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
// BinarySpikeClasswrite.g

    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P23RSaSPIKEbin.dat{mynode} /P23RSanet/P23RSa 1 {P23RSa_NX*P23RSa_NY} state P23RSaSPIKEbin
    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P23RSbSPIKEbin.dat{mynode} /P23RSbnet/P23RSb 2 {P23RSb_NX*P23RSb_NY} state P23RSbSPIKEbin
    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P23RScSPIKEbin.dat{mynode} /P23RScnet/P23RSc 3 {P23RSc_NX*P23RSc_NY} state P23RScSPIKEbin
    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P23RSdSPIKEbin.dat{mynode} /P23RSdnet/P23RSd 4 {P23RSd_NX*P23RSd_NY} state P23RSdSPIKEbin

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/B23FSSPIKEbin.dat{mynode} /B23FSnet/B23FS 5 {B23FS_NX*B23FS_NY} state B23FSSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/B23FSSPIKEbin.dat{mynode} /B23FSnet/B23FS 5 {B23FS_NX*B23FS_NY/2} state B23FSSPIKEbin

    end

    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P5IBaSPIKEbin.dat{mynode} /P5IBanet/P5IBa 6 {P5IBa_NX*P5IBa_NY} state P5IBaSPIKEbin
    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P5IBbSPIKEbin.dat{mynode} /P5IBbnet/P5IBb 7 {P5IBb_NX*P5IBb_NY} state P5IBbSPIKEbin
    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P5IBcSPIKEbin.dat{mynode} /P5IBcnet/P5IBc 8 {P5IBc_NX*P5IBc_NY} state P5IBcSPIKEbin
    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P5IBdSPIKEbin.dat{mynode} /P5IBdnet/P5IBd 9 {P5IBd_NX*P5IBd_NY} state P5IBdSPIKEbin

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/B5FSSPIKEbin.dat{mynode} /B5FSnet/B5FS 10 {B5FS_NX*B5FS_NY} state B5FSSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/B5FSSPIKEbin.dat{mynode} /B5FSnet/B5FS 10 {B5FS_NX*B5FS_NY/2} state B5FSSPIKEbin

    end

    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P6RSaSPIKEbin.dat{mynode} /P6RSanet/P6RSa 11 {P6RSa_NX*P6RSa_NY} state P6RSaSPIKEbin
    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P6RSbSPIKEbin.dat{mynode} /P6RSbnet/P6RSb 12 {P6RSb_NX*P6RSb_NY} state P6RSbSPIKEbin

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P6RScSPIKEbin.dat{mynode} /P6RScnet/P6RSc 13 {P6RSc_NX*P6RSc_NY} state P6RScSPIKEbin
         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P6RSdSPIKEbin.dat{mynode} /P6RSdnet/P6RSd 14 {P6RSd_NX*P6RSd_NY} state P6RSdSPIKEbin

    end

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/C23FSSPIKEbin.dat{mynode} /C23FSnet/C23FS 15 {C23FS_NX*C23FS_NY} state C23FSSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/C23FSSPIKEbin.dat{mynode} /C23FSnet/C23FS 15 {C23FS_NX*C23FS_NY/2} state C23FSSPIKEbin

    end

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/C5FSSPIKEbin.dat{mynode} /C5FSnet/C5FS 16 {C5FS_NX*C5FS_NY} state C5FSSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/C5FSSPIKEbin.dat{mynode} /C5FSnet/C5FS 16 {C5FS_NX*C5FS_NY/2} state C5FSSPIKEbin

    end

    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/ST4RSSPIKEbin.dat{mynode} /ST4RSnet/ST4RS 17 {ST4RS_NX*ST4RS_NY} state ST4RSSPIKEbin

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/I23LTSSPIKEbin.dat{mynode} /I23LTSnet/I23LTS 18 {I23LTS_NX*I23LTS_NY} state I23LTSSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/I23LTSSPIKEbin.dat{mynode} /I23LTSnet/I23LTS 18 {I23LTS_NX*I23LTS_NY/2} state I23LTSSPIKEbin

    end

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/I5LTSSPIKEbin.dat{mynode} /I5LTSnet/I5LTS 19 {I5LTS_NX*I5LTS_NY} state I5LTSSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/I5LTSSPIKEbin.dat{mynode} /I5LTSnet/I5LTS 19 {I5LTS_NX*I5LTS_NY/2} state I5LTSSPIKEbin

    end

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/TCRSPIKEbin.dat{mynode} /TCRnet/TCR 20 {TCR_NX*TCR_NY} state TCRSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/TCRSPIKEbin.dat{mynode} /TCRnet/TCR 20 {TCR_NX*TCR_NY/2} state TCRSPIKEbin

    end

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/nRTSPIKEbin.dat{mynode} /nRTnet/nRT 21 {nRT_NX*nRT_NY} state nRTSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/nRTSPIKEbin.dat{mynode} /nRTnet/nRT 21 {nRT_NX*nRT_NY/2} state nRTSPIKEbin

    end

    if ({columntype == 0})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P23FRBaSPIKEbin.dat{mynode} /P23FRBanet/P23FRBa 22 {P23FRBa_NX*P23FRBa_NY} state P23FRBaSPIKEbin

    end

    if ({columntype == 1})

         do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P23FRBaSPIKEbin.dat{mynode} /P23FRBanet/P23FRBa 22 {P23FRBa_NX*P23FRBa_NY/4} state P23FRBaSPIKEbin

    end

    do_classasc_filebin /home/pol/Data/GenesisData/Neocortex/P5RSaSPIKEbin.dat{mynode} /P5RSanet/P5RSa 23 {P5RSa_NX*P5RSa_NY} state P5RSaSPIKEbin




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