Gq coupled signaling pathways involved in striatal synaptic plasticity (Kim et al. 2013)

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Accession:154967
Model of Gq coupled signaling pathways underlying synaptic plasticity in striatal medium spiny projection neurons. Reactions and diffusion are implemented stochastically in a dendrite with one or more diffusionally coupled spines. Simulations demonstrate that theta burst stimulation, which produces LTP, increases the ratio of PKC:2AG as compared to 20 Hz stimulation, which produces LTD.
Reference:
1 . Kim B, Hawes SL, Gillani F, Wallace LJ, Blackwell KT (2013) Signaling pathways involved in striatal synaptic plasticity are sensitive to temporal pattern and exhibit spatial specificity. PLoS Comput Biol 9:e1002953 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network;
Brain Region(s)/Organism:
Cell Type(s): Neostriatum medium spiny direct pathway GABA cell;
Channel(s):
Gap Junctions:
Receptor(s): mGluR1;
Gene(s):
Transmitter(s):
Simulation Environment: NeuroRD;
Model Concept(s): Synaptic Plasticity; Signaling pathways;
Implementer(s): Blackwell, Avrama [avrama at gmu.edu];
Search NeuronDB for information about:  Neostriatum medium spiny direct pathway GABA cell; mGluR1;
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KimEtAl2013
MorphLong
Robust
readme.txt
discretized-tree.swc
mglu_2ag_reac12mar20desens025.xml
mglu_2ag_reac12mar20desens025Bapta.xml
mglur_2ag_init12mar1lowrGabg.xml *
mglur_2ag_init12mar1lowrGabgBapta10.xml
mglur_morph.xml
mglur_outPIKnewCaM.xml
mglur_stim20hz-10sITI-2xCa30dhpg.xml
mglur_stimTheta2xCa30dhpg.xml
mglurMaster20hz12mar20desens025lowrG.xml
mglurMaster20hz12mar20desens025lowrG-Bapta.xml
mglurMasterTheta12mar20desens025lowrG.xml
NeuroRD2.1.1newtableNP30.jar
sample_output-fast-conc.txt
sample_output-mesh.txt
sample_output-slow-conc.txt
UchiModel12mar20desen025lowrG_100ms0dhpg20sCa12.xml
UchiModel12mar20desen025lowrG_100ms1dhpg20sCa12.xml
UchiModel12mar20desen025lowrG_100ms25dhpg20sCa12.xml
UchiModel12mar20desen025lowrG_100ms5dhpg20sCa12.xml
UchiModel12mar20desen025lowrG_1s0dhpg20sCa12-3.xml
UchiModel12mar20desen025lowrG_1s1dhpg20sCa12-3.xml
UchiModel12mar20desen025lowrG_1s25dhpg20sCa12-3.xml
UchiModel12mar20desen025lowrG_1s5dhpg20sCa12-3.xml
UchiModel12mar20desen025lowrG_5s0dhpg20sCa12-3.xml
UchiModel12mar20desen025lowrG_5s1dhpg20sCa12-3.xml
UchiModel12mar20desen025lowrG_5s25dhpg20sCa12-3.xml
UchiModel12mar20desen025lowrG_5s5dhpg20sCa12-3.xml
UchiStim100ms0dhpgCaRate12.xml
UchiStim100ms1dhpg20sCa12.xml
UchiStim100ms25dhpg20sCa12.xml
UchiStim100ms5dhpg20sCa12.xml
UchiStim1s0dhpgCaRate12-3.xml
UchiStim1s1dhpg20sCa12-3.xml
UchiStim1s25dhpg20sCa12-3.xml
UchiStim1s5dhpg20sCa12-3.xml
UchiStim5s0dhpgCaRate12-3-3-2-2.xml
UchiStim5s1dhpg20sCa12-3-3-2-2.xml
UchiStim5s25dhpg20sCa12-3-3-2-2.xml
UchiStim5s5dhpg20sCa12-3-3-2-2.xml
                            
<SDRun>
    <!-- this file defines a single run of the calculation, using morphology and
         reaction data brought in from other files -->

    <reactionSchemeFile>mglu_2ag_reac12mar20desens025</reactionSchemeFile>
    <morphologyFile>       mglur_morph                      </morphologyFile>
    <stimulationFile>      UchiStim1s0dhpgCaRate12-3 </stimulationFile>
    <initialConditionsFile>mglur_2ag_init12mar1lowrGabg</initialConditionsFile>
    <outputSchemeFile>     mglur_outPIKnewCaM               </outputSchemeFile>

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet...)  -->
    <geometry>          2D           </geometry>
<!--    <depth2D>           2.0          </depth2D> -->
    <depth2D>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    971263          </simulationSeed>
    <outputQuantity>NUMBER</outputQuantity>

    <!-- run time for the calculation, milliseconds.  200 s for initial sims, 350 s later -->
    <runtime>          40000       </runtime>
    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>        9897623       </spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
<!-- Use 0.2 for rough tuning the model 
	<defaultMaxElementSide>0.2</defaultMaxElementSide> -->
<!-- make it 0.15 once rates and init values are close -->
	<defaultMaxElementSide>0.15</defaultMaxElementSide>
        
	<!-- discretization for spines, microns -->
  <spineDeltaX>0.1</spineDeltaX> 

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->

<!--
	<MaxElementSide region="head">0.2</MaxElementSide>
        <MaxElementSide region="neck">0.2</MaxElementSide>
-->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->

    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds -->
    <fixedStepDt>         0.0025       </fixedStepDt>

    <outputInterval>1000</outputInterval>

    <!-- the tolerace is not used yet -->
    <tolerance>           0.001      </tolerance>


    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for
         reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <calculation> GRID_STEPPED_STOCHASTIC  </calculation>

</SDRun>