// MS-DG-CA3-CA1 network model: Rhythm generation
// DG-GC, DG-MC, DG-BC, DG-HC, CA3-PC, CA3-BC, CA3-AAC, CA3-BSC, CA3-OLM
// CA1-PC, CA1-BC, CA1-AAC, CA1-BSC, CA1-OLM, EC-L2, EC-L3, MS-GABA-180, MS-GABA-360 (using moderate cell models)
//
// Updated: 13/3/2013 by Vassilis Cutsuridis
objref pc
pc = new ParallelContext()
STARTDEL = 50 // msecs
THETA = 140 // msecs (8 Hz)
GAMMA = 25 // msecs (40 Hz)
SIMDUR = STARTDEL + (THETA * 3) // simulation duration (msecs)
//////////////////////////////////
// Step 1: Define the cell classes
//////////////////////////////////
ndggcell=100 // DG granule cells
ndgmcell=2 // DG mossy cells
ndgbcell=2 // DG basket cells
ndghcell=1 // DG HIPP cells
nca3pcell=100 // CA3 pyramidal cells
nca3aacell=1 // CA3 axo-axonic cells
nca3bcell=2 // CA3 basket cells
nca3olm=1 // CA3 OLM cells
nECL2180=100 // EC L2 180 input
nECL2360=100 // EC L2 360 input
nSEP180=10 // Medial septal cells (180)
nSEP360=10 // Medial septal cells (360)
nca1pcell=100 // CA1 pyramidal cells (20 are active according to Amaral et al. 1990)
nca1aacell=1 // CA1 axo-axonic cells
nca1bcell=2 // CA1 basket cells
nca1bscell=1 // CA1 bistratified cells
nca1olm=1 // CA1 OLM cells
nECL3180=100 // EC L3 180 input
nECL3360=100 // EC L3 360 input
ndgcell = ndggcell+ndgmcell+ndgbcell+ndghcell // total number of DG cells
nca3cell = nca3pcell+nca3aacell+nca3bcell+nca3olm // total number of CA3 cells
//nca1cell = nca1pcell+nca1bcell+nca1aacell+nca1bscell+nca1olm // total number of CA1 cells
nca1cell = nca1pcell+nca1bcell+nca1aacell+nca1bscell // total number of CA1 cells
ncell = ndgcell+nca3cell+nca1cell // total number of cells
nstim = nECL2180+nECL2360+nSEP180+nSEP360+nECL3180+nECL3360 // total number of inputs
ntot = ncell+nstim
// gid ordering:
// DG-GCs:0..ndggcell-1
// DG-MCs:ndggcell..ndggcell+ndgmcell-1
// DG-BCs:ndggcell+ndgmcell..ndggcell+ndgmcell+ndgbcell-1
// DG-HCs:ndggcell+ndgmcell+ndgbcell..ndggcell+ndgmcell+ndgbcell+ndghcell-1
// CA3-PCs:ndggcell+ndgmcell+ndgbcell+ndghcell..ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell-1
// etc
// indices of first cell of each type in list "cells"
iDGGC=0
iDGMC=ndggcell
iDGBC=ndggcell+ndgmcell
iDGHC=ndggcell+ndgmcell+ndgbcell
iCA3PC=ndggcell+ndgmcell+ndgbcell+ndghcell
iCA3AAC=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell
iCA3BC=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell
iCA3OLM=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell
iCA1PC=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm
iCA1AAC=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell
iCA1BC=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell+nca1aacell
iCA1BSC=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell+nca1aacell+nca1bcell
iECL2180=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell+nca1aacell+nca1bcell+nca1bscell
iECL2360=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell+nca1aacell+nca1bcell+nca1bscell+nECL2180
iECL3180=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell+nca1aacell+nca1bcell+nca1bscell+nECL2180+nECL2360
iECL3360=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell+nca1aacell+nca1bcell+nca1bscell+nECL2180+nECL2360+nECL3180
iSEP180=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell+nca1aacell+nca1bcell+nca1bscell+nECL2180+nECL2360+nECL3180+nECL3360
iSEP360=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nca1pcell+nca1aacell+nca1bcell+nca1bscell+nECL2180+nECL2360+nECL3180+nECL3360+nSEP180
//iCA1OLM=ndggcell+ndgmcell+ndgbcell+ndghcell+nca3pcell+nca3aacell+nca3bcell+nca3olm+nECL2180+nECL2360+nSEP180+nSEP360+nca1pcell+nca1aacell+nca1bcell+nca1bscell+nECL3180+nECL3360
//////////////////////////////////////////////////////////////
// Steps 2 and 3 are to create the cells and connect the cells
//////////////////////////////////////////////////////////////
C_P = 1 // probability of excitatory connections received by each CA1 PC
// from CA3 inputs (1 gives full connectivity)
SPATT = 4 // number of active cells per pattern
NPATT = 1 // number of stored patterns
NSTORE = 1 // number of new patterns to store
CPATT = 1 // index of cue pattern
CFRAC = 1 // fraction of active cells in cue
iPPC=1 // index of a pattern PC (1st patt in 5 patterns)
iNPPC=0 // index of a non-pattern PC (1st patt in 5 patterns)
strdef FDGCONN, FDGPATT, FDGSTORE, FCA3CONN, FCA3PATT, FCA3STORE, FCA1CONN, FCA1PATT, FCA1STORE // file name of connection weights and patterns
// (cue and EC patterns taken from FSTORE file to implement storage)
// (use same file for FPATT and FSTORE to test recall only)
FDGCONN = "Weights/DGwgtsN100S4P1.dat"
FDGPATT = "Weights/DGpattsN100S4P1.dat" // already stored patterns
FDGSTORE = "Weights/DGpattsN100S4P1.dat" // new patterns to store
FCA3PATT = "Weights/CA3pattsN100S20P1.dat" // already stored patterns
FCA3CONN = "Weights/CA3wgtsN100S20P1.dat"
FCA3STORE = "Weights/CA3pattsN100S20P1.dat" // new patterns to store
FCA1CONN = "Weights/CA1wgtsN100S20P1.dat"
FCA1PATT = "Weights/CA1pattsN100S20P1.dat" // already stored patterns
FCA1STORE = "Weights/CA1pattsN100S20P1.dat" // new patterns to store
// Simple connectivity
// From_To = # of connections
// *** DG ***
ECL2180_DGGC = nECL2180 // # of connections received by each DG GC from EC-L2-180 cells (excit)
ECL2180_DGBC = nECL2180 // # of connections received by each DG BC from EC-L2-180 cells (excit)
ECL2180_DGMC = nECL2180 // # of connections received by each DG MC from EC-L2-180 cells (excit)
ECL2360_DGGC = nECL2360 // # of connections received by each DG GC from EC-L2-360 cells (excit)
ECL2360_DGBC = nECL2360 // # of connections received by each DG BC from EC-L2-360 cells (excit)
ECL2360_DGMC = nECL2360 // # of connections received by each DG MC from EC-L2-360 cells (excit)
SEP180_DGHC = nSEP180 // # of connections received by each DG HC from SEP 180 cells (inhib)
SEP360_DGBC = nSEP360 // # of connections received by each DG BC from SEP 360 cells (inhib)
DGGC_CA3PC = ndggcell // # of connections received by each CA3 PC from DG GC cells (excit)
DGGC_CA3AAC = ndggcell // # of connections received by each CA3 AAC from DG GC cells (excit)
DGGC_CA3BC = ndggcell // # of connections received by each CA3 BC from DG GC cells (excit)
DGGC_DGBC = ndggcell // # of connections received by each BC cell from GCs (excit)
DGGC_DGHC = ndggcell // # of connections received by each HC cell from GCs (excit)
DGGC_DGMC = ndggcell // # of connections received by each MC cell from GCs (excit)
DGMC_DGGC = ndgmcell // # of connections received by each DG GC cell from DG MCs (excit)
