Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:150284
"… We present a new event-driven algorithm to synchronize different neuronal models, which decreases computational time and avoids superfluous synchronizations. The algorithm is implemented in the TimeScales framework. We demonstrate its use by simulating a new multiscale model of the Medium Spiny Neuron of the Neostriatum. The model comprises over a thousand dendritic spines, where the electrical model interacts with the respective instances of a biochemical model. Our results show that a multiscale model is able to exhibit changes of synaptic plasticity as a result of the interaction between electrical and biochemical signaling. …"
Reference:
1 . Mattioni M, Le Novère N (2013) Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum. PLoS One 8:e66811 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Synapse;
Brain Region(s)/Organism: Striatum;
Cell Type(s): Neostriatum medium spiny direct pathway GABA cell;
Channel(s): I Na,p; I Na,t; I T low threshold; I A; I K,Ca; I CAN; I Calcium; I A, slow; I Krp; I R; I Q;
Gap Junctions:
Receptor(s):
Gene(s): Kv4.2 KCND2; Kv1.2 KCNA2; Cav1.3 CACNA1D; Cav1.2 CACNA1C; Kv2.1 KCNB1;
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Synaptic Plasticity; Signaling pathways; Calcium dynamics; Multiscale;
Implementer(s): Mattioni, Michele [mattioni at ebi.ac.uk];
Search NeuronDB for information about:  Neostriatum medium spiny direct pathway GABA cell; I Na,p; I Na,t; I T low threshold; I A; I K,Ca; I CAN; I Calcium; I A, slow; I Krp; I R; I Q;
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
  <model id="untitled" name="testSimple">
    <annotation>
      <celldesigner:modelVersion>4.0</celldesigner:modelVersion>
      <celldesigner:modelDisplay sizeX="600" sizeY="400"/>
      <celldesigner:listOfCompartmentAliases/>
      <celldesigner:listOfComplexSpeciesAliases/>
      <celldesigner:listOfSpeciesAliases>
        <celldesigner:speciesAlias id="sa1" species="s1">
          <celldesigner:activity>inactive</celldesigner:activity>
          <celldesigner:bounds x="222.0" y="246.0" w="80.0" h="40.0"/>
          <celldesigner:view state="usual"/>
          <celldesigner:usualView>
            <celldesigner:innerPosition x="0.0" y="0.0"/>
            <celldesigner:boxSize width="80.0" height="40.0"/>
            <celldesigner:singleLine width="1.0"/>
            <celldesigner:paint color="ffccffcc" scheme="Color"/>
          </celldesigner:usualView>
          <celldesigner:briefView>
            <celldesigner:innerPosition x="0.0" y="0.0"/>
            <celldesigner:boxSize width="80.0" height="60.0"/>
            <celldesigner:singleLine width="0.0"/>
            <celldesigner:paint color="3fff0000" scheme="Color"/>
          </celldesigner:briefView>
        </celldesigner:speciesAlias>
        <celldesigner:speciesAlias id="sa2" species="s3">
          <celldesigner:activity>inactive</celldesigner:activity>
          <celldesigner:bounds x="382.0" y="246.0" w="80.0" h="40.0"/>
          <celldesigner:view state="usual"/>
          <celldesigner:usualView>
            <celldesigner:innerPosition x="0.0" y="0.0"/>
            <celldesigner:boxSize width="80.0" height="40.0"/>
            <celldesigner:singleLine width="1.0"/>
            <celldesigner:paint color="ffed1051" scheme="Color"/>
          </celldesigner:usualView>
          <celldesigner:briefView>
            <celldesigner:innerPosition x="0.0" y="0.0"/>
            <celldesigner:boxSize width="80.0" height="60.0"/>
            <celldesigner:singleLine width="0.0"/>
            <celldesigner:paint color="3fff0000" scheme="Color"/>
          </celldesigner:briefView>
        </celldesigner:speciesAlias>
        <celldesigner:speciesAlias id="sa3" species="s2">
          <celldesigner:activity>inactive</celldesigner:activity>
          <celldesigner:bounds x="302.0" y="186.0" w="80.0" h="40.0"/>
          <celldesigner:view state="usual"/>
          <celldesigner:usualView>
            <celldesigner:innerPosition x="0.0" y="0.0"/>
            <celldesigner:boxSize width="80.0" height="40.0"/>
            <celldesigner:singleLine width="1.0"/>
            <celldesigner:paint color="ffccffcc" scheme="Color"/>
          </celldesigner:usualView>
          <celldesigner:briefView>
            <celldesigner:innerPosition x="0.0" y="0.0"/>
            <celldesigner:boxSize width="80.0" height="60.0"/>
            <celldesigner:singleLine width="0.0"/>
            <celldesigner:paint color="3fff0000" scheme="Color"/>
          </celldesigner:briefView>
        </celldesigner:speciesAlias>
      </celldesigner:listOfSpeciesAliases>
      <celldesigner:listOfGroups/>
      <celldesigner:listOfProteins>
        <celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
        <celldesigner:protein id="pr1" name="s1" type="GENERIC">
          <celldesigner:listOfModificationResidues>
            <celldesigner:modificationResidue angle="2.029814608249193" id="rs1" side="none"/>
          </celldesigner:listOfModificationResidues>
        </celldesigner:protein>
      </celldesigner:listOfProteins>
      <celldesigner:listOfGenes/>
      <celldesigner:listOfRNAs/>
      <celldesigner:listOfAntisenseRNAs/>
      <celldesigner:listOfLayers/>
