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
                            
echo P5IBd Synapse Definitions...
echo

//P23RS - P5IBd AMPA synapses

str s

//Load synapse location array

str locations = "apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P23RSAMPA
     setfield /P5IBd/{s}/Ex_ch9P23RSAMPA gmax {CondmaxP23RSAMPA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P23RSAMPA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P23RSAMPA VOLTAGE Vm

     ce /

end

//P23RS - P5IBd NMDA synapses

str s

//Load synapse location array

str locations = "apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P23RSNMDA
     setfield /P5IBd/{s}/Ex_ch9P23RSNMDA gmax {CondmaxP23RSNMDA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P23RSNMDA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P23RSNMDA VOLTAGE Vm

     ce /

end

//P5IB - P5IBd AMPA synapses

str s

//Load synapse location array

str locations = "apdend1 apdend2 apdend3 apdend4 apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12 apdend13 apobdistLa apobdistLb apobdistLc apobmidLa apobmidLb apobmidLc apobproxLa apobproxLb apobproxLc apobdistRa apobdistRb apobdistRc apobmidRa apobmidRb apobmidRc apobproxRa apobproxRb apobproxRc basalLsupera basalLsuperb basalLsuperc basalLmida basalLmidb basalLmidc basalRsupera basalRsuperb basalRsuperc basalRmida basalRmidb basalRmidc basaldeepa basaldeepb basaldeepc"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P5IBAMPA
     setfield /P5IBd/{s}/Ex_ch9P5IBAMPA gmax {CondmaxP5IBAMPA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P5IBAMPA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P5IBAMPA VOLTAGE Vm

     ce /

end

//P5IB - P5IBd NMDA synapses

str s

//Load synapse location array

str locations = "apdend1 apdend2 apdend3 apdend4 apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12 apdend13 apobdistLa apobdistLb apobdistLc apobmidLa apobmidLb apobmidLc apobproxLa apobproxLb apobproxLc apobdistRa apobdistRb apobdistRc apobmidRa apobmidRb apobmidRc apobproxRa apobproxRb apobproxRc basalLsupera basalLsuperb basalLsuperc basalLmida basalLmidb basalLmidc basalRsupera basalRsuperb basalRsuperc basalRmida basalRmidb basalRmidc basaldeepa basaldeepb basaldeepc"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P5IBNMDA
     setfield /P5IBd/{s}/Ex_ch9P5IBNMDA gmax {CondmaxP5IBNMDA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P5IBNMDA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P5IBNMDA VOLTAGE Vm

     ce /

end

//B5FS - P5IBd GABAa synapses

str s

//Load synapse location array

str locations = "soma apdend1 apdend2 basalLsupera basalLmida basalRsupera basalRmida basaldeepa"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Inh_ch9B5FSGABAa
     setfield /P5IBd/{s}/Inh_ch9B5FSGABAa gmax {CondmaxB5FSGABAa_P5IB}
     addmsg /P5IBd/{s}/Inh_ch9B5FSGABAa /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Inh_ch9B5FSGABAa VOLTAGE Vm

     ce /

end

//P6RS - P5IBd AMPA synapses

str s

//Load synapse location array

str locations = "apdend1 apdend2 apdend3 apdend4 apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12 apdend13 apobdistLa apobdistLb apobdistLc apobmidLa apobmidLb apobmidLc apobproxLa apobproxLb apobproxLc apobdistRa apobdistRb apobdistRc apobmidRa apobmidRb apobmidRc apobproxRa apobproxRb apobproxRc basalLsupera basalLsuperb basalLsuperc basalLmida basalLmidb basalLmidc basalRsupera basalRsuperb basalRsuperc basalRmida basalRmidb basalRmidc basaldeepa basaldeepb basaldeepc"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P6RSAMPA
     setfield /P5IBd/{s}/Ex_ch9P6RSAMPA gmax {CondmaxP6RSAMPA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P6RSAMPA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P6RSAMPA VOLTAGE Vm

