- addPlot( '/model/chem/spineMesh/SPINE/Ca_CaM[12]', 'getConc', 'sCaCaM12' )
- addPlot( '/model/chem/psdMesh/PSD/Ca_CaM_CaMKII[6]', 'getConc', 'pCaCaMCaMKII6' )
-
- addPlot( '/model/chem/psdMesh/PSD/zod[6]', 'getConc', 'zod6' )
-
- addPlot( '/model/chem/spineMesh/SPINE/foo[6]', 'getConc', 'foo6' )
- addPlot( '/model/chem/spineMesh/SPINE/bar[6]', 'getConc', 'bar6' )
-
-def testNeuroMeshMultiscale():
- elecDt = 50e-6
- chemDt = 1e-4
- plotDt = 5e-4
- plotName = 'x_compt.plot'
-
- makeNeuroMeshModel()
- """
- for i in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
- if ( i[0].diffConst > 0 ):
- grandpaname = i.parent[0].parent.name + '/'
- paname = i.parent[0].name + '/'
- print grandpaname + paname + i[0].name, i[0].diffConst
- """
- """
- moose.le( '/model/chem/spineMesh/ksolve' )
- print 'Neighbors:'
- for t in moose.element( '/model/chem/spineMesh/ksolve/junction' ).neighbors['masterJunction']:
- print 'masterJunction <-', t.path
- for t in moose.wildcardFind( '/model/chem/#Mesh/ksolve' ):
- k = moose.element( t[0] )
- print k.path + ' localVoxels=', k.numLocalVoxels, ', allVoxels= ', k.numAllVoxels
- """
-
- makeChemPlots()
- makeElecPlots()
- moose.setClock( 0, elecDt )
- moose.setClock( 1, elecDt )
- moose.setClock( 2, elecDt )
- moose.setClock( 5, chemDt )
- moose.setClock( 6, chemDt )
- moose.setClock( 7, plotDt )
- moose.setClock( 8, plotDt )
- moose.useClock( 0, '/model/elec/##[ISA=Compartment]', 'init' )
- moose.useClock( 1, '/model/elec/##[ISA=SpikeGen]', 'process' )
- moose.useClock( 2, '/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]','process')
- moose.useClock( 5, '/model/chem/##[ISA=PoolBase],/model/##[ISA=ReacBase],/model/##[ISA=EnzBase]', 'process' )
- moose.useClock( 6, '/model/chem/##[ISA=Adaptor]', 'process' )
- moose.useClock( 7, '/graphs/#', 'process' )
- moose.useClock( 8, '/graphs/elec/#', 'process' )
- moose.useClock( 5, '/model/chem/#Mesh/ksolve', 'init' )
- moose.useClock( 6, '/model/chem/#Mesh/ksolve', 'process' )
- hsolve = moose.HSolve( '/model/elec/hsolve' )
- moose.useClock( 1, '/model/elec/hsolve', 'process' )
- hsolve.dt = elecDt
- hsolve.target = '/model/elec/compt'
- moose.reinit()
- moose.reinit()
- """
- print 'pre'
- eca = moose.vec( '/model/chem/psdMesh/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'dend'
- eca = moose.vec( '/model/chem/neuroMesh/DEND/Ca' )
- for i in ( 0, 1, 2, 30, 60, 90, 120, 144 ):
- print i, eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
-
- print 'PSD'
- eca = moose.vec( '/model/chem/psdMesh/PSD/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- print 'spine'
- eca = moose.vec( '/model/chem/spineMesh/SPINE/CaM/Ca' )
- for i in range( 3 ):
- print eca[i].concInit, eca[i].conc, eca[i].nInit, eca[i].n, eca[i].volume
- """
-
- moose.start( 0.5 )
- dumpPlots( plotName )
- print('All done')
-
-
-def main():
- testNeuroMeshMultiscale()
-
-if __name__ == '__main__':
- main()
-
-#
-# loadMulti.py ends here.
diff --git a/moose-examples/snippets/RandSpikeStats.py b/moose-examples/snippets/RandSpikeStats.py
index 438de46670e7091671a5140f55b93ce09ac4d98a..377dc18b9659f1ad0c90b8a851aace2949605d60 100644
--- a/moose-examples/snippets/RandSpikeStats.py
+++ b/moose-examples/snippets/RandSpikeStats.py
@@ -67,6 +67,7 @@ def make_model():
moose.connect( plotf, 'requestOut', fire, 'getVm' )
def main():
+<<<<<<< HEAD
"""
This snippet shows the use of several objects.