DGMC_DGMC = 1 // # of connections received by each DG MC cell from DG MCs (excit)
DGMC_DGHC = ndgmcell // # of connections received by each DG HC cell from DG MCs (excit)
DGMC_DGBC = ndgmcell // # of connections received by each DG BC cell from DG MCs (excit)
DGHC_DGGC = ndghcell // # of connections received by each DG GC cell from DG HCs (inhib)
DGHC_DGMC = ndghcell // # of connections received by each DG MC cell from DG HCs (inhib)
DGHC_DGBC = ndghcell // # of connections received by each DG BC cell from DG HCs (inhib)
DGBC_DGGC = ndgbcell // # of connections received by each DG GC cell from DG BCs (inhib)
DGBC_DGMC = ndgbcell // # of connections received by each DG MC cell from DG BCs (inhib)
DGBC_DGBC = 1 // # of connections received by each DG BC cell from DG BCs (inhib)
// *** CA3 ***
ECL2180_CA3PC = nECL2180 // # of connections received by each CA3 PC from EC-L2-180 cells (excit)
ECL2180_CA3AAC = nECL2180 // # of connections received by each CA3 AAC from EC-L2-180 cells (excit)
ECL2180_CA3BC = nECL2180 // # of connections received by each CA3 BC from EC-L2-180 cells (excit)
ECL2360_CA3PC = nECL2360 // # of connections received by each CA3 PC from EC-L2-360 cells (excit)
ECL2360_CA3AAC = nECL2360 // # of connections received by each CA3 AAC from EC-L2-360 cells (excit)
ECL2360_CA3BC = nECL2360 // # of connections received by each CA3 BC from EC-L2-360 cells (excit)
SEP180_CA3OLM = nSEP180 // # of connections received by each CA3 OLM from SEP 180 cells (inhib)
SEP360_CA3AAC = nSEP360 // # of connections received by each CA3 AAC from SEP 360 cells (inhib)
SEP180_CA3BC = nSEP180 // # of connections received by each CA3 BC from SEP 180 cells (inhib)
CA3PC_CA3PC = 1 // # of connections received by each CA3-PC from other CA3-PCs (excit)
CA3PC_CA3BC = nca3pcell // # of connections received by each CA3-BC from CA3-PCs (excit)
CA3PC_CA3AAC = nca3pcell // # of connections received by each CA3-BSC from CA3-PCs (excit)
CA3PC_CA3OLM = nca3pcell // # of connections received by each CA3-OLM from CA3-PCs (excit)
CA3PC_CA1PC = nca3pcell // # of connections received by each CA1-PC from CA3-PCs (excit)
CA3PC_CA1BC = nca3pcell // # of connections received by each CA1-BC from CA3-PCs (excit)
CA3PC_CA1AAC = nca3pcell // # of connections received by each CA1-AAC from CA3-PCs (excit)
CA3PC_CA1BSC = nca3pcell // # of connections received by each CA1-BSC from CA3-PCs (excit)
CA3PC_DGMC = nca3pcell // # of connections received by each DG MC from CA3-PCs (excit)
CA3BC_CA3PC = nca3bcell // # of connections received by each CA3 PC from CA3 BCs (inhib)
CA3BC_CA3OLM = nca3bcell // # of connections received by each CA3 OLM from CA3 BCs (inhib)
CA3BC_CA3BC = 1 // # of connections received by each CA3 BC from other CA3 BCs (inhib)
CA3AAC_CA3PC = nca3aacell // # of connections received by each CA3 PC from CA3 AACs (inhib)
CA3OLM_CA3PC = nca3olm // # of connections received by each CA3 PC from CA3 OLM cells (inhib)
CA3OLM_CA3BC = nca3olm // # of connections received by each CA3 BC from CA3 OLM cells (inhib)
// *** CA1 ***
ECL3180_CA1PC = nECL3180 // # of connections received by each CA1 PC from EC-L3-180 cells (excit)
ECL3180_CA1BC = nECL3180 // # of connections received by each CA1 BC from EC-L3-180 cells (excit)
ECL3180_CA1AAC = nECL3180 // # of connections received by each CA1 AAC from EC-L3-180 cells (excit)
ECL3360_CA1PC = nECL3360 // # of connections received by each CA1 PC from EC-L3-360 cells (excit)
ECL3360_CA1BC = nECL3360 // # of connections received by each CA1 BC from EC-L3-360 cells (excit)
ECL3360_CA1AAC = nECL3360 // # of connections received by each CA1 AAC from EC-L3-360 cells (excit)
SEP360_CA1BSC = nSEP360 // # of connections received by each CA1 BSC from SEP 360 cells (inhib)
SEP360_CA1OLM = nSEP360 // # of connections received by each CA1 OLM from SEP 360 cells (inhib)
SEP180_CA1AAC = nSEP180 // # of connections received by each CA1 AAC from SEP 180 cells (inhib)
SEP180_CA1BC = nSEP180 // # of connections received by each CA1 BC from SEP 180 cells (inhib)
//SEP360_CA1AAC = nSEP360 // # of connections received by each CA1 AAC from SEP 360 cells (inhib)
//SEP360_CA1BC = nSEP360 // # of connections received by each CA1 BC from SEP 360 cells (inhib)
CA1PC_CA1PC = 1 // # of connections received by each CA1-PC from other CA1-PCs (excit)
CA1PC_CA1BC = nca1pcell // # of connections received by each CA1-BC from CA1-PCs (excit)
CA1PC_CA1BSC = nca1pcell // # of connections received by each CA1-BSC from CA1-PCs (excit)
CA1PC_CA1AAC = nca1pcell // # of connections received by each CA1-AAC from CA1-PCs (excit)
CA1PC_CA1OLM = nca1pcell // # of connections received by each CA1-OLM from CA1-PCs (excit)
CA1BC_CA1PC = nca1bcell // # of connections received by each CA1 PC from CA1 BCs (inhib)
CA1BC_CA1BSC = nca1bcell // # of connections received by each CA1 BSC from CA1 BCs (inhib)
CA1BC_CA1OLM = nca1bcell // # of connections received by each CA1 OLM from CA1 BCs (inhib)
CA1BC_CA1BC = 1 // # of connections received by each CA1 BC from other CA1 BCs (inhib)
CA1AAC_CA1PC = nca1aacell // # of connections received by each CA1 PC from CA1 AACs (inhib)
CA1BSC_CA1PC = nca1bscell // # of connections received by each CA1 PC from CA1 BSCs (inhib)
CA1BSC_CA1BC = nca1bscell // # of connections received by each CA1 BC from CA1 BSCs (inhib)
CA1OLM_CA1PC = nca1olm // # of connections received by each CA1 PC from CA1 OLM cells (inhib)
CA1OLM_CA1BC = nca1olm // # of connections received by each CA1 BC from CA1 OLM cells (inhib)
// Synaptic weights and delays
// **** DG ****
ECL2180DGGCCHWGT = 0.005 //0.0006 // EC-L2-180 weight (high) to DG-GC
ECL2180DGGCCLWGT = 0.0001 // EC-L2-180 weight (low) to DG-GC
ECL2180DGGCDEL = 1 // EC-L2-180 delay to DG-GC
ECL2180DGBCWGT = 0.002 // EC-L2-180 weight to DG-BC
ECL2180DGBCDEL = 1 // EC-L2-180 delay to DG-BC
ECL2180DGMCWGT = 0.004 / nECL2180 // EC-L2-180 weight to DG-MC
ECL2180DGMCDEL = 1 // EC-L2-180 delay to DG-MC
ECL2360DGGCCHWGT = 0.0015 //0.00025 // EC-L2-360 weight (high) to DG-GC
ECL2360DGGCCLWGT = 0.00008 // EC-L2-360 weight (low) to DG-GC
ECL2360DGGCDEL = 1 // EC-L2-360 delay to DG-GC
ECL2360DGBCWGT = 0.00008 // EC-L2-360 weight to DG-BC
ECL2360DGBCDEL = 1 // EC-L2-360 delay to DG-BC
ECL2360DGMCWGT = 0.0015 / nECL2360 // EC-L2-360 weight to DG-MC
ECL2360DGMCDEL = 1 // EC-L2-360 delay to DG-MC
SEP1802DGHCWGT = 0.06 / nSEP180 // SEP weight to DG-HCs
SEP1802DGHCDEL = 1 // SEP delay to DG-HCs
SEP3602DGBCWGT = 0.3 // SEP weight to DG-BCs
SEP3602DGBCDEL = 1 // SEP delay to DG-BCs
