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
// Neocortex - netdef.g

// Define P23RSa cells

include P23RSaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P23RSacell3Dpk.p /P23RSa

//pk Steady bias current for excitability level/heterogeneity (if randomized)
str tempChanName
foreach tempChanName ({el /P23RSa/#})
    setfield {tempChanName} Em -0.07
end
setfield /P23RSa/soma inject 0.2e-9

P23RSa_synapsedefs

//setfield /P23RSa/apdend3 inject 0.0

delete /library

// Define P23RSb cells

include P23RSbprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P23RSbcell3Dpk.p /P23RSb

//pk Steady bias current for excitability level/heterogeneity (if randomized)
//str tempChanName
foreach tempChanName ({el /P23RSb/#})
    setfield {tempChanName} Em -0.07
end
setfield /P23RSb/soma inject 0.2e-9

P23RSb_synapsedefs

delete /library

// Define P23RSc cells

include P23RScprotodefs.g 

// Build the cell from a parameter file using the cell reader
readcell P23RSccell3Dpk.p /P23RSc

//pk Steady bias current for excitability level/heterogeneity (if randomized)
//str tempChanName
foreach tempChanName ({el /P23RSc/#})
    setfield {tempChanName} Em -0.07 
end
setfield /P23RSc/soma inject 0.2e-9

P23RSc_synapsedefs

delete /library

// Define P23RSd cells

include P23RSdprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P23RSdcell3Dpk.p /P23RSd

//pk Steady bias current for excitability level/heterogeneity (if randomized)
//str tempChanName
foreach tempChanName ({el /P23RSd/#})
    setfield {tempChanName} Em -0.07 
end
setfield /P23RSd/soma inject 0.2e-9

P23RSd_synapsedefs

delete /library

// Define B23FS cells

include B23FSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell B23FScell3Dpk.p /B23FS

B23FS_synapsedefs

delete /library

// Define P5IBa cells

include P5IBaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P5IBacell3Dpk.p /P5IBa

P5IBa_synapsedefs

delete /library

// Define P5IBb cells

include P5IBbprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P5IBbcell3Dpk.p /P5IBb

P5IBb_synapsedefs

delete /library

// Define P5IBc cells
    
include P5IBcprotodefs

// Build the cell from a parameter file using the cell reader
readcell P5IBccell3Dpk.p /P5IBc

P5IBc_synapsedefs

delete /library 

// Define P5IBd cells

include P5IBdprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P5IBdcell3Dpk.p /P5IBd

P5IBd_synapsedefs

delete /library

// Define B5FS cells

include B5FSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell B5FScell3Dpk.p /B5FS

B5FS_synapsedefs

delete /library

// Define P6RSa cells

include P6RSaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P6RSacell3Dpk.p /P6RSa

P6RSa_synapsedefs

delete /library

// Define P6RSb cells

include P6RSbprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P6RSbcell3Dpk.p /P6RSb

P6RSb_synapsedefs

delete /library

if ({columntype == 0})

     // Define P6RSc cells

     include P6RScprotodefs.g

     // Build the cell from a parameter file using the cell reader
     readcell P6RSccell3Dpk.p /P6RSc

     P6RSc_synapsedefs

     delete /library

     // Define P6RSd cells

     include P6RSdprotodefs.g

     // Build the cell from a parameter file using the cell reader
     readcell P6RSdcell3Dpk.p /P6RSd

     P6RSd_synapsedefs

     delete /library

end

// Define C23FS cells

include C23FSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell C23FScell3Dpk.p /C23FS

C23FS_synapsedefs

delete /library

// Define C5FS cells

include C5FSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell C5FScell3Dpk.p /C5FS

C5FS_synapsedefs

delete /library

// Define ST4RS cells

include ST4RSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell ST4RScell3Dpk.p /ST4RS

//pk Steady bias current for excitability level/heterogeneity (if randomized)
//str tempChanName
/*foreach tempChanName ({el /ST4RS/#})
   setfield {tempChanName} inject -0.005e-9
end*/
setfield /ST4RS/soma inject -0.01e-9

ST4RS_synapsedefs

delete /library

// Define I23LTS cells

include I23LTSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell I23LTScell3Dpk.p /I23LTS

I23LTS_synapsedefs

delete /library

// Define I5LTS cells

include I5LTSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell I5LTScell3Dpk.p /I5LTS

I5LTS_synapsedefs

delete /library

// Define TCR cells

if ({thalamocortical == 1})

     include TCRprotodefs.g

// Build the cell from a parameter file using the cell reader

     readcell TCRcellpk.p /TCR

     TCR_synapsedefs

     delete /library

     include nRTprotodefs.g

// Build the cell from a parameter file using the cell reader

     readcell nRTcellpk.p /nRT

     nRT_synapsedefs

     delete /library

end

// Define P23FRBa cells

include P23FRBaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P23FRBacell3Dpk.p /P23FRBa

//pk Steady bias current for excitability level/heterogeneity (if randomized)
//str tempChanName
foreach tempChanName ({el /P23FRBa/#})
    setfield {tempChanName} inject -0.01e-9
end

P23FRBa_synapsedefs

delete /library

// Define P5RSa cells

include P5RSaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell P5RSacell3Dpk.p /P5RSa

P5RSa_synapsedefs

delete /library

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