This snippet sets up a StimulusTable to control a RandSpike which
@@ -103,6 +104,44 @@ def main():
moose.useClock( 8, '/plot#', 'process' )
'''
+=======
+ """
+ This snippet shows the use of several objects.
+ This snippet sets up a StimulusTable to control a RandSpike which
+ sends its outputs to two places: to a SimpleSynHandler on an IntFire,
+ which is used to monitor spike arrival, and to various Stats objects.
+ Each of these are recorded and plotted.
+ The StimulusTable has a sine-wave waveform.
+ """
+ make_model()
+
+ moose.reinit()
+ moose.start( runtime )
+ plots = moose.element( '/plots' )
+ plot1 = moose.element( '/plot1' )
+ plot2 = moose.element( '/plot2' )
+ plotf = moose.element( '/plotf' )
+ t = [i * dt for i in range( plot1.vector.size )]
+ pylab.plot( t, plots.vector, label='stimulus' )
+ pylab.plot( t, plot1.vector, label='spike rate mean' )
+ pylab.plot( t, plot2.vector, label='Vm mean' )
+ pylab.plot( t, plotf.vector, label='Vm' )
+ pylab.legend()
+ pylab.show()
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
+
+ '''
+ moose.useClock( 0, '/stim', 'process' )
+ moose.useClock( 1, '/spike', 'process' )
+ moose.useClock( 2, '/syn', 'process' )
+ moose.useClock( 3, '/fire', 'process' )
+ moose.useClock( 4, '/stats#', 'process' )
+ moose.useClock( 8, '/plot#', 'process' )
+ for i in range (10):
+ moose.setClock( i, dt )
+ moose.useClock( 8, '/plot#', 'process' )
+ '''
+
# Run the 'main' if this script is executed standalone.
if __name__ == '__main__':
diff --git a/moose-examples/snippets/analogStimTable.py b/moose-examples/snippets/analogStimTable.py
index f1cf3c6c21846263b634a0317f373133f90ad808..f7ce328caa05764ced9b49b6cccaf98204393e79 100644
--- a/moose-examples/snippets/analogStimTable.py
+++ b/moose-examples/snippets/analogStimTable.py
@@ -89,7 +89,11 @@ for plotting.
analogStimTable()
if __name__ == '__main__':
+<<<<<<< HEAD
main
+=======
+ main()
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
#
# stimtable.py ends here
diff --git a/moose-examples/snippets/cspaceSteadyState.py b/moose-examples/snippets/cspaceSteadyState.py
index d11b7b5dd947fab5fbf5c7139559a08e3810c82c..12ebb3b87ec413a3f6f29fd4b74f826a49041989 100644
--- a/moose-examples/snippets/cspaceSteadyState.py
+++ b/moose-examples/snippets/cspaceSteadyState.py
@@ -40,6 +40,7 @@ def main():
It looks for the fixed points 100 times, as follows:
- Set up the random initial condition that fits the conservation laws
- Run for 2 seconds. This should not be mathematically necessary, but
+<<<<<<< HEAD
for obscure numerical reasons it makes it much more likely that the
steady state solver will succeed in finding a state.
- Find the fixed point
@@ -47,6 +48,15 @@ def main():
- Run for 10 seconds. This is completely unnecessary, and is done here
just so that the resultant graph will show what kind of state has been
found.
+=======
+ for obscure numerical reasons it makes it much more likely that the
+ steady state solver will succeed in finding a state.
+ - Find the fixed point
+ - Print out the fixed point vector and various diagnostics.
+ - Run for 10 seconds. This is completely unnecessary, and is done here
+ just so that the resultant graph will show what kind of state has been
+ found.
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
After it does all this, the program runs for 100 more seconds on the last
found fixed point (which turns out to be a saddle node), then
is hard-switched in the script to the first attractor basin from which
@@ -55,6 +65,7 @@ def main():
seconds.
Looking at the output you will see many features of note:
- the first attractor (stable point) and the saddle point
+<<<<<<< HEAD
(unstable fixed point) are both found quite often. But the second
attractor is found just once. Has a very small basin of attraction.
- The values found for each of the fixed points match well with the
@@ -62,6 +73,15 @@ def main():
- There are a large number of failures to find a fixed point. These are
found and reported in the diagnostics. They show up on the plot
as cases where the 10-second runs are not flat.