DGMC2DGGCw = 0.001 * 2 / ndgmcell //0.0006 * 2 / ndgmcell
DGMC2DGGCd = 1
DGMC2DGMCw = 0.001 * 2 / ndgmcell
DGMC2DGMCd = 1
DGMC2DGBCw = 0.0 //0.001 * 2 / ndgmcell
DGMC2DGBCd = 1
DGMC2DGHCw = 0.001 * 2 / ndgmcell
DGMC2DGHCd = 1
DGHC2DGGCw = 0.25
DGHC2DGGCd = 1
DGHC2DGMCw = 0.0001 / ndghcell
DGHC2DGMCd = 1
DGHC2DGBCw = 0.005 / ndghcell
DGHC2DGBCd = 1
DGBC2DGGCw = 0.02
DGBC2DGGCd = 1
DGBC2DGMCw = 0.0095 * 2 / ndgbcell
DGBC2DGMCd = 1
DGBC2DGBCw = 0.0005 * 2 / ndgbcell
DGBC2DGBCd = 1
DGGC2DGMCw = 0.0005 * 3 / ndggcell
DGGC2DGMCd = 1
DGGC2DGBCw = 0.001 * 3 / ndggcell
DGGC2DGBCd = 1
DGGC2DGHCw = 0.09
DGGC2DGHCd = 1
DGGC2CA3PCCHw = 0.2 * 3 / ndggcell
DGGC2CA3PCCLw = 0.005 * 3 / ndggcell
DGGC2CA3PCd = 1
DGGC2CA3AACw = 0.007 * 3 / ndggcell
DGGC2CA3AACd = 1
DGGC2CA3BCw = 0.08 * 3 / ndggcell
DGGC2CA3BCd = 1
// **** CA3 ****
ECL2180CA3PCWGT = 0.00006 // EC-L2-180 weight to CA3-PC
ECL2180CA3PCDEL = 1 // EC-L2-180 delay to CA3-PC
ECL2180CA3AACWGT = 0.0004 // EC-L2-180 weight to CA3-AAC
ECL2180CA3AACDEL = 1 // EC-L2-180 delay to CA3-AAC
ECL2180CA3BCWGT = 0.00008 // EC-L2-180 weight to CA3-BC
ECL2180CA3BCDEL = 1 // EC-L2-180 delay to CA3-BC
ECL2360CA3PCWGT = 0.00002 // EC-L2-360 weight to CA3-PC
ECL2360CA3PCDEL = 1 // EC-L2-360 delay to CA3-PC
ECL2360CA3AACWGT = 0.00001 // EC-L2-360 weight to CA3-AAC
ECL2360CA3AACDEL = 1 // EC-L2-360 delay to CA3-AAC
ECL2360CA3BCWGT = 0.00024 // EC-L2-360 weight to CA3-BC
ECL2360CA3BCDEL = 1 // EC-L2-360 delay to CA3-BC
SEP1802CA3BCWGT = 0.05 // SEP weight to CA3-BC
SEP1802CA3BCDEL = 1 // SEP delay to CA3-BC
SEP1802CA3OLMWGT = 0.007 // SEP weight to CA3-OLM
SEP1802CA3OLMDEL = 1 // SEP delay to CA3-OLM
SEP3602CA3AACWGT = 2.9 // SEP weight to CA3-AAC
SEP3602CA3AACDEL = 1 // SEP delay to CA3-AAC
CA3PC2DGMCw = 0.003 * 3 / nca3pcell //0.0009 * 3 / nca3pcell
CA3PC2DGMCd = 1
CA3PC2CA1PCCHw = 0.00025 //0.001
CA3PC2CA1PCCLw = 0.00007
CA3PC2CA1PCCHwn = 0.00012
CA3PC2CA1PCd = 1
CA3PC2CA1AACw = 0.0 //0.006
CA3PC2CA1AACd = 1
CA3PC2CA1BCw = 0.0 //0.006
CA3PC2CA1BCd = 1
CA3PC2CA1BSCw = 0.6
CA3PC2CA1BSCd = 1
CA3PC2CA3PCw = 0.0005 * 3 / nca3pcell
CA3PC2CA3PCd = 1
CA3PC2CA3AACw = 0.0 //0.00005 * 3 / nca3pcell
CA3PC2CA3AACd = 1
CA3PC2CA3BCw = 0.0 //0.00005 * 3 / nca3pcell
CA3PC2CA3BCd = 1
CA3PC2CA3OLMw = 0.0001
CA3PC2CA3OLMd = 1
CA3BC2CA3PCw = 0.5 * 2 / nca3bcell
CA3BC2CA3PCd = 1
CA3BC2CA3BCw = 0.005 * 2 / nca3bcell
CA3BC2CA3BCd = 1
CA3BC2CA3OLMw = 0.0 * 2 / nca3bcell
CA3BC2CA3OLMd = 1
CA3AAC2CA3PCw = 0.9 / nca3aacell
CA3AAC2CA3PCd = 1
CA3OLM2CA3PCw = 2.8 / nca3olm
CA3OLM2CA3PCgbw = 0.0 //0.0004 / nca3olm
CA3OLM2CA3PCd = 1
CA3OLM2CA3BCw = 0.0 //0.01 / nca3olm
CA3OLM2CA3BCd = 1
// **** CA1 ****
ECL3180CA1PCCHWGT = 0.064 // EC-L3-180 weight to CA1-PC
ECL3180CA1PCCLWGT = 0.00001 // EC-L3-180 weight to CA1-PC
ECL3180CA1PCDEL = 1 // EC-L3-180 delay to CA1-PC
ECL3180CA1AACWGT = 0.00014 // EC-L3-180 weight to CA1-AAC
ECL3180CA1AACDEL = 1 // EC-L3-180 delay to CA1-AAC
ECL3180CA1BCWGT = 0.00014 // EC-L3-180 weight to CA1-BC
ECL3180CA1BCDEL = 1 // EC-L3-180 delay to CA1-BC
ECL3360CA1PCCHWGT = 0.008 // EC-L3-360 weight to CA1-PC
ECL3360CA1PCCLWGT = 0.00001 // EC-L3-360 weight to CA1-PC
ECL3360CA1PCDEL = 1 // EC-L3-360 delay to CA1-PC
ECL3360CA1AACWGT = 0.00052 // EC-L3-360 weight to CA1-AAC
ECL3360CA1AACDEL = 1 // EC-L3-360 delay to CA1-AAC
ECL3360CA1BCWGT = 0.00052 // EC-L3-360 weight to CA1-BC
ECL3360CA1BCDEL = 1 // EC-L3-360 delay to CA1-BC
SEP1802CA1AACWGT = 0.8 // SEP weight to CA1-AAC
SEP1802CA1AACDEL = 1 // SEP delay to CA1-AAC
SEP1802CA1BCWGT = 0.8 // SEP weight to CA1-BC
SEP1802CA1BCDEL = 1 // SEP delay to CA1-BC
SEP3602CA1BSCWGT = 0.3 // SEP weight to CA1-BSC
SEP3602CA1BSCDEL = 1 // SEP delay to CA1-BSC
SEP3602CA1OLMWGT = 0.3 // SEP weight to CA1-OLM
SEP3602CA1OLMDEL = 1 // SEP delay to CA1-OLM
CA1PC2CA1PCw = 0.0001 * 3 / nca1pcell
CA1PC2CA1PCd = 1
CA1PC2CA1AACw = 0.0005 * 3 / nca1pcell
CA1PC2CA1AACd = 1
CA1PC2CA1BCw = 0.0005 * 3 / nca1pcell
CA1PC2CA1BCd = 1
CA1PC2CA1BSCw = 0.0005 * 3 / nca1pcell
CA1PC2CA1BSCd = 1
CA1PC2CA1OLMw = 0.005 * 3 / nca1pcell
CA1PC2CA1OLMd = 1
CA1BC2CA1PCw = 0.09
CA1BC2CA1PCd = 1
CA1BC2CA1BCw = 0.01
CA1BC2CA1BCd = 1
CA1BC2CA1BSCw = 0.08
CA1BC2CA1BSCd = 1
CA1BC2CA1OLMw = 0.0 * 2 / nca1bcell
CA1BC2CA1OLMd = 1
CA1AAC2CA1PCw = 0.09
CA1AAC2CA1PCd = 1
CA1BSC2CA1PCw = 0.2
CA1BSC2CA1PCd = 1
CA1BSC2CA1PCgbw = 0.08 / nca1bscell
CA1BSC2CA1PCgbd = 1
CA1BSC2CA1BCw = 0.06 / nca1bscell
CA1BSC2CA1BCd = 1
CA1OLM2CA1PCw = 0.04
CA1OLM2CA1PCgbw = 0.0 //0.0004 / nca1olm
CA1OLM2CA1PCd = 1
CA1OLM2CA1BCw = 0.0 //0.01 / nca1olm
CA1OLM2CA1BCd = 1
// Synapse indices
// onto DG GCs
E_EC_GC = 0 // EC AMPA to gcdend1[3] (2 of)
E_MC_GC = 2 // MC AMPA to gcdend1[1] (2 of)
I_HC_GC = 4 // HIPP GABA-A to gcdend1[3] (2 of)
I_BC_GC = 6 // BC GABA-A to GC soma
EM_EC_GC = 9 // EC-L2 AMPA modifiable (STDP) to DG GC dist dendrites (2 of)
// onto DG MCs
E_EC_MC = 0 // EC AMPA to mcdend1[3] (4 of)
E_GC_MC = 4 // GC AMPA to mcdend1[0] (4 of)
E_MC_MC = 8 // MC AMPA to mcdend1[0] (4 of)
I_BC_MC = 12 // BC GABA-A to MC soma
I_HC_MC = 13 // HIPP GABA-A to mcdend1[2] (4 of)
E_CA3PC_MC = 17 // CA3 PC AMPA to mcdend1[0] (4 of)
// onto DG BCs
E_EC_BC = 0 // EC AMPA to bcdend1[3] (2 of)
E_GC_BC = 2 // GC AMPA to bcdend1[0] (4 of)
E_MC_BC = 6 // MC AMPA to bcdend1[1] (2 of)
I_BC_BC = 8 // BC GABA-A to bddend1[1] (2 of)
I_HC_BC = 10 // HIPP GABA-A to bcdend1[3] (2 of)
I_SEP180_BC = 12 // SEP180 GABA-A to BC soma
I_SEP360_BC = 12 // SEP360 GABA-A to BC soma
// onto DG HCs
E_GC_HC = 0 // GC AMPA to hcdend1[0] (4 of)
E_MC_HC = 4 // MC AMPA to hcdend1[1] (4 of)
I_SEP180_HC = 8 // SEP180 GABA-A to HC soma
I_SEP360_HC = 8 // SEP360 GABA-A to HC soma
// onto CA3 PCs
E_ECL2_CA3PC = 0 // EC AMPA to CA3 PC LM dendrites (8 of)
E_GC_CA3PC = 8 // GC AMPA to CA3 PC SR prox dendrites (4 of)
EN_GC_CA3PC = 12 // GC NMDA to CA3 PC SR prox dendrites (4 of)
E_CA3PC_CA3PC = 16 // CA3 PC recurrent AMPA to CA3 PC SR med dendrites (4 of)
I_BC_CA3PC = 20 // BC GABA-A to CA3 PC soma
I_AAC_CA3PC = 21 // AAC GABA-A to CA3 PC axon
I_OLM_CA3PC = 22 // OLM GABA-A to CA3 PC LM dendrites (8 of)
IB_OLM_CA3PC = 30 // OLM GABA-B to CA3 PC LM dendrites (8 of)
// onto CA1 PCs
//E_ECL3_CA1PC = 0 // EC AMPA to CA1 PC LM dendrites (2 of) *** DON'T USE THIS (USE INSTEAD FROM 26 ONWARDS) ***
//E_CA3PC_CA1PC = 2 // CA3 AMPA to CA1 PC SR med dendrites *** DON'T USE THIS (USE INSTEAD FROM 44 ONWARDS) ***
//EN_CA3PC_CA1PC = 3 // CA3 NMDA to CA1 PC SR med dendrites *** DON'T USE THIS (USE INSTEAD FROM 53 ONWARDS) ***
E_CA1PC_CA1PC = 4 // CA1 PC recurrent AMPA to CA1 PC SR med dendrites