      <celldesigner:listOfBlockDiagrams/>
    </annotation>
    <listOfFunctionDefinitions>
      <functionDefinition id="function_4_re1_1" name="function_4_re1_1">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <lambda>
            <bvar>
              <ci> default </ci>
            </bvar>
            <bvar>
              <ci> k1 </ci>
            </bvar>
            <bvar>
              <ci> s1 </ci>
            </bvar>
            <bvar>
              <ci> s2 </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> s1 </ci>
                <ci> s2 </ci>
                <ci> k1 </ci>
              </apply>
              <ci> default </ci>
            </apply>
          </lambda>
        </math>
      </functionDefinition>
    </listOfFunctionDefinitions>
    <listOfCompartments>
      <compartment id="default" name="default" size="1"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="s2" name="s2" compartment="default" initialAmount="0.5" charge="0">
        <annotation>
          <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
          <celldesigner:speciesIdentity>
            <celldesigner:class>PROTEIN</celldesigner:class>
            <celldesigner:proteinReference>pr2</celldesigner:proteinReference>
          </celldesigner:speciesIdentity>
          <celldesigner:listOfCatalyzedReactions>
            <celldesigner:catalyzed reaction="re1"/>
          </celldesigner:listOfCatalyzedReactions>
        </annotation>
      </species>
      <species id="s1" name="s1" compartment="default" initialAmount="0.8" charge="0">
        <annotation>
          <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
          <celldesigner:speciesIdentity>
            <celldesigner:class>PROTEIN</celldesigner:class>
            <celldesigner:proteinReference>pr1</celldesigner:proteinReference>
          </celldesigner:speciesIdentity>
        </annotation>
      </species>
      <species id="s3" name="s1_2" compartment="default" initialAmount="0">
        <annotation>
          <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
          <celldesigner:speciesIdentity>
            <celldesigner:class>PROTEIN</celldesigner:class>
            <celldesigner:proteinReference>pr1</celldesigner:proteinReference>
            <celldesigner:state>
              <celldesigner:listOfModifications>
                <celldesigner:modification residue="rs1" state="phosphorylated"/>
              </celldesigner:listOfModifications>
            </celldesigner:state>
          </celldesigner:speciesIdentity>
        </annotation>
      </species>
    </listOfSpecies>
    <listOfReactions>
      <reaction id="re1" name="re1" reversible="false" fast="false">
        <annotation>
          <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
          <celldesigner:baseReactants>
            <celldesigner:baseReactant species="s1" alias="sa1">
              <celldesigner:linkAnchor position="E"/>
            </celldesigner:baseReactant>
          </celldesigner:baseReactants>
          <celldesigner:baseProducts>
            <celldesigner:baseProduct species="s3" alias="sa2">
              <celldesigner:linkAnchor position="W"/>
            </celldesigner:baseProduct>
          </celldesigner:baseProducts>
          <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
            <celldesigner:listOfLineDirection>
              <celldesigner:lineDirection index="0" value="unknown"/>
            </celldesigner:listOfLineDirection>
          </celldesigner:connectScheme>
          <celldesigner:line width="1.0" color="ff000000"/>
          <celldesigner:listOfModification>
            <celldesigner:modification type="CATALYSIS" modifiers="s2" aliases="sa3" targetLineIndex="-1,2">
              <celldesigner:connectScheme connectPolicy="direct">
                <celldesigner:listOfLineDirection>
                  <celldesigner:lineDirection index="0" value="unknown"/>
                </celldesigner:listOfLineDirection>
              </celldesigner:connectScheme>
              <celldesigner:linkTarget species="s2" alias="sa3">
                <celldesigner:linkAnchor position="S"/>
              </celldesigner:linkTarget>
              <celldesigner:line width="1.0" color="ff000000"/>
            </celldesigner:modification>
          </celldesigner:listOfModification>
        </annotation>
        <listOfReactants>
          <speciesReference species="s1">
            <annotation>
              <celldesigner:alias>sa1</celldesigner:alias>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="s3">
            <annotation>
              <celldesigner:alias>sa2</celldesigner:alias>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="s2">
            <annotation>
              <celldesigner:alias>sa3</celldesigner:alias>
            </annotation>
          </modifierSpeciesReference>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> default </ci>
              <apply>
                <ci> function_4_re1_1 </ci>
                <ci> default </ci>
                <ci> k1 </ci>
                <ci> s1 </ci>
                <ci> s2 </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="k1" value="0.4"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>

Loading data, please wait...