Merge pull request #230 from NeuroML/experimental

Add examples with tests for various ways to include <morphology> and …

.gitignore

@@ -68,3 +68,15 @@ examples/*.pov
 /LEMSexamples/tmp
 arm64
 /examples/NML2_SingleCompHHCell.nml__flattened.xml
+/LEMSexamples/morphologies/*.mod
+/LEMSexamples/morphologies/*.c
+/LEMSexamples/morphologies/*.so
+*eden.py
+*netpyne.py
+*nrn.py
+/LEMSexamples/morphologies/*.dat
+/LEMSexamples/morphologies/*.hoc
+/LEMSexamples/morphologies/NET_m_in_b_in.net.nml
+/LEMSexamples/morphologies/simulator.props
+/LEMSexamples/morphologies/NET_m_in_b_out.net.nml
+/LEMSexamples/morphologies/NET_m_out_b_in.net.nml

LEMSexamples/morphologies/.test.jnml.omt

@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.004018425953151025

LEMSexamples/morphologies/.test.jnmleden.multi.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_EDEN
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.017719626168224333
+
+
+

LEMSexamples/morphologies/.test.jnmleden.multi.out.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_out.xml
+engine: jNeuroML_EDEN
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.017719626168224333
+
+
+

LEMSexamples/morphologies/.test.jnmleden.omt

@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML_EDEN
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.0024858998690222445

LEMSexamples/morphologies/.test.jnmleden.out.omt

@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_out_b_out.xml
+engine: jNeuroML_EDEN
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.0024858998690222445

LEMSexamples/morphologies/.test.jnmlnetpyne.multi.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_NetPyNE
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnetpyne.multi.out.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_out.xml
+engine: jNeuroML_NetPyNE
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnetpyne.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML_NetPyNE
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnetpyne.out.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_out_b_out.xml
+engine: jNeuroML_NetPyNE
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnrn.multi.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_NEURON
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnrn.multi.out.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_out.xml
+engine: jNeuroML_NEURON
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnrn.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML_NEURON
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnrn.out.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_out_b_out.xml
+engine: jNeuroML_NEURON
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.mep

@@ -0,0 +1,6 @@
+system: Testing a single compartment cell
+
+experiments:
+  Current clamp pyramidal:
+    expected:
+        spike times: [102.49, 120.78, 148.66, 256.3125, 330.84000000000003, 408.0575, 484.6375, 561.1650000000001]

LEMSexamples/morphologies/.test.multi.mep

@@ -0,0 +1,6 @@
+system: Testing a cell
+
+experiments:
+  Current clamp pyramidal:
+    expected:
+        spike times: [134.24, 401.25]

LEMSexamples/morphologies/.test.validate.omt

@@ -0,0 +1,5 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+# This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml
+target: "*cell.nml *channel.nml C*.nml"
+engine: jNeuroML_validate

LEMSexamples/morphologies/Ca_conc.nml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="Ca_conc">
+
+    <notes>NeuroML file describing intracellular Calcium dynamics, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+
+    <fixedFactorConcentrationModel id="Ca_conc" restingConc="0.0mM" decayConstant="0.1s" ion="ca" rho="9543.150099999999mol_per_m_per_A_per_s"/>
+
+</neuroml>