I_BC_CA1PC = 5 // BC GABA-A to CA1 PC soma
I_AAC_CA1PC = 6 // AAC GABA-A to CA1 PC axon
I_OLM_CA1PC = 7 // OLM GABA-A to CA1 PC LM dendrites (2 of)
IB_OLM_CA1PC = 9 // OLM GABA-B to CA1 PC LM dendrites (2 of)
I_BSC_CA1PC = 11 // BSC GABA-A to CA1 PC SR med dendrites (6 of GABA-A)
IB_BSC_CA1PC = 17 // BSC GABA-B to CA1 PC SR med dendrites (6 of GABA-B)
E_ECL3_CA1PC = 23 // EC AMPA to CA1 PC LM dendrites (18 of)
E_CA3PC_CA1PC = 41 // CA3 AMPA to CA1 PC SR med dendrites (9 of)
EN_CA3PC_CA1PC = 50 // CA3 NMDA to CA1 PC SR med dendrites (5 of)
EN_ECL3_CA1PC = 55 // EC NMDA to CA1 PC LM thick dendrites (2 of)
// onto CA3/CA1 INs (CA3/CA1 BC, CA3/CA1 AAC, CA3/CA1 BSC)
EI_EC = 0 // EC AMPA excit (2 of; not onto BSC)
EI_CA3 = 2 // CA3 AMPA excit (4 of)
EI_PC = 6 // CA3/CA1 PC AMPA excit (2 of)
II_SAME = 8 // inhib from neighbouring INs (BC->BC; BSC->BSC)
II_OPP = 9 // inhib from other INs (BSC->BC; BC->BSC)
II_SEP = 10 // GABA-A inhib from septum (2 of)
IIB_SEP = 12 // GABA_B inhib from septum (2 of)
EI_GC = 14 // DG GC AMPA excit (2 of)
// onto CA3/CA1 INs (CA3/CA1 OLM)
EO_PC = 0 // CA3/CA1 PC AMPA excit to OLM dendrites (2 of)
IO_IN = 2 // Septal GABA-A to OLM soma
IOB_IN = 3 // Septal GABA-B to OLM soma
// Background excitation (theta spiking)
ENUM = 4 // number of spikes
ESTART = 0 // time of first spike
EINT = 10 // spike ISI
ENOISE = 1 // ISI noise
EWGT = 0.001 // excitatory weights (AMPA)
ENWGT = 0.002 // excitatory weights (NMDA)
EDEL = 1 // delay (msecs)
// EC-L2-180 excitation
ECL2180NUM = 1000 // number of EC-L2-180 spikes
ECL2180START = STARTDEL // time of first EC-L2-180 spike
ECL2180INT = THETA // EC-L2-180 spike ISI
ECL2180NOISE = 0.08 // EC-L2-180 ISI noise
//ECL2180NOISE = 0.0 // EC-L2-180 ISI noise
ECL2180BINT = THETA // EC-L2-180 interburst interval
ECL2180BLEN = THETA / 2 // EC-L2-180 burst length
// EC-L2-360 excitation
ECL2360NUM = 1000 // number of EC-L2-360 spikes
ECL2360START = STARTDEL + (THETA / 2) // time of first EC-L2-360 spike
ECL2360INT = THETA // EC-L2-360 spike ISI
ECL2360NOISE = 0.08 // EC-L2-360 ISI noise
//ECL2360NOISE = 0.0 // EC-L2-360 ISI noise
ECL2360BINT = THETA // EC-L2-360 interburst interval
ECL2360BLEN = THETA / 2 // EC-L2-360 burst length
// EC-L3-180 excitation
ECL3180NUM = 1000 // number of EC-L3-180 spikes
ECL3180START = STARTDEL // time of first EC-L3-180 spike
ECL3180INT = THETA // EC-L3-180 spike ISI (during burst)
//ECL3180NOISE = 0.0 // EC-L3-180 ISI noise
ECL3180NOISE = 0.08 // EC-L3-180 ISI noise
ECL3180BINT = THETA // EC-L3-180 interburst interval
ECL3180BLEN = THETA / 2 // EC-L3-180 burst length
// EC-L3-360 excitation
ECL3360NUM = 1000 // number of EC-L3-360 spikes
ECL3360START = STARTDEL + (THETA / 2) // time of first EC-L3-360 spike
ECL3360INT = THETA // EC-L3-360 spike ISI (during burst)
//ECL3360NOISE = 0.0 // EC-L3-360 ISI noise
ECL3360NOISE = 0.08 // EC-L3-360 ISI noise
ECL3360BINT = THETA // EC-L3-360 interburst interval
ECL3360BLEN = THETA / 2 // EC-L3-360 burst length
// Septal 180 inhibition
SEP180NUM = 1000 // number of SEP spikes
SEP180START = STARTDEL // time of first SEP 180 spike
SEP180INT = THETA // SEP spike ISI (during burst)
//SEP180NOISE = 0.0 // SEP ISI noise
SEP180NOISE = 0.08 // SEP ISI noise
SEP180BINT = THETA / 2 // SEP interburst interval
SEP180BLEN = THETA / 2 // SEP burst length
// Septal 360 inhibition
SEP360NUM = 1000 // number of SEP spikes
SEP360START = STARTDEL + (THETA / 2) // time of first SEP spike
SEP360INT = THETA // SEP spike ISI (during burst)
//SEP360NOISE = 0.0 // SEP ISI noise
SEP360NOISE = 0.08 // SEP ISI noise
SEP360BINT = THETA / 2 // SEP interburst interval
SEP360BLEN = THETA / 2 // SEP burst length
// EC excitation
ECPATT = 1 // index of output pattern
connect_random_low_start_ = 1 // low seed for mcell_ran4_init()
objref cells, nclist, ncslist, ncelist, ncilist // cells will be a List that holds
// all instances of network cells that exist on this host
// nclist will hold all NetCon instances that exist on this host
// and connect network spike sources to targets on this host (nclist)
// ncslist holds NetConns from input spike sources (NetStims)
objref ranlist // for RandomStreams on this host
objref stims, stimlist, cuelist, cuelistECL2180, cuelistECL2360, cuelistECL3180, cuelistECL3360, ECL2list, ECL2180list, ECL2360list, ECL3180list, ECL3360list, EClist
objref gidvec // to associate gid and position in cells List
// useful for setting up connections and reporting connectivity
// Make the network
proc mknet() {
print "Make cells..."
mkcells() // create the cells
print "Make inputs..."
mkinputs() // create the CA3, EC and septal inputs
print "Connect cells..."
mcell_ran4_init(connect_random_low_start_)
nclist = new List()
print "**** DG ****"
print " EC..."
// EC-L2-180 to DG-GC
//connectcells(ndggcell, iDGGC, nECL2180, iECL2180, ECL2180_DGGC, E_EC_GC, E_EC_GC+1, ECL2180DGGCDEL, ECL2180DGGCCHWGT)
//connectcells(ndggcell, iDGGC, nECL2180, iECL2180, ECL2180_DGGC, EM_EC_GC, EM_EC_GC+1, ECL2180DGGCDEL, ECL2180DGGCWGT)
// EC-L2-180 to DG-BC
connectcells(ndgbcell, iDGBC, nECL2180, iECL2180, ECL2180_DGBC, E_EC_BC, E_EC_BC+1, ECL2180DGBCDEL, ECL2180DGBCWGT)
// EC-L2-180 to DG-MC
//connectcells(ndgmcell, iDGMC, nECL2180, iECL2180, ECL2180_DGMC, E_EC_MC, E_EC_MC+3, ECL2180DGMCDEL, ECL2180DGMCWGT)
// EC-L2-360 to DG-GC
//connectcells(ndggcell, iDGGC, nECL2360, iECL2360, ECL2360_DGGC, E_EC_GC, E_EC_GC+1, ECL2360DGGCDEL, ECL2360DGGCCHWGT)
//connectcells(ndggcell, iDGGC, nECL2360, iECL2360, ECL2360_DGGC, EM_EC_GC, EM_EC_GC+1, ECL2360DGGCDEL, ECL2360DGGCWGT)
// EC-L2-360 to DG-BC
connectcells(ndgbcell, iDGBC, nECL2360, iECL2360, ECL2360_DGBC, E_EC_BC, E_EC_BC+1, ECL2360DGBCDEL, ECL2360DGBCWGT)
// EC-L2-360 to DG-MC
//connectcells(ndgmcell, iDGMC, nECL2360, iECL2360, ECL2360_DGMC, E_EC_MC, E_EC_MC+3, ECL2360DGMCDEL, ECL2360DGMCWGT)
print " SEP180..."
// SEP180 to DG-HC
connectcells(ndghcell, iDGHC, nSEP180, iSEP180, SEP180_DGHC, I_SEP180_HC, I_SEP180_HC, SEP1802DGHCDEL, SEP1802DGHCWGT)
print " SEP360..."
// SEP360 to DG-BC
connectcells(ndgbcell, iDGBC, nSEP360, iSEP360, SEP360_DGBC, I_SEP360_BC, I_SEP360_BC, SEP3602DGBCDEL, SEP3602DGBCWGT)
print " GC..."
//DG-GC to DG-BC
connectcells(ndgbcell, iDGBC, ndggcell, iDGGC, DGGC_DGBC, E_GC_BC, E_GC_BC+3, DGGC2DGBCd, DGGC2DGBCw)
//DG-GC to DG-MC
connectcells(ndgmcell, iDGMC, ndggcell, iDGGC, DGGC_DGMC, E_GC_MC, E_GC_MC+3, DGGC2DGMCd, DGGC2DGMCw)
//DG-GC to DG-HC
connectcells(ndghcell, iDGHC, ndggcell, iDGGC, DGGC_DGHC, E_GC_HC, E_GC_HC+3, DGGC2DGHCd, DGGC2DGHCw)
print " INs..."
