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NeuroML · Oct 27, 2017 · 7b1b50a · 7b1b50a
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+/target
diff --git a/LICENSE b/LICENSE
diff --git a/pom.xml b/pom.xml
@@ -0,0 +1,50 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<name>NeuroML2 model lite</name>
+	<url>https://neuroml.org/</url>
+	<packaging>bundle</packaging>
+	<groupId>org.neuroml.neuroml2modelLite</groupId>
+	<artifactId>neuroml2modelLite</artifactId>
+	<version>0.0.6</version>
+
+	<dependencies>
+
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.11</version>
+        </dependency>
+
+	</dependencies>
+
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<version>2.3.7</version>
+				<extensions>true</extensions>
+				<configuration>
+					<manifestLocation>src/main/java/META-INF</manifestLocation>
+					<supportedProjectTypes>
+						<supportedProjectType>jar</supportedProjectType>
+						<supportedProjectType>bundle</supportedProjectType>
+					</supportedProjectTypes>
+					<instructions>
+						<Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
+						<Bundle-Version>${project.version}</Bundle-Version>
+					</instructions>
+				</configuration>
+			</plugin>
+        </plugins>
+
+
+
+
+
+	</build>
+
+
+</project>
diff --git a/src/main/java/META-INF/MANIFEST.MF b/src/main/java/META-INF/MANIFEST.MF
@@ -0,0 +1,11 @@
+Manifest-Version: 1.0
+Bnd-LastModified: 1509096768302
+Build-Jdk: 1.8.0_91
+Built-By: padraig
+Bundle-ManifestVersion: 2
+Bundle-Name: NeuroML2 model lite
+Bundle-SymbolicName: neuroml2modelLite
+Bundle-Version: 0.0.6
+Created-By: Apache Maven Bundle Plugin
+Export-Package: org.neuroml2.model;version="0.0.6"
+Tool: Bnd-1.50.0
diff --git a/src/main/java/org/neuroml2/model/NeuroML2ModelReader.java b/src/main/java/org/neuroml2/model/NeuroML2ModelReader.java
@@ -0,0 +1,29 @@
+package org.neuroml2.model;
+
+import java.io.File;
+import java.io.IOException;
+
+
+public class NeuroML2ModelReader {
+
+
+
+
+
+    public static void main(String[] args) throws IOException
+    {
+        String ionChannelFile = "src/test/resources/Ca_LVAst.channel.nml";
+        ionChannelFile = "../../geppetto/org.geppetto.model.neuroml/src/test/resources/traub/k2.channel.nml";
+        ionChannelFile = "../../geppetto/org.geppetto.model.neuroml/src/test/resources/hhcell/NML2_SingleCompHHCell.nml";
+        if (args.length==1)
+            ionChannelFile = args[0];
+        File nmlFile = new File(ionChannelFile);
+
+
+        NeuroML2ModelReader nmlr;
+
+            System.out.println("Opening file: "+nmlFile.getCanonicalPath());
+
+    }
+
+}
diff --git a/src/test/java/org/neuroml2/model/AllTests.java b/src/test/java/org/neuroml2/model/AllTests.java
@@ -0,0 +1,30 @@
+package org.neuroml2.model;
+
+import java.io.File;
+import org.junit.Before;
+import org.junit.Test;
+
+
+
+public class AllTests {
+
+
+
+	@Before
+	public void setUp() throws Throwable {
+        NeuroML2ModelReader nmlReader = new NeuroML2ModelReader();
+
+
+	}
+
+	@Test
+	public void testChannels() throws Throwable {
+
+            System.out.println("Testing...");
+	}
+
+	protected File getLocalFile(String fname) {
+		return new File(getClass().getResource(fname).getFile());
+	}
+
+}
diff --git a/src/test/resources/Ca_LVAst.channel.nml b/src/test/resources/Ca_LVAst.channel.nml
@@ -0,0 +1,76 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<neuroml2>
+
+    <notes>NeuroML file containing a single Channel description</notes>
+
+    <ionChannel id="Ca_LVAst" conductance="10pS" type="ionChannelHH" species="ca">
+
+        <notes>Low voltage activated Ca2+ current
+
+Comment from original mod file: 
+Note: mtau is an approximation from the plots
+:Reference : :		Avery and Johnston 1996, tau from Randall 1997