+=======
+ (unstable fixed point) are both found quite often. But the second
+ attractor is found just once. Has a very small basin of attraction.
+ - The values found for each of the fixed points match well with the
+ values found by running the system to steady-state at the end.
+ - There are a large number of failures to find a fixed point. These are
+ found and reported in the diagnostics. They show up on the plot
+ as cases where the 10-second runs are not flat.
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
If you wanted to find fixed points in a production model, you would
not need to do the 10-second runs, and you would need to eliminate the
diff --git a/moose-examples/snippets/funcInputToPools.py b/moose-examples/snippets/funcInputToPools.py
index f773a3652e77ac6995811770fd7f8a9bfa140c53..3a8d06fa28d574001d48d4282f01c713e4c9d4fe 100644
--- a/moose-examples/snippets/funcInputToPools.py
+++ b/moose-examples/snippets/funcInputToPools.py
@@ -12,6 +12,7 @@ import pylab
import numpy
import moose
import sys
+<<<<<<< HEAD
def makeModel():
if len( sys.argv ) == 1:
@@ -99,22 +100,123 @@ To run in deterministic mode::
"""
+=======
+
+def makeModel():
+ if len( sys.argv ) == 1:
+ useGsolve = True
+ else:
+ useGsolve = ( sys.argv[1] == 'True' )
+ # create container for model
+ model = moose.Neutral( 'model' )
+ compartment = moose.CubeMesh( '/model/compartment' )
+ compartment.volume = 1e-22
+ # the mesh is created automatically by the compartment
+ moose.le( '/model/compartment' )
+ mesh = moose.element( '/model/compartment/mesh' )
+
+ # create molecules and reactions
+ a = moose.Pool( '/model/compartment/a' )
+ b = moose.Pool( '/model/compartment/b' )
+
+ # create functions of time
+ f1 = moose.Function( '/model/compartment/f1' )
+ f2 = moose.Function( '/model/compartment/f2' )
+
+ # connect them up for reactions
+ moose.connect( f1, 'valueOut', a, 'setConc' )
+ moose.connect( f2, 'valueOut', b, 'increment' )
+
+ # Assign parameters
+ a.concInit = 0
+ b.concInit = 1
+ #f1.numVars = 1
+ #f2.numVars = 1
+ f1.expr = '1 + sin(t)'
+ f2.expr = '10 * cos(t)'
+
+ # Create the output tables
+ graphs = moose.Neutral( '/model/graphs' )
+ outputA = moose.Table2 ( '/model/graphs/nA' )
+ outputB = moose.Table2 ( '/model/graphs/nB' )
+
+ # connect up the tables
+ moose.connect( outputA, 'requestOut', a, 'getN' );
+ moose.connect( outputB, 'requestOut', b, 'getN' );
+
+ # Set up the solvers
+ if useGsolve:
+ gsolve = moose.Gsolve( '/model/compartment/gsolve' )
+ gsolve.useClockedUpdate = True
+ else:
+ gsolve = moose.Ksolve( '/model/compartment/gsolve' )
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = gsolve
+ stoich.path = '/model/compartment/##'
+ '''
+ '''
+
+ # We need a finer timestep than the default 0.1 seconds,
+ # in order to get numerical accuracy.
+ for i in range (10, 19 ):
+ moose.setClock( i, 0.1 ) # for computational objects
+
+def main():
+ """
+ This example describes the special (and discouraged) use case where
+ functions provide input to a reaction system. Here we have two functions of
+ time which control the pool # and pool rate of change, respectively::
+
+ number of molecules of a = 1 + sin(t)
+ rate of change of number of molecules of b = 10 * cos(t)
+
+ In the stochastic case one must set a special flag *useClockedUpdate*
+ in order to achieve clock-triggered updates from the functions. This is
+ needed because the functions do not have reaction events to trigger them,
+ and even if there were reaction events they might not be frequent enough to
+ track the periodic updates. The use of this flag slows down the calculations,
+ so try to use a table to control a pool instead.
+
+ To run in stochastic mode::
+
+ ''python funcInputToPools''
+
+ To run in deterministic mode::
+
+ ''python funcInputToPools false''
+
+ """
+
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
makeModel()
moose.seed()
moose.reinit()
+<<<<<<< HEAD
moose.start( 50.0 ) # Run the model for 50 seconds.
+=======
+ moose.start( 50.0 ) # Run the model for 100 seconds.
