Testing changing ca2o to 2mM

Related to #8
OpenSourceBrain · Jan 15, 2016 · 4a102f6 · 4a102f6
1 parent f831524
commit 4a102f6
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Showing 6 changed files with 12 additions and 11 deletions.
diff --git a/.gitignore b/.gitignore
@@ -9,6 +9,7 @@
 /NeuroML2/*.hoc
 /NeuroML2/*.dat
 
+/NEURON*/old
 /NEURON*/test/*.dat
 /NEURON*/*.dat
 /NEURON*/Golgi_count.txt

diff --git a/NEURON/Golgi_template.hoc b/NEURON/Golgi_template.hoc
@@ -6,7 +6,7 @@ Data Analysis: Sergio Solinas
 
 Work Progress: April 2004 - May 2007
 
-Developed At:  Universit� Degli Studi Di Pavia
+Developed At:  Universit� Degli Studi Di Pavia
 	       Dipartimento Di Scienze Fisiologiche
 	       Pavia - Italia
 
@@ -85,11 +85,14 @@ proc init() {
 
 	cai0_ca_ion = 50e-6
 	ca2i0_ca2_ion = cai0_ca_ion
+
 
 	cai = cai0_ca_ion
 
 	ca2i = cai
 	ca2o = cao
+	cao0_ca_ion = 2
+	ca2o0_ca2_ion = 2
 
 	cai0_Golgi_CALC = cai0_ca_ion
 	ca2i0_Golgi_CALC_ca2 = cai0_ca_ion

diff --git a/NEURON/Test_golgi.hoc b/NEURON/Test_golgi.hoc
@@ -34,11 +34,11 @@ objref Golgi[1]
 Golgi[0] = new Goc()
 
 v_init = -60
-dt = 0.025
+dt = 0.0025
 
 access Golgi[0].soma
 
-cvode.active(1)
+//cvode.active(1)
 
 
 // Set output

diff --git a/NEURON/test/.test.mep b/NEURON/test/.test.mep
@@ -5,5 +5,5 @@ system: Testing Golgi
 experiments:
   pacemaking:
     expected:
-      spike times: [0.041562, 0.200095, 0.364031, 0.527852, 0.691267, 0.854141, 1.016794, 1.179499, 1.341892, 1.504193, 1.666397, 1.828394, 1.990712, 2.152964, 2.315255, 2.477304, 2.639469, 2.80132, 2.963057, 3.125055, 3.287089, 3.448934, 3.610879, 3.772468, 3.934263]
+      spike times: [0.041427, 0.199477, 0.36273, 0.525698, 0.68832, 0.850668, 1.012803, 1.174773, 1.336615, 1.498358, 1.66002, 1.82161, 1.983145, 2.144625, 2.306065, 2.466482, 2.6278, 2.78912, 2.950412, 3.11167, 3.272897, 3.434092, 3.595257, 3.756392, 3.917502]
 
diff --git a/neuroConstruct/pythonScripts/RegenerateNml2.py b/neuroConstruct/pythonScripts/RegenerateNml2.py
@@ -27,19 +27,16 @@
 
 projFile = File(os.getcwd(), "../SolinasEtAl-GolgiCell.ncx")
 
-simConfigs = []
-simConfigs.append("TestNML2")
-
 print("Generating NeuroML v1.8.1 files...")
 nc.generateNeuroML1(projFile, ['Fig. 2A: Pacemaking'])
 
 
 print("Generating NeuroML v2 files...")
-nc.generateNeuroML2(projFile, simConfigs)
+nc.generateNeuroML2(projFile, ['Fig. 2A: Pacemaking'])
 
 # Some extra files have been committed for testing or to provide other LEMS/NeuroML 2 examples
 # This just pulls them from the repository, since they get wiped by the generateNeuroML2 function 
-extra_files = ['.test.*', 'channel_summary', 'analyse_chans.sh','compare_nml2_mods.py']
+extra_files = ['.test.*', 'channel_summary', 'analyse_chans.sh', 'compare_nml2_mods.py', '../generatedNeuroML/.test.validate.omt']
 
 if len(sys.argv)==2 and sys.argv[1] == "-f":
     extra_files.append('SolinasEtAl-GolgiCell.net.nml')

diff --git a/neuroConstruct/pythonScripts/RunTestsPace.py b/neuroConstruct/pythonScripts/RunTestsPace.py
@@ -37,7 +37,7 @@
 
 simConfigs.append("PacemakerTest")
 
-simDt =                 0.001
+simDt =                 0.0025
 
 simulators =            ["NEURON"]
 
@@ -88,7 +88,7 @@ def testAll(argv=None):
     spikeTimesToCheck = {'Golgi_CML_0': spike_times}
 
 
-    spikeTimeAccuracy = 2.6 # ms in 4000 ms
+    spikeTimeAccuracy = 7.2 # ms in 4000 ms
 
     report = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
                                   spikeTimeAccuracy = spikeTimeAccuracy)