     ce /

end

//P6RS - P5IBd NMDA synapses

str s

//Load synapse location array

str locations = "apdend1 apdend2 apdend3 apdend4 apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12 apdend13 apobdistLa apobdistLb apobdistLc apobmidLa apobmidLb apobmidLc apobproxLa apobproxLb apobproxLc apobdistRa apobdistRb apobdistRc apobmidRa apobmidRb apobmidRc apobproxRa apobproxRb apobproxRc basalLsupera basalLsuperb basalLsuperc basalLmida basalLmidb basalLmidc basalRsupera basalRsuperb basalRsuperc basalRmida basalRmidb basalRmidc basaldeepa basaldeepb basaldeepc"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P6RSNMDA
     setfield /P5IBd/{s}/Ex_ch9P6RSNMDA gmax {CondmaxP6RSNMDA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P6RSNMDA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P6RSNMDA VOLTAGE Vm

     ce /

end

//C23FS - P5IBd GABAa synapses

ce /P5IBd/axona

make_Inh_ch9C23FSGABAa
setfield /P5IBd/axona/Inh_ch9C23FSGABAa gmax {CondmaxC23FSGABAa_P5IB}
addmsg /P5IBd/axona/Inh_ch9C23FSGABAa /P5IBd/axona CHANNEL Gk Ek
addmsg /P5IBd/axona /P5IBd/axona/Inh_ch9C23FSGABAa VOLTAGE Vm

ce /

//C5FS - P5IBd GABAa synapses

ce /P5IBd/axona

make_Inh_ch9C5FSGABAa
setfield /P5IBd/axona/Inh_ch9C5FSGABAa gmax {CondmaxC5FSGABAa_P5IB}
addmsg /P5IBd/axona/Inh_ch9C5FSGABAa /P5IBd/axona CHANNEL Gk Ek
addmsg /P5IBd/axona /P5IBd/axona/Inh_ch9C5FSGABAa VOLTAGE Vm

ce /

//ST4RS - P5IBd AMPA synapses

str s

//Load synapse location array

str locations = "apdend2 apdend3 apdend4 apdend5 apdend6 apdend7 apobdistLa apobmidLa apobproxLa apobdistRa apobmidRa apobproxRa"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9ST4RSAMPA
     setfield /P5IBd/{s}/Ex_ch9ST4RSAMPA gmax {CondmaxST4RSAMPA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9ST4RSAMPA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9ST4RSAMPA VOLTAGE Vm

     ce /

end

//ST4RS - P5IBd NMDA synapses

str s

//Load synapse location array

str locations = "apdend2 apdend3 apdend4 apdend5 apdend6 apdend7 apobdistLa apobmidLa apobproxLa apobdistRa apobmidRa apobproxRa"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9ST4RSNMDA
     setfield /P5IBd/{s}/Ex_ch9ST4RSNMDA gmax {CondmaxST4RSNMDA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9ST4RSNMDA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9ST4RSNMDA VOLTAGE Vm

     ce /

end



//I23LTS - P5IBd GABAa synapses

str s

//Load synapse location array

str locations = "apdend4 apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12 apdend13 apdend14aR apdend14bR apdend14cR apdend14dR apdend14aL apdend14bL apdend14cL apdend14dL basalLsuperb basalLsuperc basalLmidb basalLmidc basalRsuperb basalRsuperc basalRmidb basalRmidc basaldeepb basaldeepc apobdistRb apobdistRc apobmidRb apobmidRc apobproxRb apobproxRc apobdistLb apobdistLc apobmidLb apobmidLc apobproxLb apobproxLc"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Inh_ch9I23LTSGABAa
     setfield /P5IBd/{s}/Inh_ch9I23LTSGABAa gmax {CondmaxI23LTSGABAa_P5IB}
     addmsg /P5IBd/{s}/Inh_ch9I23LTSGABAa /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Inh_ch9I23LTSGABAa VOLTAGE Vm

     ce /

end

//I5LTS - P5IBd GABAa synapses

str s

//Load synapse location array

str locations = "apdend4 apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12 apdend13 apdend14aR apdend14bR apdend14cR apdend14dR apdend14aL apdend14bL apdend14cL apdend14dL basalLsuperb basalLsuperc basalLmidb basalLmidc basalRsuperb basalRsuperc basalRmidb basalRmidc basaldeepb basaldeepc apobdistRb apobdistRc apobmidRb apobmidRc apobproxRb apobproxRc apobdistLb apobdistLc apobmidLb apobmidLc apobproxLb apobproxLc"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Inh_ch9I5LTSGABAa
     setfield /P5IBd/{s}/Inh_ch9I5LTSGABAa gmax {CondmaxI5LTSGABAa_P5IB}
     addmsg /P5IBd/{s}/Inh_ch9I5LTSGABAa /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Inh_ch9I5LTSGABAa VOLTAGE Vm