//DG-MC to DG-GC
connectcells(ndggcell, iDGGC, ndgmcell, iDGMC, DGMC_DGGC, E_MC_GC, E_MC_GC+1, DGMC2DGGCd, DGMC2DGGCw)
//DG-MC to DG-BC
connectcells(ndgbcell, iDGBC, ndgmcell, iDGMC, DGMC_DGBC, E_MC_BC, E_MC_BC+1, DGMC2DGBCd, DGMC2DGBCw)
//DG-MC to DG-MC
connectcells(ndgmcell, iDGMC, ndgmcell, iDGMC, DGMC_DGMC, E_MC_MC, E_MC_MC+3, DGMC2DGMCd, DGMC2DGMCw)
//DG-MC to DG-HC
connectcells(ndghcell, iDGHC, ndgmcell, iDGMC, DGMC_DGHC, E_MC_HC, E_MC_HC+3, DGMC2DGHCd, DGMC2DGHCw)
//DG-BC to DG-GC
connectcells(ndggcell, iDGGC, ndgbcell, iDGBC, DGBC_DGGC, I_BC_GC, I_BC_GC, DGBC2DGGCd, DGBC2DGGCw)
//DG-BC to DG-BC
connectcells(ndgbcell, iDGBC, ndgbcell, iDGBC, DGBC_DGBC, I_BC_BC, I_BC_BC+1, DGBC2DGBCd, DGBC2DGBCw)
//DG-BC to DG-MC
connectcells(ndgmcell, iDGMC, ndgbcell, iDGBC, DGBC_DGMC, I_BC_MC, I_BC_MC, DGBC2DGMCd, DGBC2DGMCw)
//DG-HC to DG-GC
connectcells(ndggcell, iDGGC, ndghcell, iDGHC, DGHC_DGGC, I_HC_GC, I_HC_GC+1, DGHC2DGGCd, DGHC2DGGCw)
//DG-HC to DG-BC
connectcells(ndgbcell, iDGBC, ndghcell, iDGHC, DGHC_DGBC, I_HC_BC, I_HC_BC+1, DGHC2DGBCd, DGHC2DGBCw)
//DG-HC to DG-MC
connectcells(ndgmcell, iDGMC, ndghcell, iDGHC, DGHC_DGMC, I_HC_MC, I_HC_MC+3, DGHC2DGMCd, DGHC2DGMCw)
print "**** CA3 ****"
print " EC..."
// EC-L2-180 to CA3-PC
connectcells(nca3pcell, iCA3PC, nECL2180, iECL2180, ECL2180_CA3PC, E_ECL2_CA3PC, E_ECL2_CA3PC+7, ECL2180CA3PCDEL, ECL2180CA3PCWGT)
//connectcells(nca3pcell, iCA3PC, nECL2180, iECL2180, ECL2180_CA3PC, EM_ECL2_CA3PC, EM_ECL2_CA3PC+7, ECL2180CA3PCDEL, ECL2180CA3PCWGT)
// EC-L2-180 to CA3-AAC
connectcells(nca3aacell, iCA3AAC, nECL2180, iECL2180, ECL2180_CA3AAC, EI_EC, EI_EC+1, ECL2180CA3AACDEL, ECL2180CA3AACWGT)
// EC-L2-180 to CA3-BC
connectcells(nca3bcell, iCA3BC, nECL2180, iECL2180, ECL2180_CA3BC, EI_EC, EI_EC+1, ECL2180CA3BCDEL, ECL2180CA3BCWGT)
// EC-L2-360 to CA3-PC
connectcells(nca3pcell, iCA3PC, nECL2360, iECL2360, ECL2360_CA3PC, E_ECL2_CA3PC, E_ECL2_CA3PC+7, ECL2360CA3PCDEL, ECL2360CA3PCWGT)
//connectcells(nca3pcell, iCA3PC, nECL2360, iECL2360, ECL2360_CA3PC, EM_ECL2_CA3PC, EM_ECL2_CA3PC+7, ECL2360CA3PCDEL, ECL2360CA3PCWGT)
// EC-L2-360 to CA3-AAC
connectcells(nca3aacell, iCA3AAC, nECL2360, iECL2360, ECL2360_CA3AAC, EI_EC, EI_EC+1, ECL2360CA3AACDEL, ECL2360CA3AACWGT)
// EC-L2-360 to CA3-BC
connectcells(nca3bcell, iCA3BC, nECL2360, iECL2360, ECL2360_CA3BC, EI_EC, EI_EC+1, ECL2360CA3BCDEL, ECL2360CA3BCWGT)
print " SEP180..."
// SEP180 to CA3-BC
connectcells(nca3bcell, iCA3BC, nSEP180, iSEP180, SEP180_CA3BC, II_SEP, II_SEP+1, SEP1802CA3BCDEL, SEP1802CA3BCWGT)
// SEP180 to CA3-OLM
connectcells(nca3olm, iCA3OLM, nSEP180, iSEP180, SEP180_CA3OLM, IO_IN, IO_IN, SEP1802CA3OLMDEL, SEP1802CA3OLMWGT)
print " SEP360..."
// SEP360 to CA3-AAC
connectcells(nca3aacell, iCA3AAC, nSEP360, iSEP360, SEP360_CA3AAC, II_SEP, II_SEP+1, SEP3602CA3AACDEL, SEP3602CA3AACWGT)
print " GC..."
// DG-GC to CA3-PC
connectDGGCtoCA3PC(nca3pcell, iCA3PC, ndggcell, iDGGC, DGGC_CA3PC, E_GC_CA3PC, E_GC_CA3PC+3, DGGC2CA3PCd, DGGC2CA3PCCHw, ECPATT, NPATT) // AMPA
connectDGGCtoCA3PC(nca3pcell, iCA3PC, ndggcell, iDGGC, DGGC_CA3PC, EN_GC_CA3PC, EN_GC_CA3PC+3, DGGC2CA3PCd, DGGC2CA3PCCHw, ECPATT, NPATT) // NMDA
//connectDGGC2CA3PC(FDGPATT, FCA3PATT, ECPATT, NPATT, E_GC_CA3PC, E_GC_CA3PC+3)
//connectcells(nca3pcell, iCA3PC, ndggcell, iDGGC, DGGC_CA3PC, E_GC_CA3PC, E_GC_CA3PC+3, DGGC2CA3PCd, DGGC2CA3PCw)
//connectcells(nca3pcell, iCA3PC, ndggcell, iDGGC, DGGC_CA3PC, EM_GC_CA3PC, EM_GC_CA3PC+3, DGGC2CA3PCd, DGGC2CA3PCw)
// DG-GC to CA3-AAC
connectcells(nca3aacell, iCA3AAC, ndggcell, iDGGC, DGGC_CA3AAC, EI_GC, EI_GC+1, DGGC2CA3AACd, DGGC2CA3AACw)
// DG-GC to CA3-BC
connectcells(nca3bcell, iCA3BC, ndggcell, iDGGC, DGGC_CA3BC, EI_GC, EI_GC+1, DGGC2CA3BCd, DGGC2CA3BCw)
print " CA3-PC..."
// CA3-PC to CA3-PC
connectcells(nca3pcell, iCA3PC, nca3pcell, iCA3PC, CA3PC_CA3PC, E_CA3PC_CA3PC, E_CA3PC_CA3PC, CA3PC2CA3PCd, CA3PC2CA3PCw)
//connectCA3pcells(nca3pcell, iCA3PC, nca3pcell, iCA3PC, CA3PC_CA3PC, E_CA3PC_CA3PC, E_CA3PC_CA3PC, CA3PC2CA3PCd, CA3PC2CA3PCw)
// CA3-PC to CA3-BC
connectcells(nca3bcell, iCA3BC, nca3pcell, iCA3PC, CA3PC_CA3BC, EI_PC, EI_PC+1, CA3PC2CA3BCd, CA3PC2CA3BCw)
// CA3-PC to CA3-AAC
connectcells(nca3aacell, iCA3AAC, nca3pcell, iCA3PC, CA3PC_CA3AAC, EI_PC, EI_PC+1, CA3PC2CA3AACd, CA3PC2CA3AACw)
// CA3-PC to CA3-OLM
connectcells(nca3olm, iCA3OLM, nca3pcell, iCA3PC, CA3PC_CA3OLM, EO_PC, EO_PC+1, CA3PC2CA3OLMd, CA3PC2CA3OLMw)
// CA3-PC to DG-MC
connectcells(ndgmcell, iDGMC, nca3pcell, iCA3PC, CA3PC_DGMC, E_CA3PC_MC, E_CA3PC_MC+3, CA3PC2DGMCd, CA3PC2DGMCw)
print " CA3-INs..."
// CA3-BC to CA3-PC
connectcells(nca3pcell, iCA3PC, nca3bcell, iCA3BC, CA3BC_CA3PC, I_BC_CA3PC, I_BC_CA3PC, CA3BC2CA3PCd, CA3BC2CA3PCw)
// CA3-BC to CA3-BC
connectcells(nca3bcell, iCA3BC, nca3bcell, iCA3BC, CA3BC_CA3BC, II_SAME, II_SAME, CA3BC2CA3BCd, CA3BC2CA3BCw)
// CA3-AAC to CA3-PC
connectcells(nca3pcell, iCA3PC, nca3aacell, iCA3AAC, CA3AAC_CA3PC, I_AAC_CA3PC, I_AAC_CA3PC, CA3AAC2CA3PCd, CA3AAC2CA3PCw)
// CA3-OLM to CA3-PC
connectcells(nca3pcell, iCA3PC, nca3olm, iCA3OLM, CA3OLM_CA3PC, I_OLM_CA3PC, I_OLM_CA3PC+7, CA3OLM2CA3PCd, CA3OLM2CA3PCw)
//connectcells(nca3pcell, iCA3PC, nca3olm, iCA3OLM, CA3OLM_CA3PC, IB_OLM_CA3PC, IB_OLM_CA3PC+7, CA3OLM2CA3PCd, CA3OLM2CA3PCgbw)
print "**** CA1 ****"
print " EC..."