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
a = moose.element( '/model/compartment/a' )
b = moose.element( '/model/compartment/b' )
# Iterate through all plots, dump their contents to data.plot.
for x in moose.wildcardFind( '/model/graphs/n#' ):
+<<<<<<< HEAD
#x.xplot( 'scriptKineticModel.plot', x.name )
t = numpy.arange( 0, x.vector.size, 1 ) * x.dt # sec
pylab.plot( t, x.vector, label=x.name )
pylab.legend()
pylab.show()
+=======
+ #x.xplot( 'scriptKineticModel.plot', x.name )
+ t = numpy.arange( 0, x.vector.size, 1 ) * x.dt # sec
+ pylab.plot( t, x.vector, label=x.name )
+ pylab.legend()
+ pylab.show()
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
quit()
diff --git a/moose-examples/snippets/intfire.py b/moose-examples/snippets/intfire.py
index 5b3b30b21a80cb436176de2b25b513dcbcc3a57d..35f8fcb9ea245df9b65b40afe7e5ee96ccb5115c 100644
--- a/moose-examples/snippets/intfire.py
+++ b/moose-examples/snippets/intfire.py
@@ -1,4 +1,7 @@
+<<<<<<< HEAD
+=======
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
# intfire.py ---
#
# Filename: intfire.py
@@ -52,6 +55,10 @@ def connect_two_intfires():
"""
Connect two IntFire neurons so that spike events in one gets
transmitted to synapse of the other.
+<<<<<<< HEAD
+=======
+
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
"""
if1 = moose.IntFire('if1')
if2 = moose.IntFire('if2')
@@ -68,8 +75,13 @@ Connect a SpikeGen object to an IntFire neuron such that spike
events in spikegen get transmitted to the synapse of the IntFire
neuron.
+<<<<<<< HEAD
"""
if3 = moose.IntFire('if3')
+=======
+if3 = moose.IntFire('if3')
+ """
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
sf3 = moose.SimpleSynHandler( 'if3/sh' )
moose.connect( sf3, 'activationOut', if3, 'activation' )
sf3.synapse.num = 1
@@ -80,6 +92,10 @@ neuron.
def setup_synapse():
"""
Create an intfire object and create two synapses on it.
+<<<<<<< HEAD
+=======
+
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
"""
if4 = moose.IntFire('if4')
sf4 = moose.SimpleSynHandler( 'if4/sh' )
@@ -97,6 +113,10 @@ def main():
"""
Demonstrates connection between 2 IntFire neurons to observe
spike generation.
+<<<<<<< HEAD
+=======
+
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
"""
connect_two_intfires()
connect_spikegen()
diff --git a/moose-examples/snippets/loadKineticModel.py b/moose-examples/snippets/loadKineticModel.py
index 0eeb1cc095233e5842f9a4aa5271d35f9ab70972..25c3f69e5144bc7419ca827e16314e41d1b4c0cb 100644
--- a/moose-examples/snippets/loadKineticModel.py
+++ b/moose-examples/snippets/loadKineticModel.py
@@ -54,9 +54,13 @@ def main():
This example illustrates loading, running, and saving a kinetic
model defined in kkit format. It uses a default kkit model but
you can specify another using the command line
+<<<<<<< HEAD
``python filename runtime solver``.
+=======
+ ``python filename runtime solver``.
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
We use the gsl solver here.
The model already defines a couple of plots and sets the runtime 20 secs.
