Adding first channe: it.channel.nml

OpenSourceBrain · Nov 5, 2015 · e21fa90 · e21fa90
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Showing 10 changed files with 466 additions and 319 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 /NEURON/temp.pkl
 /NEURON/saveClass.pyc
 /NEURON/libcell.pyc
+/NEURON/test/*.dat
 *.bak
 *~
 generatedNeuroML
@@ -19,6 +20,7 @@ NeuroML2/*.log
 NeuroML2/*.hoc
 NeuroML2/*.props
 NeuroML2/*nrn.py
+NeuroML2/LEMS_Test*
 
 x86_64
 umac

diff --git a/NEURON/test/analyse_mods.sh b/NEURON/test/analyse_mods.sh
@@ -0,0 +1 @@
+pynml-modchananalysis it -stepV 5 -temperature [26,34] -modFile '../mod.files/CaT.mod'
diff --git a/NeuroML2/.test.validate.omt b/NeuroML2/.test.validate.omt
@@ -0,0 +1,6 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
+# Still in development, subject to change without notice!!
+
+# This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml
+target: "*.nml"
+engine: jNeuroML_validate
diff --git a/NeuroML2/L23_morph.cell.nml b/NeuroML2/L23_morph.cell.nml
diff --git a/NeuroML2/analyse_chans.sh b/NeuroML2/analyse_chans.sh
@@ -0,0 +1,4 @@
+
+pynml-channelanalysis it.channel.nml \
+                      -caConc 4.3e-4 -temperature 35 -datSuffix '.35' -html -md
+
diff --git a/NeuroML2/channel_summary/ChannelInfo.html b/NeuroML2/channel_summary/ChannelInfo.html
@@ -0,0 +1,25 @@
+<html>
+    <title>Channel information</title>
+
+    <body>
+        <p style="font-family:arial">Channel information at: T = 35.0 degC, E_rev = 0 mV, [Ca2+] = 0.00043 mM</p>
+        <table>
+            <tr>
+        <td width="130px">
+            <p style="font-size:80%;font-family:arial"><b>it</b></p>
+            <p style="font-size:80%;font-family:arial"><a href="../it.channel.nml">it.channel.nml</a></p>
+            <p style="font-size:80%;background-color:#8FBC8F;"><b>Ion: ca</b></p>
+            <p style="font-size:80%;font-family:arial">g = gmax * m<sup>2</sup> * h </p><br/>
+            <p style="font-size:80%;font-family:arial">...</p><br/>
+        </td>
+        <td>
+        <a href="it.inf.png"><img alt="it steady state" src="it.inf.png" height="300"/></a>
+        </td>
+        <td>
+        <a href="it.tau.png"><img alt="it time course" src="it.tau.png" height="300"/></a>
+        </td>
+        </tr>
+        </table>
+    </body>
+
+</html>
diff --git a/NeuroML2/channel_summary/README.md b/NeuroML2/channel_summary/README.md
@@ -0,0 +1,23 @@
+Channel information
+===================
+
+<p style="font-family:arial">Channel information at: T = 35.0 degC, E_rev = 0 mV, [Ca2+] = 0.00043 mM</p>
+
+<table>
+    <tr>
+<td width="120px">
+            <sup><b>it</b><br/>
+            <a href="../it.channel.nml">it.channel.nml</a><br/>
+            <b>Ion: ca</b><br/>
+            <i>g = gmax * m<sup>2</sup> * h </i><br/>
+            ...</sup>
+</td>
+<td>
+<a href="it.inf.png"><img alt="it steady state" src="it.inf.png" height="220"/></a>
+</td>
+<td>
+<a href="it.tau.png"><img alt="it time course" src="it.tau.png" height="220"/></a>
+</td>
+</tr>
+</table>
+
diff --git a/NeuroML2/channel_summary/it.inf.png b/NeuroML2/channel_summary/it.inf.png
diff --git a/NeuroML2/channel_summary/it.tau.png b/NeuroML2/channel_summary/it.tau.png
diff --git a/NeuroML2/it.channel.nml b/NeuroML2/it.channel.nml
@@ -0,0 +1,76 @@
+<?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="it">
+
+    <notes>NeuroML file containing a single Channel description</notes>
+
+    <ionChannel id="it" conductance="0 pS" type="ionChannelHH" species="ca">
+
+        <notes>...</notes>
+
+        <annotation>
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                <rdf:Description rdf:about="IT">
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>....</rdf:li>
+                            <rdf:li rdf:resource="..."/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Calcium channels</rdf:li>
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/channelGene2.aspx#table1"/>
+                        </rdf:Bag>
+                    </bqbiol:isVersionOf>
+
+                </rdf:Description>
+            </rdf:RDF>
+        </annotation>
+
+        <gate id="m" type="gateHHtauInf" instances="2">
+            <timeCourse type="CaT_m_tau_tau"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="7.4mV" midpoint="-50mV"/>
+        </gate>
+
+        <gate id="h" type="gateHHtauInf" instances="1">
+            <timeCourse type="CaT_h_tau_tau"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="-5.0mV" midpoint="-78mV"/>
+        </gate>
+
+    </ionChannel>
+
+
+    <ComponentType name="CaT_m_tau_tau" extends="baseVoltageDepTime">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+
+        <Constant name="am" dimension="none" value="3"/>
+        <Constant name="vm1" dimension="voltage" value="25 mV"/>
+        <Constant name="wm1" dimension="voltage" value="20 mV"/>
+        <Constant name="vm2" dimension="voltage" value="100 mV"/>
+        <Constant name="wm2" dimension="voltage" value="15 mV"/>
+
+        <Dynamics>
+            <DerivedVariable name="t" exposure="t" dimension="time" value="( am + 1.0 / ( exp((v+vm1)/wm1) + exp(-(v+vm2)/wm2) ) ) * TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="CaT_h_tau_tau" extends="baseVoltageDepTime">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+
+        <Constant name="ah" dimension="none" value="85"/>
+        <Constant name="vh1" dimension="voltage" value="46 mV"/>
+        <Constant name="wh1" dimension="voltage" value="4 mV"/>
+        <Constant name="vh2" dimension="voltage" value="405 mV"/>
+        <Constant name="wh2" dimension="voltage" value="50 mV"/>
+
+        <Dynamics>
+            <DerivedVariable name="t" exposure="t" dimension="time" value="( ah + 1.0 / ( exp((v+vh1)/wh1) + exp(-(v+vh2)/wh2) ) ) * TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+
+</neuroml>
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		pynml-modchananalysis it -stepV 5 -temperature [26,34] -modFile '../mod.files/CaT.mod'
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,4 @@

		pynml-channelanalysis it.channel.nml \
		-caConc 4.3e-4 -temperature 35 -datSuffix '.35' -html -md