+:Comment: shifted by -10 mv to correct for junction potential
+:Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21</notes>
+
+        <annotation>
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                <rdf:Description rdf:about="Ca_LVAst">
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
+            Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Ca 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">
+            <q10Settings type="q10Fixed" fixedQ10="2.95288264"/>
+            <timeCourse type="Ca_LVAst_m_tau_tau"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="6mV" midpoint="-40mV"/>
+        </gate>
+
+        <gate id="h" type="gateHHtauInf" instances="1">
+            <q10Settings type="q10Fixed" fixedQ10="2.95288264"/>
+            <timeCourse type="Ca_LVAst_h_tau_tau"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="-6.4mV" midpoint="-90mV"/>
+        </gate>
+
+    </ionChannel>
+
+    <ComponentType name="Ca_LVAst_m_tau_tau" extends="baseVoltageDepTime">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="t" exposure="t" dimension="time" value="(5 + 20 / (1 + (exp ((V+35)/5) ))) * TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="Ca_LVAst_h_tau_tau" extends="baseVoltageDepTime">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="t" exposure="t" dimension="time" value="(20 + 50 / (1 + (exp ((V+50)/7) ))) * TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+</neuroml2>
diff --git a/src/test/resources/Ih.channel.nml b/src/test/resources/Ih.channel.nml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<neuroml2>
+
+    <notes>NeuroML file containing a single Channel description</notes>
+
+    <ionChannel id="Ih" conductance="10pS" type="ionChannelHH" species="hcn">
+
+        <notes>Non-specific cation current
+
+Comment from original mod file: 
+Reference : :		Kole,Hallermann,and Stuart, J. Neurosci. 2006</notes>
+
+        <annotation>
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                <rdf:Description rdf:about="Ih">
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
+            Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+                </rdf:Description>
+            </rdf:RDF>
+        </annotation>
+
+        <gate id="m" type="gateHHrates" instances="1">
+            <forwardRate type="HHExpLinearRate" rate="0.076517per_ms" scale="-11.9mV" midpoint="-154.9mV"/>
+            <reverseRate type="HHExpRate" rate="0.193per_ms" scale="33.1mV" midpoint="0mV"/>
+        </gate>
+
+    </ionChannel>
+
+</neuroml2>
diff --git a/src/test/resources/NML2_SingleCompHHCell.nml b/src/test/resources/NML2_SingleCompHHCell.nml
@@ -0,0 +1,85 @@
+<neuroml2>
+
+    <!-- Single compartment cell with HH channels -->
+
+    <!-- This is a "pure" NeuroML 2 file. It can be included in a LEMS file for use in a simulaton
+    by the LEMS interpreter, see LEMS_NML2_Ex5_DetCell.xml -->
+
+    <ionChannelHH id="passiveChan" conductance="10pS">
+        <notes>Leak conductance</notes>
+    </ionChannelHH>
+
+
+    <ionChannelHH id="naChan" conductance="10pS" species="na">
+        <notes>Na channel</notes>
+
+        <gateHHrates id="m" instances="3">
+            <forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-40mV" scale="10mV"/>
+            <reverseRate type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>
+        </gateHHrates>
+
+        <gateHHrates id="h" instances="1">
+            <forwardRate type="HHExpRate" rate="0.07per_ms" midpoint="-65mV" scale="-20mV"/>
+            <reverseRate type="HHSigmoidRate" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
+        </gateHHrates>
+
+    </ionChannelHH>
+
+
+    <ionChannelHH id="kChan" conductance="10pS" species="k">
+
+        <gateHHrates id="n" instances="4">
