From 4a102f6c0f5276395ae80243fc48be21f24ed4e7 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 15 Jan 2016 16:35:54 +0000 Subject: [PATCH] Testing changing ca2o to 2mM Related to #8 --- .gitignore | 1 + NEURON/Golgi_template.hoc | 5 ++++- NEURON/Test_golgi.hoc | 4 ++-- NEURON/test/.test.mep | 2 +- neuroConstruct/pythonScripts/RegenerateNml2.py | 7 ++----- neuroConstruct/pythonScripts/RunTestsPace.py | 4 ++-- 6 files changed, 12 insertions(+), 11 deletions(-) diff --git a/.gitignore b/.gitignore index 91f56ec..9702564 100644 --- 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 index 582f3b9..1841478 100644 --- 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: Università 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 index 574f13e..f6c3b8e 100644 --- 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 index 2268f40..cd71efb 100644 --- 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 index 6acaeaf..eec3cc7 100644 --- 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 index 091fb44..da7a829 100644 --- 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)