From d7d4cd0d0410d788ec8ba7847ebb74922e1b7ca5 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Fri, 28 Apr 2017 10:07:27 +0100
Subject: [PATCH] Better testing of synapses

---
 NEURON/test/testSyns.py    | 20 ++++++++++----------
 NeuroML2/AMPA.synapse.nml  |  2 +-
 NeuroML2/GABA.synapse.nml  |  2 +-
 NeuroML2/LEMS_testSyns.xml |  2 +-
 NeuroML2/NMDA.synapse.nml  |  5 +++--
 5 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/NEURON/test/testSyns.py b/NEURON/test/testSyns.py
index 83eb2a5..09cb5f5 100644
--- a/NEURON/test/testSyns.py
+++ b/NEURON/test/testSyns.py
@@ -201,10 +201,10 @@ def add_AMPA_NMDAsyns(gmaxa=0.5, tau1a=0.5, tau2a=1, gmaxn=0.5, tau1n=2, tau2n=2
 stim.amp = 0.06
 inputs.append(stim)
 
-ampa1 = add_AMPAsyns()
-gaba1 = add_GABAsyns()
-nmda1 = add_NMDAsyns()
-ampa2, nmda2 = add_AMPA_NMDAsyns()
+ampa1 = add_AMPAsyns(gmax=1)
+gaba1 = add_GABAsyns(gmax=1,rev=-80)
+nmda1 = add_NMDAsyns(gmax=1)
+ampa2, nmda2 = add_AMPA_NMDAsyns(gmaxa=1,gmaxn=1)
 
 
 h('forall psection()')
@@ -216,7 +216,7 @@ def add_AMPA_NMDAsyns(gmaxa=0.5, tau1a=0.5, tau2a=1, gmaxn=0.5, tau1n=2, tau2n=2
 ds3 = create_dumps(comp3, varlist)
 ds4 = create_dumps(comp4, varlist)
 
-run(400, 0.01)
+run(400, 0.005)
 
 if not nogui:
     from pylab import show
@@ -227,11 +227,11 @@ def add_AMPA_NMDAsyns(gmaxa=0.5, tau1a=0.5, tau2a=1, gmaxn=0.5, tau1n=2, tau2n=2
     plot_timeseries(ds4, varlist)
     show()
     
-dump_to_file(ds0, varlist, fname='v0.dat')
-dump_to_file(ds1, varlist, fname='v1.dat')
-dump_to_file(ds2, varlist, fname='v2.dat')
-dump_to_file(ds3, varlist, fname='v3.dat')
-dump_to_file(ds4, varlist, fname='v4.dat')
+dump_to_file(ds0, varlist, fname='s0.dat')
+dump_to_file(ds1, varlist, fname='s1.dat')
+dump_to_file(ds2, varlist, fname='s2.dat')
+dump_to_file(ds3, varlist, fname='s3.dat')
+dump_to_file(ds4, varlist, fname='s4.dat')
 
 
 if nogui:
diff --git a/NeuroML2/AMPA.synapse.nml b/NeuroML2/AMPA.synapse.nml
index 7fb025d..3190ac3 100644
--- a/NeuroML2/AMPA.synapse.nml
+++ b/NeuroML2/AMPA.synapse.nml
@@ -3,7 +3,7 @@
 
     <notes>NeuroML 2 file describing a single synaptic mechanism</notes>
 
-    <expTwoSynapse id="AMPA" tauRise="0.5ms" tauDecay="1ms" gbase="0.5nS" erev="0.0V">
+    <expTwoSynapse id="AMPA" tauRise="0.5ms" tauDecay="1ms" gbase="1nS" erev="0.0V">
         <notes>AMPA synapse</notes>
     </expTwoSynapse>
 
diff --git a/NeuroML2/GABA.synapse.nml b/NeuroML2/GABA.synapse.nml
index 8630dfe..aa8dac1 100644
--- a/NeuroML2/GABA.synapse.nml
+++ b/NeuroML2/GABA.synapse.nml
@@ -6,7 +6,7 @@
 
     <notes>NeuroML 2 file describing a single synaptic mechanism</notes>
 
-    <expTwoSynapse id="GABA" tauRise="0.1ms" tauDecay="4ms" gbase="0.5nS" erev="-75mV">
+    <expTwoSynapse id="GABA" tauRise="0.1ms" tauDecay="4ms" gbase="1nS" erev="-80mV">
         <notes>GABA synapse</notes>
     </expTwoSynapse>
 
diff --git a/NeuroML2/LEMS_testSyns.xml b/NeuroML2/LEMS_testSyns.xml
index 5b3be9f..9d6c9c2 100644
--- a/NeuroML2/LEMS_testSyns.xml
+++ b/NeuroML2/LEMS_testSyns.xml
@@ -12,7 +12,7 @@
   <Include file="testSyns.net.nml"/>
   
   
-  <Component type="Simulation" id="sim1" length="400ms" step="0.01 ms" target="net">
+  <Component type="Simulation" id="sim1" length="400ms" step="0.005 ms" target="net">
 
     <Display id="" title="v"  xmin="0" xmax="400" ymin="-75.0" ymax="-10" timeScale="1ms">
       <Line id="V0" timeScale="1ms" quantity="pop0/0/cell/v" scale="1 mV" color="#000000"/>
diff --git a/NeuroML2/NMDA.synapse.nml b/NeuroML2/NMDA.synapse.nml
index 2c15312..a01eeeb 100644
--- a/NeuroML2/NMDA.synapse.nml
+++ b/NeuroML2/NMDA.synapse.nml
@@ -6,11 +6,12 @@
 
     <notes>NeuroML 2 file describing a single synaptic mechanism</notes>
      
-    <blockingPlasticSynapse id="NMDA" gbase="0.485nS"
+    <!--                                     0.97nS to scale for (1-pf) with pf=0.03 in exp2synNMDA.mod -->
+    <blockingPlasticSynapse id="NMDA" gbase="0.97nS"  
                             erev="0mV" tauRise="2ms" tauDecay="20ms">
         <notes>NMDA synapse</notes>
         <blockMechanism type="voltageConcDepBlockMechanism" species="mg" blockConcentration="1 mM"
-                                      scalingConc="3.57 mM" scalingVolt="16.129 mV"/>
+                                      scalingConc="3.57 mM" scalingVolt="16.129032258 mV"/>
     </blockingPlasticSynapse>
 
 </neuroml>