//// EC-L3-180 to CA1-PC
//connectcells(nca1pcell, iCA1PC, nECL3180, iECL3180, ECL3180_CA1PC, E_ECL3_CA1PC, E_ECL3_CA1PC+1, ECL3180CA1PCDEL, ECL3180CA1PCWGT)
////connectcells(nca1pcell, iCA1PC, nECL3180, iECL3180, ECL3180_CA1PC, EM_ECL3_CA1PC, EM_ECL3_CA1PC+1, ECL3180CA1PCDEL, ECL3180CA1PCWGT)
// EC-L3-180 to CA1-AAC
connectcells(nca1aacell, iCA1AAC, nECL3180, iECL3180, ECL3180_CA1AAC, EI_EC, EI_EC+1, ECL3180CA1AACDEL, ECL3180CA1AACWGT)
// EC-L3-180 to CA1-BC
connectcells(nca1bcell, iCA1BC, nECL3180, iECL3180, ECL3180_CA1BC, EI_EC, EI_EC+1, ECL3180CA1BCDEL, ECL3180CA1BCWGT)
//// EC-L3-360 to CA1-PC
//connectcells(nca1pcell, iCA1PC, nECL3360, iECL3360, ECL3360_CA1PC, E_ECL3_CA1PC, E_ECL3_CA1PC+1, ECL3360CA1PCDEL, ECL3360CA1PCWGT)
////connectcells(nca1pcell, iCA1PC, nECL3360, iECL3360, ECL3360_CA1PC, EM_ECL3_CA1PC, EM_ECL3_CA1PC+1, ECL3360CA1PCDEL, ECL3360CA1PCWGT)
// EC-L3-360 to CA1-AAC
connectcells(nca1aacell, iCA1AAC, nECL3360, iECL3360, ECL3360_CA1AAC, EI_EC, EI_EC+1, ECL3360CA1AACDEL, ECL3360CA1AACWGT)
// EC-L3-360 to CA1-BC
connectcells(nca1bcell, iCA1BC, nECL3360, iECL3360, ECL3360_CA1BC, EI_EC, EI_EC+1, ECL3360CA1BCDEL, ECL3360CA1BCWGT)
print " SEP180..."
// SEP180 to CA1-AAC
connectcells(nca1aacell, iCA1AAC, nSEP180, iSEP180, SEP180_CA1AAC, II_SEP, II_SEP+1, SEP1802CA1AACDEL, SEP1802CA1AACWGT)
// SEP180 to CA1-BC
connectcells(nca1bcell, iCA1BC, nSEP180, iSEP180, SEP180_CA1BC, II_SEP, II_SEP+1, SEP1802CA1BCDEL, SEP1802CA1BCWGT)
print " SEP360..."
// SEP360 to CA1-BSC
connectcells(nca1bscell, iCA1BSC, nSEP360, iSEP360, SEP360_CA1BSC, II_SEP, II_SEP+1, SEP3602CA1BSCDEL, SEP3602CA1BSCWGT)
// // SEP360 to CA1-OLM
// connectcells(nca1olm, iCA1OLM, nSEP360, iSEP360, SEP360_CA1OLM, IO_IN, IO_IN, SEP3602CA1OLMDEL, SEP3602CA1OLMWGT)
print " CA3..."
// CA3-PC to CA1-PC
connectCA3PCtoCA1PC(nca1pcell, iCA1PC, nca3pcell, iCA3PC, CA3PC_CA1PC, E_CA3PC_CA1PC, E_CA3PC_CA1PC+8, CA3PC2CA1PCd, CA3PC2CA1PCCHw, ECPATT, NPATT)
connectCA3PCtoCA1PC(nca1pcell, iCA1PC, nca3pcell, iCA3PC, CA3PC_CA1PC, EN_CA3PC_CA1PC, EN_CA3PC_CA1PC+4, CA3PC2CA1PCd, CA3PC2CA1PCCHwn, ECPATT, NPATT)
//connectCA3PCtoCA1PC(nca1pcell, iCA1PC, nca3pcell, iCA3PC, CA3PC_CA1PC, EM_CA3PC_CA1PC, EM_CA3PC_CA1PC+8, CA3PC2CA1PCd, CA3PC2CA1PCCHw, ECPATT, NPATT)
//connectCA3PCtoCA1PC(nca1pcell, iCA1PC, nca3pcell, iCA3PC, CA3PC_CA1PC, E_CA3PC_CA1PC, E_CA3PC_CA1PC, CA3PC2CA1PCd, CA3PC2CA1PCCHw)
//connectCA3PCtoCA1PC(nca1pcell, iCA1PC, nca3pcell, iCA3PC, CA3PC_CA1PC, EM_CA3PC_CA1PC, EM_CA3PC_CA1PC, CA3PC2CA1PCd, CA3PC2CA1PCCHw)
// CA3-PC to CA1-AAC
connectcells(nca1aacell, iCA1AAC, nca3pcell, iCA3PC, CA3PC_CA1AAC, EI_GC, EI_GC+1, CA3PC2CA1AACd, CA3PC2CA1AACw)
// CA3-PC to CA1-BC
connectcells(nca1bcell, iCA1BC, nca3pcell, iCA3PC, CA3PC_CA1BC, EI_GC, EI_GC+1, CA3PC2CA1BCd, CA3PC2CA1BCw)
// CA3-PC to CA1-BSC
connectcells(nca1bscell, iCA1BSC, nca3pcell, iCA3PC, CA3PC_CA1BSC, EI_GC, EI_GC+1, CA3PC2CA1BSCd, CA3PC2CA1BSCw)
print " CA1-PC..."
// CA1-PC to CA1-PC
connectCA1pcells(nca1pcell, iCA1PC, nca1pcell, iCA1PC, CA1PC_CA1PC, E_CA1PC_CA1PC, E_CA1PC_CA1PC, CA1PC2CA1PCd, CA1PC2CA1PCw)
// // CA1-PC to CA1-BC
// //connectcells(nca1bcell, iCA1BC, nca1pcell, iCA1PC, CA1PC_CA1BC, EI_PC, EI_PC+1, CA1PC2CA1BCd, CA1PC2CA1BCw)
// // CA1-PC to CA1-AAC
// //connectcells(nca1aacell, iCA1AAC, nca1pcell, iCA1PC, CA1PC_CA1AAC, EI_PC, EI_PC+1, CA1PC2CA1AACd, CA1PC2CA1AACw)
// // CA1-PC to CA1-BSC
// //connectcells(nca1bscell, iCA1BSC, nca1pcell, iCA1PC, CA1PC_CA1BSC, EI_PC, EI_PC+1, CA1PC2CA1BSCd, CA1PC2CA1BSCw)
// // CA1-PC to CA1-OLM
// connectcells(nca1olm, iCA1OLM, nca1pcell, iCA1PC, CA1PC_CA1OLM, EO_PC, EO_PC+1, CA1PC2CA1OLMd, CA1PC2CA1OLMw)
print " CA1-INs..."
// CA1-BC to CA1-PC
connectcells(nca1pcell, iCA1PC, nca1bcell, iCA1BC, CA1BC_CA1PC, I_BC_CA1PC, I_BC_CA1PC, CA1BC2CA1PCd, CA1BC2CA1PCw)
// CA1-BC to CA1-BC
connectcells(nca1bcell, iCA1BC, nca1bcell, iCA1BC, CA1BC_CA1BC, II_SAME, II_SAME, CA1BC2CA1BCd, CA1BC2CA1BCw)
// CA1-BC to CA1-BSC
connectcells(nca1bscell, iCA1BSC, nca1bcell, iCA1BC, CA1BC_CA1BSC, II_OPP, II_OPP, CA1BC2CA1BSCd, CA1BC2CA1BSCw)
// CA1-AAC to CA1-PC
connectcells(nca1pcell, iCA1PC, nca1aacell, iCA1AAC, CA1AAC_CA1PC, I_AAC_CA1PC, I_AAC_CA1PC, CA1AAC2CA1PCd, CA1AAC2CA1PCw)
// CA1-BSC to CA1-PC
connectcells(nca1pcell, iCA1PC, nca1bscell, iCA1BSC, CA1BSC_CA1PC, I_BSC_CA1PC+2, I_BSC_CA1PC+2, CA1BSC2CA1PCd, CA1BSC2CA1PCw) // GABA-A
//connectcells(nca1pcell, iCA1PC, nca1bscell, iCA1BSC, CA1BSC_CA1PC, IB_BSC_CA1PC+1, IB_BSC_CA1PC+3, CA1BSC2CA1PCgbd, CA1BSC2CA1PCgbw) // GABA-B
// CA1-BSC to CA1-BC
connectcells(nca1bcell, iCA1BC, nca1bscell, iCA1BSC, CA1BSC_CA1BC, II_OPP, II_OPP, CA1BSC2CA1BCd, CA1BSC2CA1BCw)
// CA1-OLM to CA1-PC
//connectcells(nca1pcell, iCA1PC, nca1olm, iCA1OLM, CA1OLM_CA1PC, I_OLM_CA1PC, I_OLM_CA1PC+2, CA1OLM2CA1PCd, CA1OLM2CA1PCw) // GABA-A
//connectcells(nca1pcell, iCA1PC, nca1olm, iCA1OLM, CA1OLM_CA1PC, IB_OLM_CA1PC, IB_OLM_CA1PC+2, CA1OLM2CA1PCd, CA1OLM2CA1PCgbw) // GABA-B
print "Connect inputs..."
