A multilayer cortical model to study seizure propagation across microdomains (Basu et al. 2015)

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Accession:206238
A realistic neural network was used to simulate a region of neocortex to obtain extracellular LFPs from ‘virtual micro-electrodes’ and produce test data for comparison with multisite microelectrode recordings. A model was implemented in the GENESIS neurosimulator. A simulated region of cortex was represented by layers 2/3, 5/6 (interneurons and pyramidal cells) and layer 4 stelate cells, spaced at 25 µm in each horizontal direction. Pyramidal cells received AMPA and NMDA inputs from neighboring cells at the basal and apical dendrites. The LFP data was generated by simulating 16-site electrode array with the help of ‘efield’ objects arranged at the predetermined positions with respect to the surface of the simulated network. The LFP for the model is derived from a weighted average of the current sources summed over all cellular compartments. Cell models were taken from from Traub et al. (2005) J Neurophysiol 93(4):2194-232.
References:
1 . Basu I, Kudela P, Korzeniewska A, Franaszczuk PJ, Anderson WS (2015) A study of the dynamics of seizure propagation across micro domains in the vicinity of the seizure onset zone. J Neural Eng 12:046016 [PubMed]
2 . Basu I, Kudela P, Anderson WS (2014) Determination of seizure propagation across microdomains using spectral measures of causality. Conf Proc IEEE Eng Med Biol Soc 2014:6349-52 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Thalamus reticular nucleus GABA cell; Neocortex spiking low threshold (LTS) neuron; Neocortex spiking regular (RS) neuron; Neocortex layer 2-3 interneuron; Neocortex layer 5 interneuron;
Channel(s): I Na,p; I Na,t; I K; I A; I M; I h; I K,Ca; I A, slow; I L high threshold; I T low threshold; I Calcium;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; GabaA; NMDA;
Gene(s):
Transmitter(s): Glutamate; Gaba; Amino Acids;
Simulation Environment: GENESIS;
Model Concept(s): Activity Patterns; Epilepsy;
Implementer(s): Anderson, WS ; Kudela, Pawel ;
Search NeuronDB for information about:  Thalamus reticular nucleus GABA cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow; Amino Acids; Gaba; Glutamate;
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BasuEtAl2015
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ModelDescription.pdf
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P6RSd_P6RSc.g
P6RSd_P6RSd.g
P6RSd_P6RSd_Gap.g
P6RSd_raninput.g
P6RSd_ST4RS.g
P6RSd_synapsedefs.g
P6RSd_TCR.g
P6RSdcell3Dpk.p
P6RSdchanpk.g
P6RSdprotodefs.g
P6RSsyncond.g
pgenesis_command
protodefs.g
protospikeB23FS.g
protospikeB5FS.g
protospikeC23FS.g
protospikeC5FS.g
protospikeI23LTS.g
protospikeI5LTS.g
protospikenRT.g
protospikeP23FRBa.g
protospikeP23RSa.g
protospikeP23RSb.g
protospikeP23RSc.g
protospikeP23RSd.g
protospikeP5IBa.g
protospikeP5IBb.g
protospikeP5IBc.g
protospikeP5IBd.g
protospikeP5RSa.g
protospikeP6RSa.g
protospikeP6RSb.g
protospikeP6RSc.g
protospikeP6RSd.g
protospikeST4RS.g
protospikeTCR.g
randominputdefs.g
spikedefs.g
ST4RS.g
ST4RS_B23FS.g
ST4RS_B5FS.g
ST4RS_C23FS.g
ST4RS_C5FS.g
ST4RS_I23LTS.g
ST4RS_I5LTS.g
ST4RS_P23FRBa.g
ST4RS_P23RSa.g
ST4RS_P23RSb.g
ST4RS_P23RSc.g
ST4RS_P23RSd.g
ST4RS_P5IBa.g
ST4RS_P5IBb.g
ST4RS_P5IBc.g
ST4RS_P5IBd.g
ST4RS_P5RSa.g
ST4RS_P6RSa.g
ST4RS_P6RSb.g
ST4RS_P6RSc.g
ST4RS_P6RSd.g
ST4RS_raninput.g
ST4RS_ST4RS.g
ST4RS_ST4RS_Gap.g
ST4RS_synapsedefs.g
ST4RScell3Dpk.p
ST4RSchanpk.g
ST4RSprotodefs.g
ST4RSsyncond.g
synapticdelays.g *
synapticprobsTraub.g
synchansB23FS.g *
synchansB5FS.g *
synchansC23FS.g *
synchansC5FS.g *
synchansI23LTS.g *
synchansI5LTS.g *
synchansnRT.g *
synchansP23FRBa.g *
synchansP23RSa.g *
synchansP23RSb.g *
synchansP23RSc.g *
synchansP23RSd.g *
synchansP5IBa.g *
synchansP5IBb.g *
synchansP5IBc.g *
synchansP5IBd.g *
synchansP5RSa.g *
synchansP6RSa.g *
synchansP6RSb.g *
synchansP6RSc.g *
synchansP6RSd.g *
synchansSPIKEs.g *
synchansSPIKEs_base.g
synchansST4RS.g
synchansTCR.g *
syncond.g
syncond2.g
TCR.g
TCR_B23FS.g
TCR_B5FS.g
TCR_C23FS.g
TCR_C5FS.g
TCR_nRT.g
TCR_P23FRBa.g
TCR_P23RSa.g
TCR_P23RSb.g
TCR_P23RSc.g
TCR_P23RSd.g
TCR_P5IBa.g
TCR_P5IBb.g
TCR_P5IBc.g
TCR_P5IBd.g
TCR_P5RSa.g
TCR_P6RSa.g
TCR_P6RSb.g
TCR_P6RSc.g
TCR_P6RSd.g
TCR_raninput.g
TCR_ST4RS.g
TCR_synapsedefs.g
TCRcellpk.p
TCRchanpk.g
TCRprotodefs.g
TCRsyncond.g
                            
