diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..432ae3c14c9c75282c3870c576369b716a8fe667
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+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/docs/source/user/py/cookbook/chem_sim_eg.rst b/docs/source/user/py/cookbook/chem_sim_eg.rst
index 96b19eafd6c7ec1f14c44ffc69e2035f739fea56..5eac01de87afc208e0aa2d65d4d60b9357c13fbb 100644
--- a/docs/source/user/py/cookbook/chem_sim_eg.rst
+++ b/docs/source/user/py/cookbook/chem_sim_eg.rst
@@ -215,9 +215,6 @@ A Turing Model
 .. automodule:: TuringOneDim
    :members:
 
-A Spatial Bistable Model
-------------------------
-
 Reaction Diffusion in Neurons
 -----------------------------
 
diff --git a/moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py b/moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py
index 556639dbfb2c0477f3bbe56316ad4d3fca1bce19..6034281770d63f62a1e38701c1825aa70b9e80ef 100644
--- a/moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py
+++ b/moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py
@@ -1,3 +1,10 @@
+"""
+Simulate a pseudo-STDP protocol and plot the STDP kernel
+that emerges from Ca plasticity of Graupner and Brunel 2012.
+Author: Aditya Gilra, NCBS, Bangalore, October, 2014.
+
+"""
+
 import moose
 from pylab import *
 
@@ -19,7 +26,7 @@ refrT = 2e-3 # s
 
 ## two neurons: index 0 will be presynaptic, 1 will be postsynaptic
 network = moose.LIF( 'network', 2 );
-moose.le( '/network' )
+moose.le( network )
 network.vec.Em = Vrest
 network.vec.thresh = Vt_base
 network.vec.refractoryPeriod = refrT
@@ -184,12 +191,6 @@ make a neuron spike
     network.vec[nrnidx].inject = 0.
 
 def main():
-    """
-Simulate a pseudo-STDP protocol and plot the STDP kernel
-that emerges from Ca plasticity of Graupner and Brunel 2012.
-Author: Aditya Gilra, NCBS, Bangalore, October, 2014.
-
-    """
     dwlist_neg = []
     ddt = 2e-3 # s
     # since CaPlasticitySynHandler is event based
diff --git a/moose-examples/snippets/interpol2d.py b/moose-examples/snippets/interpol2d.py
index b4642cae49a38e8e0e9c860b2953af3f3f63aae2..af2344517a03f2a4f9c81308cf59eac1df2ba234 100644
--- a/moose-examples/snippets/interpol2d.py
+++ b/moose-examples/snippets/interpol2d.py
@@ -44,15 +44,13 @@
 #
 
 # Code:
-"""Example of Interpol object in 2 dimensions."""
-
 import numpy as np
 import sys
 sys.path.append('../../python')
 import moose
 
-
 def interpolation_demo():
+    """Example of Interpol object in 2 dimensions."""
     interpol = moose.Interpol2D('/interpol2D')
     interpol.xmin = 0.0
     interpol.xmax = 1.0
diff --git a/moose-examples/snippets/rxdSpineSize.py b/moose-examples/snippets/rxdSpineSize.py
index 6e150e2bb3d9d09bee17e54c383fdff994f89580..b404a34ec5dbd728966a3d09e39140f93deea49c 100644
--- a/moose-examples/snippets/rxdSpineSize.py
+++ b/moose-examples/snippets/rxdSpineSize.py
@@ -28,8 +28,6 @@ spineSpacing = 10e-6
 spineSpacingDistrib = 1e-6
 spineSize = 1.0
 spineSizeDistrib = 0.5
-spineAngle= PI / 2.0
-spineAngleDistrib = 0.0
 
 def makeCellProto( name ):
     elec = moose.Neuron( '/library/' + name )
@@ -79,6 +77,9 @@ def makeSpineProto2( name ):
     moose.connect( shaft, 'axial', head, 'raxial' )
 
 def makeModel():
+    spineAngle= PI / 2.0
+    spineAngleDistrib = 0.0
+
     moose.Neutral( '/library' )
     makeCellProto( 'cellProto' )
     makeChemProto( 'cProto' )
diff --git a/moose-examples/snippets/testRdesigneur.py b/moose-examples/snippets/testRdesigneur.py
index 1de81ad641c079b18d2cc25aad0ecc16943330ca..4087a3fbaa16a14bbe68cabc803e36f36270009b 100644
--- a/moose-examples/snippets/testRdesigneur.py
+++ b/moose-examples/snippets/testRdesigneur.py
@@ -22,8 +22,6 @@ spineSpacing = 2.0e-6
 spineSpacingDistrib = 0.0
 spineSize = 1.0
 spineSizeDistrib = 0.2
-spineAngle= 0.0
-spineAngleDistrib = 2*PI
 
 # Here we define a function that is used to make a cell prototype. Normally
 # it would load in a model from a file.
@@ -60,6 +58,9 @@ def makeChemProto( name ):
 
 
 def makeModel():
+    spineAngle= 0.0
+    spineAngleDistrib = 2*PI
+    
     moose.Neutral( '/library' )
     # Here we illustrate building the chem proto directly. This is not
     # good practice as it takes the model definition away from the
diff --git a/moose-examples/snippets/testWigglySpines.py b/moose-examples/snippets/testWigglySpines.py
index a85bf1efef7b47793518c033cc22083a20fa4336..7992e4050cd2b99c37e2521f3271ee0e20b5c2bc 100644
--- a/moose-examples/snippets/testWigglySpines.py
+++ b/moose-examples/snippets/testWigglySpines.py
@@ -26,9 +26,6 @@ spineSpacing = 1.5e-6
 spineSpacingDistrib = 1e-10
 spineSize = 1.0
 spineSizeDistrib = 0
-spineAngle= PI / 2.0
-spineAngleDistrib = 0.0
-
 
 def makeCellProto( name ):
     elec = moose.Neuron( '/library/' + name )
@@ -53,6 +50,9 @@ def makeSpineProto2( name ):
     moose.connect( shaft, 'axial', head, 'raxial' )
 
 def makeModel():
+    spineAngle= PI / 2.0
+    spineAngleDistrib = 0.0
+
     moose.Neutral( '/library' )
     makeCellProto( 'cellProto' )
     makeChemProto( 'cProto' )