diff --git a/moose-examples/snippets/multiComptSigNeur.py b/moose-examples/snippets/multiComptSigNeur.py
index 04b31283ab29b35f60c86fa7ee30b0597c6f50e6..bb964baf2e27fc021677298e6147ad1df665f66e 100644
--- a/moose-examples/snippets/multiComptSigNeur.py
+++ b/moose-examples/snippets/multiComptSigNeur.py
@@ -26,7 +26,8 @@ import os
import math
import moose
-
+import numpy
+import matplotlib.pyplot as plt
EREST_ACT = -70e-3
# Gate equations have the form:
@@ -215,12 +216,16 @@ def makeElecPlots():
#addPlot( '/n/head0/gluR', 'getGk', 'elec/head0Gk' )
#addPlot( '/n/head2/gluR', 'getGk', 'elec/head2Gk' )
-def dumpPlots( fname ):
+def dumpPlots( fname,runtime ):
if ( os.path.exists( fname ) ):
os.remove( fname )
for x in moose.wildcardFind( '/graphs/##[ISA=Table]' ):
x.xplot( fname, x.name )
-
+ t = numpy.linspace( 0, runtime, x.vector.size ) # sec
+ plt.plot( t, x.vector, label=x.name )
+ plt.legend()
+ plt.show()
+ quit()
def makeSpinyCompt():
comptLength = 30e-6
comptDia = 6e-6
@@ -494,7 +499,8 @@ def testCubeMultiscale( useSolver ):
makeSolvers( elecDt )
moose.reinit()
moose.start( 1.0 )
- dumpPlots( plotName )
+ runtime = 1.0
+ dumpPlots( plotName,runtime )
def main():
"""
diff --git a/moose-examples/snippets/reacDiffBranchingNeuron.py b/moose-examples/snippets/reacDiffBranchingNeuron.py
index b8213d879745c5e978429ed1087c207722a380fe..ac4de98234afd462ae5ad11d15ad4cc14ef605c4 100644
--- a/moose-examples/snippets/reacDiffBranchingNeuron.py
+++ b/moose-examples/snippets/reacDiffBranchingNeuron.py
@@ -112,19 +112,29 @@ def finalizeDisplay( plotlist, cPlotDt ):
line1, = plotlist[0].plot( pos, x.vector, label=x.name )
plt.legend()
plotlist[1].canvas.draw()
- print( "Hit 'enter' to exit" )
- eval(input())
+ print( "Hit '0' to exit" )
+ eval(str(input()))
+
def makeChemModel( compt ):
"""
This function sets up a simple oscillatory chemical system within
the script. The reaction system is::
+<<<<<<< HEAD
+
+ s ---a---> a // s goes to a, catalyzed by a.
+ s ---a---> b // s goes to b, catalyzed by a.
+ a ---b---> s // a goes to s, catalyzed by b.
+ b -------> s // b is degraded irreversibly to s.
+
+=======
s ---a---> a // s goes to a, catalyzed by a.
s ---a---> b // s goes to b, catalyzed by a.
a ---b---> s // a goes to s, catalyzed by b.
b -------> s // b is degraded irreversibly to s.
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
in sum, **a** has a positive feedback onto itself and also forms **b**.
**b** has a negative feedback onto **a**.
Finally, the diffusion constant for **a** is 1/10 that of **b**.
diff --git a/moose-examples/snippets/scaleVolumes.py b/moose-examples/snippets/scaleVolumes.py
index 9ff1894c5b0ae91db46b8c464f9275fd8d310fc3..965a8562f28d6b0c2b01825a2977df5064a854b5 100644
--- a/moose-examples/snippets/scaleVolumes.py
+++ b/moose-examples/snippets/scaleVolumes.py
@@ -12,6 +12,12 @@ import pylab
import numpy
import moose
+# Ugly python hack to make input behave the same on python2 and python3.
+try:
+ input = raw_input
+except NameError as e:
+ pass
+
def makeModel():
# create container for model
model = moose.Neutral( 'model' )
@@ -149,11 +155,16 @@ def main():
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
pylab.show( block=False )
+<<<<<<< HEAD
print(('vol = ', vol, 'hit 0 to go to next plot'))
eval(str(input()))
+=======
+ print( 'vol = %f ' % vol )
+ response = input( "Press enter to go to next plot... " )
+>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
quit()
# Run the 'main' if this script is executed standalone.
if __name__ == '__main__':
- main()
+ main( )
diff --git a/moose-examples/tutorials/ChemicalBistables/scaleVolumes.py b/moose-examples/tutorials/ChemicalBistables/scaleVolumes.py
index ca9e8ce6b6ebe492c0a026f26797d19bd5757fb4..66b869ff67ba7e6f12b76e54c582bc91401b39d3 100644
--- a/moose-examples/tutorials/ChemicalBistables/scaleVolumes.py
+++ b/moose-examples/tutorials/ChemicalBistables/scaleVolumes.py
@@ -12,6 +12,12 @@ import pylab
import numpy
import moose
+# Hack to make sure input works with both python2 and python3.
+try:
+ input = raw_input
+except Exception as e:
+ pass
+
def makeModel():
# create container for model
model = moose.Neutral( 'model' )
@@ -148,7 +154,7 @@ def main():
displayPlots()
pylab.show( block=False )
print(('vol = ', vol, 'hit enter to go to next plot'))
- eval(input())
+ input()
quit()