     ce /

end

//TCR - P5IBd AMPA synapses

str s

//Load synapse location array

str locations = "apdend13 apdend14aR apdend14bR apdend14cR apdend14dR apdend14aL apdend14bL apdend14cL apdend14dL"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9TCRAMPA
     setfield /P5IBd/{s}/Ex_ch9TCRAMPA gmax {CondmaxTCRAMPA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9TCRAMPA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9TCRAMPA VOLTAGE Vm

     ce /

end

//TCR - P5IBd NMDA synapses

str s

//Load synapse location array

str locations = "apdend13 apdend14aR apdend14bR apdend14cR apdend14dR apdend14aL apdend14bL apdend14cL apdend14dL"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9TCRNMDA
     setfield /P5IBd/{s}/Ex_ch9TCRNMDA gmax {CondmaxTCRNMDA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9TCRNMDA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9TCRNMDA VOLTAGE Vm

     ce /

end

//P23FRB - P5IBd AMPA synapses

str s

//Load synapse location array

str locations = "apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P23FRBAMPA
     setfield /P5IBd/{s}/Ex_ch9P23FRBAMPA gmax {CondmaxP23FRBAMPA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P23FRBAMPA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P23FRBAMPA VOLTAGE Vm

     ce /

end

//P23FRB - P5IBd NMDA synapses

str s

//Load synapse location array

str locations = "apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P23FRBNMDA
     setfield /P5IBd/{s}/Ex_ch9P23FRBNMDA gmax {CondmaxP23FRBNMDA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P23FRBNMDA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P23FRBNMDA VOLTAGE Vm

     ce /

end

//P5RS - P5IBd AMPA synapses

str s

//Load synapse location array

str locations = "apdend1 apdend2 apdend3 apdend4 apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12 apdend13 apobdistLa apobdistLb apobdistLc apobmidLa apobmidLb apobmidLc apobproxLa apobproxLb apobproxLc apobdistRa apobdistRb apobdistRc apobmidRa apobmidRb apobmidRc apobproxRa apobproxRb apobproxRc basalLsupera basalLsuperb basalLsuperc basalLmida basalLmidb basalLmidc basalRsupera basalRsuperb basalRsuperc basalRmida basalRmidb basalRmidc basaldeepa basaldeepb basaldeepc"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P5RSAMPA
     setfield /P5IBd/{s}/Ex_ch9P5RSAMPA gmax {CondmaxP5RSAMPA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P5RSAMPA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P5RSAMPA VOLTAGE Vm

     ce /

end

//P5RS - P5IBd NMDA synapses

str s

//Load synapse location array

str locations = "apdend1 apdend2 apdend3 apdend4 apdend5 apdend6 apdend7 apdend8 apdend9 apdend10 apdend11 apdend12 apdend13 apobdistLa apobdistLb apobdistLc apobmidLa apobmidLb apobmidLc apobproxLa apobproxLb apobproxLc apobdistRa apobdistRb apobdistRc apobmidRa apobmidRb apobmidRc apobproxRa apobproxRb apobproxRc basalLsupera basalLsuperb basalLsuperc basalLmida basalLmidb basalLmidc basalRsupera basalRsuperb basalRsuperc basalRmida basalRmidb basalRmidc basaldeepa basaldeepb basaldeepc"

foreach s ({arglist {locations}})

     ce /P5IBd/{s}

     make_Ex_ch9P5RSNMDA
     setfield /P5IBd/{s}/Ex_ch9P5RSNMDA gmax {CondmaxP5RSNMDA_P5IB}
     addmsg /P5IBd/{s}/Ex_ch9P5RSNMDA /P5IBd/{s} CHANNEL Gk Ek
     addmsg /P5IBd/{s} /P5IBd/{s}/Ex_ch9P5RSNMDA VOLTAGE Vm

     ce /

end

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