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

// Setting the axonal propagation velocity
float CABLE_VEL = 1	// scale factor = 1/(cable velocity) sec/meter

float destlim = {nRT_TCR_destlim}

/*
 * Usage :
 * volumeconnect source-path destination-path
 *		 [-relative]
 *		 [-sourcemask {box,ellipse} x1 y1 x2 y2]
 *		 [-sourcehole {box,ellipse} x1 y1 x2 y2]
 *		 [-destmask   {box,ellipse} x1 y1 x2 y2]
 *		 [-desthole   {box,ellipse} x1 y1 x2 y2]
 *		 [-probability p]
 */

echo Making connections from the nRT cells to the TCR cells.

//nRT - TCR GABAa

str s

//Load synapse location array

str locations = "proxdendNNW31 proxdendNNW32 proxdendNNW33 proxdendNNE31 proxdendNNE32 proxdendNNE33 proxdendNE31 proxdendNE32 proxdendNE33 proxdendE31 proxdendE32 proxdendE33 proxdendSE31 proxdendSE32 proxdendSE33 proxdendSSE31 proxdendSSE32 proxdendSSE33 proxdendSSW31 proxdendSSW32 proxdendSSW33 proxdendSW31 proxdendSW32 proxdendSW33 proxdendW31 proxdendW32 proxdendW33 proxdendNW31 proxdendNW32 proxdendNW33 proxdendNNW21 proxdendNNW22 proxdendNNW23 proxdendNNE21 proxdendNNE22 proxdendNNE23 proxdendNE21 proxdendNE22 proxdendNE23 proxdendE21 proxdendE22 proxdendE23 proxdendSE21 proxdendSE22 proxdendSE23 proxdendSSE21 proxdendSSE22 proxdendSSE23 proxdendSSW21 proxdendSSW22 proxdendSSW23 proxdendSW21 proxdendSW22 proxdendSW23 proxdendW21 proxdendW22 proxdendW23 proxdendNW21 proxdendNW22 proxdendNW23 proxdendNNW11 proxdendNNW12 proxdendNNW13 proxdendNNE11 proxdendNNE12 proxdendNNE13 proxdendNE11 proxdendNE12 proxdendNE13 proxdendE11 proxdendE12 proxdendE13 proxdendSE11 proxdendSE12 proxdendSE13 proxdendSSE11 proxdendSSE12 proxdendSSE13 proxdendSSW11 proxdendSSW12 proxdendSSW13 proxdendSW11 proxdendSW12 proxdendSW13 proxdendW11 proxdendW12 proxdendW13 proxdendNW11 proxdendNW12 proxdendNW13"

foreach s ({arglist {locations}})

    rvolumeconnect /nRTnet/nRT[]/soma/spk21  \
	      /TCRnet/TCR[]/{s}/Inh_ch20nRTGABAa@all	    \
	      -relative			    \
	      -sourcemask box -1 -1  -1  1  1  1  \
	      -destmask   box -{destlim} -{destlim}  -1 {destlim}  {destlim}  1   \
          -probability 0.01111*{nRT_TCR_prob}

end

echo Setting weights and delays for nRT->TCR connections.
// assigning delays using the volumedelay function

/* 
 * Usage :
 * volumedelay path 
 * [-fixed delay]
 * [-radial propagation_velocity] 
 * [-uniform range]   (not used here)
 * [-gaussian sd max] (not used here)
 * [-exp mid max]     (not used here)
 * [-absoluterandom]  (not used here)
 */

rvolumedelay /nRTnet/nRT[]/soma/spk21 -fixed  {nRT_TCR_axdelayCV} -add -gaussian {nRT_TCR_axdelaystdev} {nRT_TCR_axdelaymaxdev}

// nRT - TCR GABAa

str s

//Load synapse location array

str locations = "proxdendNNW31 proxdendNNW32 proxdendNNW33 proxdendNNE31 proxdendNNE32 proxdendNNE33 proxdendNE31 proxdendNE32 proxdendNE33 proxdendE31 proxdendE32 proxdendE33 proxdendSE31 proxdendSE32 proxdendSE33 proxdendSSE31 proxdendSSE32 proxdendSSE33 proxdendSSW31 proxdendSSW32 proxdendSSW33 proxdendSW31 proxdendSW32 proxdendSW33 proxdendW31 proxdendW32 proxdendW33 proxdendNW31 proxdendNW32 proxdendNW33 proxdendNNW21 proxdendNNW22 proxdendNNW23 proxdendNNE21 proxdendNNE22 proxdendNNE23 proxdendNE21 proxdendNE22 proxdendNE23 proxdendE21 proxdendE22 proxdendE23 proxdendSE21 proxdendSE22 proxdendSE23 proxdendSSE21 proxdendSSE22 proxdendSSE23 proxdendSSW21 proxdendSSW22 proxdendSSW23 proxdendSW21 proxdendSW22 proxdendSW23 proxdendW21 proxdendW22 proxdendW23 proxdendNW21 proxdendNW22 proxdendNW23 proxdendNNW11 proxdendNNW12 proxdendNNW13 proxdendNNE11 proxdendNNE12 proxdendNNE13 proxdendNE11 proxdendNE12 proxdendNE13 proxdendE11 proxdendE12 proxdendE13 proxdendSE11 proxdendSE12 proxdendSE13 proxdendSSE11 proxdendSSE12 proxdendSSE13 proxdendSSW11 proxdendSSW12 proxdendSSW13 proxdendSW11 proxdendSW12 proxdendSW13 proxdendW11 proxdendW12 proxdendW13 proxdendNW11 proxdendNW12 proxdendNW13"

foreach s ({arglist {locations}})

    syndelay    /TCRnet/TCR[]/{s}/Inh_ch20nRTGABAa {nRT_TCR_syndelay} -add -gaussian {nRT_TCR_syndelaystdev} {nRT_TCR_syndelaymaxdev}

end

// assigning weights using the volumeweight function

/* 
 * Usage :
 *  volumeweight sourcepath 
 *          [-fixed weight]
 *          [-decay decay_rate max_weight min_weight]
 *          [-uniform range] 
 *          [-gaussian sd max] 
 *          [-exponential mid max]
 *          [-absoluterandom]
 */

rvolumeweight /nRTnet/nRT[]/soma/spk21 -decay {nRTdecayrate} {nRTmaxwgt} {nRTminwgt}
//volumeweight /nRTnet/nRT[]/soma/spk21 -fixed 0.50




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