// EC-L2 input to GCs
//connectECL2DG(FDGPATT, ECPATT, NPATT, E_EC_GC, E_EC_GC+1) // with fixed synapses
//connectECL2DG(FDGPATT, ECPATT, NSTORE, EM_EC_GC, EM_EC_GC+1) // store new pattern
print "Connect EC-L2 to DG-GC"
connectECL2toDG($s1, $2, E_EC_GC, E_EC_GC+1) // with fixed synapses
//connectECL2toDG($s1, $2, EM_EC_GC, EM_EC_GC+1) // with modifiable synapses
// EC-L3 input to CA1-PCs
print "Connect EC-L3 to CA1-PC"
connectECL3toCA1PC(FCA1CONN, 1, E_ECL3_CA1PC, E_ECL3_CA1PC+17) // with fixed synapses
//connectECL3toCA1PC(FCA1CONN, 1, EN_ECL3_CA1PC, EN_ECL3_CA1PC+1) // with fixed synapses
//connectECL3toCA1PC(FCA1PATT, ECPATT, NSTORE, EM_ECL3_CA1PC, EM_ECL3_CA1PC+17) // store new pattern
}
// creates the cells and appends them to a List called cells
// argument is the number of cells to be created
proc mkcells() {local i,j localobj cell, nc, nil
cells = new List()
ranlist = new List()
gidvec = new Vector()
// each host gets every nhost'th cell,
// starting from the id of the host
// and continuing until no more cells are left
for i=0, ntot {
if (i < iDGMC) {
cell = new GranuleCell() // DG Granule cell
} else if (i < iDGBC) {
cell = new MossyCell() // DG Mossy cell
} else if (i < iDGHC) {
cell = new BC() // DG Basket cell
} else if (i < iCA3PC) {
cell = new HIPPCell() // DG HIPP cell
} else if (i < iCA3AAC) {
cell = new CA3PyramidalCell() // CA3 Pyramidal cell
} else if (i < iCA3BC) {
cell = new CA3AACell() // CA3 Axoaxonic cell
} else if (i < iCA3OLM) {
cell = new CA3BasketCell() // CA3 Basket cell
} else if (i < iCA1PC) {
cell = new CA3OLMCell() // CA3 OLM cell
} else if (i < iCA1AAC) {
cell = new CA1PyramidalCell() // CA1 Pyramidal cell
} else if (i < iCA1BC) {
cell = new CA1AACell() // CA1 Axo-axonic cell
} else if (i < iCA1BSC) {
cell = new CA1BasketCell() // CA1 Basket cell
} else if (i < iECL2180) {
cell = new CA1BistratifiedCell() // CA1 Bistratified cell
} else if (i < iECL2360) {
cell = new StimCell() // EC-L2-180
} else if (i < iECL3180) {
cell = new StimCell() // EC-L2-360
} else if (i < iECL3360) {
cell = new StimCell() // EC-L3-180
} else if (i < iSEP180) {
cell = new StimCell() // EC-L3-360
} else if (i < iSEP360) {
cell = new BurstCell() // SEP 180 input
} else {
// } else if (i < iCA1OLM) {
cell = new BurstCell() // SEP 360 input
// } else {
// cell = new CA1OLMCell() // CA1 OLM cell
}
cells.append(cell)
pc.set_gid2node(i, pc.id) // associate gid i with this host
nc = cell.connect2target(nil) // attach spike detector to cell
pc.cell(i, nc) // associate gid i with spike detector
ranlist.append(new RandomStream(i)) // ranlist.o(i) corresponds to
gidvec.append(i)
}
}
// reports distribution of cells across hosts
proc report_gidvecs() { local i, rank
pc.barrier() // wait for all hosts to get to this point
if (pc.id==0) printf("\ngidvecs on the various hosts\n")
for rank=0, pc.nhost-1 { // host 0 first, then 1, 2, etc.
if (rank==pc.id) {
print "host ", pc.id
gidvec.printf()
}
pc.barrier() // wait for all hosts to get to this point
}
}
// sets the CA3, EC and Septal background inputs
proc mkinputs() {local i localobj stim, rs
for i=0, cells.count-1 {
gid = gidvec.x[i] // id of cell
if (gid >= iECL2180 && gid < iECL2180+nECL2180) { // appropriate target cell
// set background activity for excitatory inputs
stim = cells.object(i).stim
//stim.number = ECL2180NUM
//stim.start = ECL2180START
//stim.interval = ECL2180INT
//stim.noise = ECL2180NOISE
//stim.burstint = ECL2180BINT
//stim.burstlen = ECL2180BLEN
stim.number = ECL2180NUM
stim.start = ECL2180START
stim.interval = ECL2180INT
stim.noise = ECL2180NOISE
}
if (gid >= iECL2360 && gid < iECL2360+nECL2360) { // appropriate target cell
// set background activity for excitatory inputs
stim = cells.object(i).stim
//stim.number = ECL2360NUM
//stim.start = ECL2360START
//stim.interval = ECL2360INT
//stim.noise = ECL2360NOISE
//stim.burstint = ECL2360BINT
//stim.burstlen = ECL2360BLEN
stim.number = ECL2360NUM
stim.start = ECL2360START
stim.interval = ECL2360INT
stim.noise = ECL2360NOISE
}
if (gid >= iSEP180 && gid < iSEP180+nSEP180) { // appropriate target cell
// set background activity for septum
stim = cells.object(i).stim
stim.number = SEP180NUM
stim.start = SEP180START
stim.interval = SEP180INT
stim.noise = SEP180NOISE
stim.burstint = SEP180BINT
stim.burstlen = SEP180BLEN
}
if (gid >= iSEP360 && gid < iSEP360+nSEP360) { // appropriate target cell
// set background activity for septum
stim = cells.object(i).stim
stim.number = SEP360NUM
stim.start = SEP360START
stim.interval = SEP360INT
stim.noise = SEP360NOISE
stim.burstint = SEP360BINT
stim.burstlen = SEP360BLEN
}
if (gid >= iECL3180 && gid < iECL3180+nECL3180) { // appropriate target cell
stim = cells.object(i).stim
//stim.number = ECL3180NUM
//stim.start = ECL3180START
//stim.interval = ECL3180INT
//stim.noise = ECL3180NOISE
//stim.burstint = ECL3180BINT
//stim.burstlen = ECL3180BLEN
stim.number = ECL3180NUM
stim.start = ECL3180START
stim.interval = ECL3180INT
stim.noise = ECL3180NOISE
}
if (gid >= iECL3360 && gid < iECL3360+nECL3360) { // appropriate target cell
stim = cells.object(i).stim
rs = ranlist.object(i)
//stim.number = ECL3360NUM
//stim.start = ECL3360START
//stim.interval = ECL3360INT
//stim.noise = ECL3360NOISE
//stim.burstint = ECL3360BINT
//stim.burstlen = ECL3360BLEN
stim.number = ECL3360NUM
stim.start = ECL3360START
stim.interval = ECL3360INT
stim.noise = ECL3360NOISE
// Use the gid-specific random generator so random streams are
// independent of where and how many stims there are.
stim.noiseFromRandom(rs.r)
rs.r.negexp(1)
rs.start()
}
}
}
// connects the EC input layer to GC cells
// read active GCs from pattern file
// all-to-all connectivity between EC and GC pattern cells
// appends the GC NetCons to a List called ncelist
proc connectECL2DG() {local i, j1, j2, gid, ncue localobj cue, cstim, syn, src, nc, fp, target
ncelist = new List()
// open patterns file
fp = new File($s1)
fp.ropen()
cue = new Vector(ndggcell)
cue.scanf(fp, $2, $3) // read pattern
fp.close()
ncue = 0
// find active cells in pattern
for i=0, cue.size()-1 {
//if (!pc.gid_exists(i+iDGGC)) { continue }
if (cue.x[i] == 1) {
print "Pattern cell ", i
//target = pc.gid2cell(i+iDGGC)
target = cells.object(i+iDGGC)
// target synapses
for k = $4, $5 {
syn = target.pre_list.object(k) // excitatory synapse
// create pattern stimulus
for j1=0, nECL2180-1 {
src = cells.object(j1+iECL2180).stim
// set up connection from source to target
//nc = pc.gid_connect(j+iEC, syn)
nc = new NetCon(src, syn)
ncelist.append(nc)
nc.delay = ECL2180DGGCDEL
nc.weight = ECL2180DGGCCHWGT
}
for j2=0, nECL2360-1 {
src = cells.object(j2+iECL2360).stim
// set up connection from source to target
//nc = pc.gid_connect(j+iEC, syn)
nc = new NetCon(src, syn)
ncelist.append(nc)
nc.delay = ECL2360DGGCDEL
nc.weight = ECL2360DGGCCHWGT
}
}
} else {
//print "Non-pattern cell ", i
//target = pc.gid2cell(i+iDGGC)
target = cells.object(i+iDGGC)
// target synapses
for k = $4, $5 {
syn = target.pre_list.object(k) // excitatory synapse
// create pattern stimulus
for j1=0, nECL2180-1 {
src = cells.object(j1+iECL2180).stim
// set up connection from source to target
//nc = pc.gid_connect(j+iEC, syn)
nc = new NetCon(src, syn)
ncelist.append(nc)
nc.delay = ECL2180DGGCDEL
nc.weight = ECL2180DGGCCLWGT
}
for j2=0, nECL2360-1 {
src = cells.object(j2+iECL2360).stim
// set up connection from source to target
//nc = pc.gid_connect(j+iEC, syn)
nc = new NetCon(src, syn)
ncelist.append(nc)
nc.delay = ECL2360DGGCDEL
nc.weight = ECL2360DGGCCLWGT
}
}
}
}
}
// connects the EC-L2 input layer to output cells (DG-GCs and INs)
// read DG-GC connections from a file, with connections to
// a target being a column with index i for target cell i
// appends the DG-GC NetCons to a List called ncslist
proc connectECL2toDG() {local i, j1, j2, cp, gid localobj src, syn, synN, nc, fc, rs, conns, rc
cp = $2 // connection probability
mcell_ran4_init(connect_random_low_start_)
conns = new Vector(nECL2180) // connection weights
rc = new Vector(nECL2180) // random physical connectivity
ncslist = new List()
// inputs to DG-GCs determined by weight matrix
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid >= iDGGC && gid < ndggcell+iDGGC) { // appropriate target cell
//print "cell ", gid
for k = $3, $4 {
syn = cells.object(i).pre_list.object(k) // AMPA synapse with STDP
rs = ranlist.object(i) // the corresponding RandomStream
rs.start()
rs.r.uniform(0, 1) // return integer in range 0..1
rc.setrand(rs.r) // generate random connectivity
// open connections file
fc = new File($s1)
fc.ropen()
conns.scanf(fc, gid+1, nECL2180) // read incoming weights for cell gid
fc.close()
for j1=0, nECL2180-1 {
// only connection if physical connection exists