+            <forwardRate type="HHExpLinearRate" rate="0.1per_ms" midpoint="-55mV" scale="10mV"/>
+            <reverseRate type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
+        </gateHHrates>
+
+    </ionChannelHH>
+
+
+
+    <cell id="hhcell">
+
+        <morphology id="morph1">
+            <segment id="0" name="soma">
+                <proximal x="0" y="0" z="0" diameter="17.841242"/> <!--Gives a convenient surface area of 1000.0 ?m�-->
+                <distal x="0" y="0" z="0" diameter="17.841242"/>
+            </segment>
+
+            <segmentGroup id="soma_group">
+                <member segment="0"/>
+            </segmentGroup>
+
+        </morphology>
+
+        <biophysicalProperties id="bioPhys1">
+
+            <membraneProperties>
+
+                <channelDensity id="leak" ionChannel="passiveChan" condDensity="3.0 S_per_m2" erev="-54.3mV"/>
+                <channelDensity id="naChans" ionChannel="naChan" condDensity="120.0 mS_per_cm2" erev="50.0 mV" ion="na"/>
+                <channelDensity id="kChans" ionChannel="kChan" condDensity="360 S_per_m2" erev="-77mV" ion="k"/>
+
+                <spikeThresh value="-20mV"/>
+                <specificCapacitance value="1.0 uF_per_cm2"/>
+                <initMembPotential value="-65mV"/>
+
+            </membraneProperties>
+
+            <intracellularProperties>
+                <resistivity value="0.03 kohm_cm"/>   <!-- Note: not used in single compartment simulations -->
+            </intracellularProperties>
+
+        </biophysicalProperties>
+
+    </cell>
+
+    <pulseGenerator id="pulseGen1" delay="100ms" duration="100ms" amplitude="0.08nA"/>
+
+
+    <network id="net1">
+        <population id="hhpop" component="hhcell" size="1"/>
+        <explicitInput target="hhpop[0]" input="pulseGen1"/>
+    </network>
+
+</neuroml2>
+
diff --git a/src/test/resources/SK_E2.channel.nml b/src/test/resources/SK_E2.channel.nml
@@ -0,0 +1,71 @@
+<?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="SK_E2">
+
+    <notes>NeuroML file containing a single Channel description</notes>
+
+    <ionChannel id="SK_E2" conductance="10pS" type="ionChannelHH" species="k">
+
+        <notes>Small-conductance, Ca2+ activated K+ current
+
+Comment from original mod file: 
+: SK-type calcium-activated potassium current
+: Reference : Kohler et al. 1996</notes>
+
+        <annotation>
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                <rdf:Description rdf:about="SK_E2">
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
+            Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>K channels</rdf:li>
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/channelGene2.aspx#table3"/>
+                        </rdf:Bag>
+                    </bqbiol:isVersionOf>
+
+                </rdf:Description>
+            </rdf:RDF>
+        </annotation>
+
+        <gate id="z" type="gateHHtauInf" instances="1">
+            <timeCourse type="SK_E2_z_tau_tau"/>
+            <steadyState type="SK_E2_z_inf_inf"/>
+        </gate>
+
+    </ionChannel>
+
+    <ComponentType name="SK_E2_z_tau_tau" extends="baseVoltageConcDepTime">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="CONC_SCALE" dimension="concentration" value="1 mol_per_cm3"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
+            <DerivedVariable name="t" exposure="t" dimension="time" value="(1) * TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="SK_E2_z_inf_inf" extends="baseVoltageConcDepVariable">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="CONC_SCALE" dimension="concentration" value="1 mol_per_cm3"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
+            <DerivedVariable name="x" exposure="x" dimension="none" value="1/(1+(4.3e-10/ca_conc)^4.8)"/>
+        </Dynamics>
+
+    </ComponentType>
+
+</neuroml>