// genesis
//Gapdefs.g

// Create Gap Junctions

     include P23RSa_P23RSa_Gap.g
     include P23RSa_P23RSb_Gap.g
     include P23RSa_P23RSc_Gap.g
     include P23RSa_P23RSd_Gap.g

     include P23RSb_P23RSb_Gap.g
     include P23RSb_P23RSc_Gap.g
     include P23RSb_P23RSd_Gap.g

     include P23RSc_P23RSc_Gap.g
     include P23RSc_P23RSd_Gap.g

     include P23RSd_P23RSd_Gap.g

if ({columntype == 0})

     include B23FS_B23FS_Gap.g

end

if ({columntype == 1})

     include B23FS_B23FS_TraubGap.g

end

     include P5IBa_P5IBa_Gap.g
     include P5IBa_P5IBb_Gap.g
     include P5IBa_P5IBc_Gap.g
     include P5IBa_P5IBd_Gap.g

     include P5IBb_P5IBb_Gap.g
     include P5IBb_P5IBc_Gap.g
     include P5IBb_P5IBd_Gap.g

     include P5IBc_P5IBc_Gap.g
     include P5IBc_P5IBd_Gap.g

     include P5IBd_P5IBd_Gap.g

if ({columntype == 0})

     include B5FS_B5FS_Gap.g

end

if ({columntype == 1})

     include B5FS_B5FS_TraubGap.g

end

if ({columntype == 0})

     include P6RSa_P6RSa_Gap.g
     include P6RSa_P6RSb_Gap.g
     include P6RSa_P6RSc_Gap.g
     include P6RSa_P6RSd_Gap.g

     include P6RSb_P6RSb_Gap.g
     include P6RSb_P6RSc_Gap.g
     include P6RSb_P6RSd_Gap.g

     include P6RSc_P6RSc_Gap.g
     include P6RSc_P6RSd_Gap.g

     include P6RSd_P6RSd_Gap.g

end

if ({columntype == 1})

     include P6RSa_P6RSa_Gap.g
     include P6RSa_P6RSb_Gap.g

     include P6RSb_P6RSb_Gap.g

end

     include ST4RS_ST4RS_Gap.g

if ({columntype == 0})

     include I23LTS_I23LTS_Gap.g

end

if ({columntype == 1})

     include I23LTS_I23LTS_TraubGap.g

end

if ({columntype == 0})

     include I5LTS_I5LTS_Gap.g

end

if ({columntype == 1})

     include I5LTS_I5LTS_TraubGap.g

end

if ({thalamocortical == 1})

     if ({columntype == 0})

          include nRT_nRT_Gap.g

     end

     if ({columntype == 1})

          include nRT_nRT_TraubGap.g

     end

end

    include P5IBa_P5RSa_Gap.g
    include P5IBb_P5RSa_Gap.g
    include P5IBc_P5RSa_Gap.g
    include P5IBd_P5RSa_Gap.g

    include P5RSa_P5RSa_Gap.g

if ({columntype == 1})

          include P23RSa_P23FRBa_TraubGap.g //these give Error messages
          include P23RSb_P23FRBa_TraubGap.g
          include P23RSc_P23FRBa_TraubGap.g
          include P23RSd_P23FRBa_TraubGap.g 

end

if ({columntype == 0})

          include P23RSa_P23FRBa_Gap.g 
          include P23RSb_P23FRBa_Gap.g
          include P23RSc_P23FRBa_Gap.g
          include P23RSd_P23FRBa_Gap.g

end

    include P23FRBa_P23FRBa_Gap.g

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