From fce2c76b471a26f9355540c0aac1b374d0ad41ad Mon Sep 17 00:00:00 2001
From: Sam Yates <halfflat@gmail.com>
Date: Thu, 14 Jul 2016 19:31:57 +0200
Subject: [PATCH] Adapt NEURON's standard exp2syn for use and validation
* Add a tweaked version of exp2syn.mod that is modparser compatible.
* Add option to simple_synapse.py to choose which syn type to use.
* Compatibility tweak for runinng nrn scripts with nrniv -python
---
mechanisms/CMakeLists.txt | 2 +-
mechanisms/mod/exp2syn.mod | 50 ++++++++++++++++++++++++++++++++++++++
nrn/simple_synapse.py | 29 +++++++++++++++++++---
3 files changed, 76 insertions(+), 5 deletions(-)
create mode 100755 mechanisms/mod/exp2syn.mod
diff --git a/mechanisms/CMakeLists.txt b/mechanisms/CMakeLists.txt
index 203dedff..cf183d75 100644
--- a/mechanisms/CMakeLists.txt
+++ b/mechanisms/CMakeLists.txt
@@ -1,4 +1,4 @@
-set(mechanisms pas hh expsyn)
+set(mechanisms pas hh expsyn exp2syn)
set(modcc "${CMAKE_BINARY_DIR}/external/bin/modcc")
diff --git a/mechanisms/mod/exp2syn.mod b/mechanisms/mod/exp2syn.mod
new file mode 100755
index 00000000..da2d2ae6
--- /dev/null
+++ b/mechanisms/mod/exp2syn.mod
@@ -0,0 +1,50 @@
+NEURON {
+ POINT_PROCESS Exp2Syn
+ RANGE tau1, tau2, e
+ NONSPECIFIC_CURRENT i
+}
+
+UNITS {
+ (nA) = (nanoamp)
+ (mV) = (millivolt)
+ (uS) = (microsiemens)
+}
+
+PARAMETER {
+ tau1=.1 (ms) : <1e-9,1e9>
+ tau2 = 10 (ms) : <1e-9,1e9>
+ e=0 (mV)
+}
+
+ASSIGNED {
+ factor
+}
+
+STATE {
+ A : (uS)
+ B : (uS)
+}
+
+INITIAL {
+ LOCAL tp
+ A = 0
+ B = 0
+ tp = (tau1*tau2)/(tau2 - tau1) * log(tau2/tau1)
+ factor = -exp(-tp/tau1) + exp(-tp/tau2)
+ factor = 1/factor
+}
+
+BREAKPOINT {
+ SOLVE state METHOD cnexp
+ i = (B - A)*(v - e)
+}
+
+DERIVATIVE state {
+ A' = -A/tau1
+ B' = -B/tau2
+}
+
+NET_RECEIVE(weight) {
+ A = A + weight*factor
+ B = B + weight*factor
+}
diff --git a/nrn/simple_synapse.py b/nrn/simple_synapse.py
index 1779799f..de7bf22d 100644
--- a/nrn/simple_synapse.py
+++ b/nrn/simple_synapse.py
@@ -8,7 +8,20 @@ from neuron import gui, h
parser = argparse.ArgumentParser(description='generate spike train ball and stick model with hh channels at soma and pas channels in dendrite')
parser.add_argument('--plot', action='store_true', dest='plot')
-args = parser.parse_args()
+parser.add_argument('--synapse', metavar='SYN', dest='synapse',
+ choices=['exp', 'exp2'],
+ default='exp',
+ help='use synapse type SYN (exp or exp2)')
+
+# hack to make things work with nrniv ... -python:
+# throw away args before -python foo.py if -python present.
+
+if '-python' in sys.argv:
+ argv = sys.argv[sys.argv.index('-python')+2:]
+else:
+ argv = sys.argv
+
+args = parser.parse_args(argv)
soma = h.Section(name='soma')
dend = h.Section(name='dend')
@@ -62,8 +75,16 @@ for nseg in [5, 11, 51, 101] :
dend.nseg=nseg
# add a synapse
- syn_ = h.ExpSyn(dend(0.5))
- syn_.tau = 2
+ if args.synapse == 'exp':
+ syn_ = h.ExpSyn(dend(0.5))
+ syn_.tau = 2
+ elif args.synapse == 'exp2':
+ syn_ = h.Exp2Syn(dend(0.5))
+ syn_.tau1 = 0.5 # artificially slow onset
+ syn_.tau2 = 2
+ else:
+ raise RuntimeError('unrecognized synapse type')
+
ncstim = h.NetCon(stim, syn_)
ncstim.delay = 1 # 1 ms delay (arrives at 10ms)
ncstim.weight[0] = 0.04 # NetCon weight is a vector
@@ -127,7 +148,7 @@ end = timer()
print "took ", end-start, " seconds"
# save the spike info as in json format
-fp = open('simple_synapse.json', 'w')
+fp = open('simple_'+args.synapse+'_synapse.json', 'w')
json.dump(results, fp, indent=2)
if args.plot :
--
GitLab