if (rc.x[j1] <= cp) {
//print " src ", j
src = cells.object(j1+iECL2180).stim
// high AMPA if weight is 1
if (conns.x[j1] == 1) {
// set up connection from source to target
//nc = pc.gid_connect(j1+iECL2180, syn)
nc = new NetCon(src, syn)
ncslist.append(nc)
nc.delay = ECL2180DGGCDEL
nc.weight = ECL2180DGGCCHWGT
} else {
// set up connection from source to target
//nc = pc.gid_connect(j1+iECL2180, syn)
nc = new NetCon(src, syn)
ncslist.append(nc)
nc.delay = ECL2180DGGCDEL
nc.weight = ECL2180DGGCCLWGT
}
}
}
for j2=0, nECL2360-1 {
// only connection if physical connection exists
if (rc.x[j2] <= cp) {
//print " src ", j
src = cells.object(j2+iECL2360).stim
// high AMPA if weight is 1
if (conns.x[j2] == 1) {
// set up connection from source to target
//nc = pc.gid_connect(j2+iECL2360, syn)
nc = new NetCon(src, syn)
ncslist.append(nc)
nc.delay = ECL2360DGGCDEL
nc.weight = ECL2360DGGCCHWGT
} else {
// set up connection from source to target
//nc = pc.gid_connect(j2+iECL2360, syn)
nc = new NetCon(src, syn)
ncslist.append(nc)
nc.delay = ECL2360DGGCDEL
nc.weight = ECL2360DGGCCLWGT
}
}
}
}
}
}
}
// Target cells receive "convergence" number of inputs from
// the pool of source cells (only one input per source cell at most)
// ("convergence" not reached if no. of sources < convergence)
// connectcells(number of targets, first target cell,
// number of source cells, first source cell,
// convergence, first synapse,
// last synapse, connection delay, weight)
// appends the NetCons to a List called nclist
objref f
strdef fn
proc connectDGGCtoCA3PC() {local i, j, k, gid, nsyn, r localobj syn, nc, rs, u, rr, vca3pc, ca3pc, conns, fp
// initialize the pseudorandom number generator
u = new Vector($3) // for sampling without replacement
conns = new Vector(nca3pcell)
jj = 0
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid >= $2 && gid < $2+$1) { // appropriate CA3-PC target cell
// open CA3-PC active cells file
fp = new File(FCA3CONN)
fp.ropen()
conns.scanf(fp, gid-iCA3PC+1, nca3pcell) // read pattern
fp.close()
// print "conns.size = ", conns.size(), "gid-iCA3PC+1 = ", gid-iCA3PC+1
if (conns.x[jj] == 1) {
// print "jj = ", jj, "pattern ca3 cell = ", conns.x[jj]
//if (gid == ca3pc.x[jj]) {
//f.printf("%d\n", 1)
//print "pattern ca3-pc = ", i - iCA3PC
print "jj = ", jj, "i = ", i, ", gid = ", gid, ", pattern ca3 cell = ", conns.x[jj]
//print "i = ", i, "gid = ", gid, "pattern ca3pc.x[jj] = ", ca3pc.x[jj]
rs = ranlist.object(i) // RandomStream for cells.object(i)
rs.start()
rs.r.discunif($4, $4+$3-1) // return source cell index
u.fill(0) // u.x[i]==1 means spike source i has already been chosen
nsyn = 0
while (nsyn < $5 && nsyn < $3) {
r = rs.repick()
// no self-connection and only one connection from any source
if (r != gidvec.x[i]) if (u.x[r-$4] == 0) {
// target synapses
for j = $6, $7 {
// set up connection from source to target
syn = cells.object(i).pre_list.object(j)
nc = pc.gid_connect(r, syn)
nclist.append(nc)
nc.delay = DGGC2CA3PCd
nc.weight = DGGC2CA3PCCHw
}
u.x[r-$4] = 1
nsyn += 1
}
}
//jj = jj + 1
} else {
print "jj = ", jj, "non-pattern ca3 cell = ", conns.x[jj]
//f.printf("%d\n", 0)
//print "non-pattern ca3-pc = ", i - iCA3PC
rs = ranlist.object(i) // RandomStream for cells.object(i)
rs.start()
rs.r.discunif($4, $4+$3-1) // return source cell index
u.fill(0) // u.x[i]==1 means spike source i has already been chosen
nsyn = 0
while (nsyn < $5 && nsyn < $3) {
r = rs.repick()
// no self-connection and only one connection from any source
if (r != gidvec.x[i]) if (u.x[r-$4] == 0) {
// target synapses
for j = $6, $7 {
// set up connection from source to target
syn = cells.object(i).pre_list.object(j)
nc = pc.gid_connect(r, syn)
nclist.append(nc)
nc.delay = DGGC2CA3PCd
nc.weight = DGGC2CA3PCCLw
}
u.x[r-$4] = 1
nsyn += 1
}
}
}
jj = jj + 1
}
}
//fp.close()
}
// Target cells receive "convergence" number of inputs from
// the pool of source cells (only one input per source cell at most)
// ("convergence" not reached if no. of sources < convergence)
// connectcells(number of targets, first target cell,
// number of source cells, first source cell,
// convergence, first synapse,
// last synapse, connection delay, weight)
// appends the NetCons to a List called nclist
proc connectcells() {local i, j, gid, nsyn, r localobj syn, nc, rs, u
// initialize the pseudorandom number generator
u = new Vector($3) // for sampling without replacement
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid >= $2 && gid < $1+$2) { // appropriate target cell
rs = ranlist.object(i) // RandomStream for cells.object(i)
rs.start()
rs.r.discunif($4, $4+$3-1) // return source cell index
u.fill(0) // u.x[i]==1 means spike source i has already been chosen
nsyn = 0
while (nsyn < $5 && nsyn < $3) {
r = rs.repick()
// no self-connection and only one connection from any source
if (r != gidvec.x[i]) if (u.x[r-$4] == 0) {
// target synapses
for j = $6, $7 {
// set up connection from source to target
syn = cells.object(i).pre_list.object(j)
nc = pc.gid_connect(r, syn)
nclist.append(nc)
nc.delay = $8
nc.weight = $9
}
u.x[r-$4] = 1
nsyn += 1
}
}
}
}
}
// Target cells receive "convergence" number of inputs from
// the pool of source cells (only one input per source cell at most)
// ("convergence" not reached if no. of sources < convergence)
// connectCA3pcells(number of targets, first target cell,
// number of source cells, first source cell,
// convergence, first synapse,
// last synapse, connection delay, weight)
// appends the NetCons to a List called nclist
proc connectCA3pcells() {local i, j, C_E, gid, nsyn, r localobj syn, nc, rs, u
C_E = 0.1 * nca3pcell
// initialize the pseudorandom number generator
u = new Vector($3) // for sampling without replacement
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid >= $2 && gid < $1+$2) { // appropriate target cell
rs = ranlist.object(i) // RandomStream for cells.object(i)
rs.start()
rs.r.discunif($4, $4+$3-1) // return source cell index
u.fill(0) // u.x[i]==1 means spike source i has already been chosen
nsyn = 0
while (nsyn < C_E) { // C_E: 10% of nca3pcell randomly selected
r = rs.repick()
// no self-connection and only one connection from any source
if (r != gidvec.x[i]) if (u.x[r-$4] == 0) {
// target synapses
for j = $6, $7 {
// set up connection from source to target
syn = cells.object(i).pre_list.object(j)
nc = pc.gid_connect(r, syn)
nclist.append(nc)
nc.delay = $8
nc.weight = $9
}
u.x[r-$4] = 1
nsyn += 1
}
}
}
}
}
// Target cells receive "convergence" number of inputs from
// the pool of source cells (only one input per source cell at most)
// ("convergence" not reached if no. of sources < convergence)
// connectCA1pcells(number of targets, first target cell,
// number of source cells, first source cell,
// convergence, first synapse,
// last synapse, connection delay, weight)
// appends the NetCons to a List called nclist
proc connectCA1pcells() {local i, j, C_E, gid, nsyn, r localobj syn, nc, rs, u
C_E = 0.011 * nca1pcell
// initialize the pseudorandom number generator
u = new Vector($3) // for sampling without replacement
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid >= $2 && gid < $1+$2) { // appropriate target cell
rs = ranlist.object(i) // RandomStream for cells.object(i)
rs.start()
rs.r.discunif($4, $4+$3-1) // return source cell index
u.fill(0) // u.x[i]==1 means spike source i has already been chosen
nsyn = 0
while (nsyn < C_E) { // C_E: 1% of nca1pcell randomly selected
r = rs.repick()
// no self-connection and only one connection from any source
if (r != gidvec.x[i]) if (u.x[r-$4] == 0) {
// target synapses
for j = $6, $7 {
// set up connection from source to target
syn = cells.object(i).pre_list.object(j)
nc = pc.gid_connect(r, syn)
nclist.append(nc)
nc.delay = $8
nc.weight = $9
}
u.x[r-$4] = 1
nsyn += 1
}
}
}
}
}
// connects the EC-L3 input layer to output cells (CA1-PCs and INs)
// read CA1-PC connections from a file, with connections to
// a target being a column with index i for target cell i
// appends the CA1-PC NetCons to a List called ncslist
proc connectECL3toCA1PC() {local i, j1, j2, cp, gid localobj src, syn, synN, nc, fc, rs, conns, rc
cp = $2 // connection probability
mcell_ran4_init(connect_random_low_start_)
conns = new Vector(nECL3180) // connection weights
rc = new Vector(nECL3180) // random physical connectivity
ncilist = new List()
// inputs to CA1-PCs determined by weight matrix
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid >= iCA1PC && gid < nca1pcell+iCA1PC) { // appropriate target cell
//print "cell ", gid
for k = $3, $4 {
syn = cells.object(i).pre_list.object(k) // AMPA synapse with STDP
rs = ranlist.object(i) // the corresponding RandomStream
rs.start()
rs.r.uniform(0, 1) // return integer in range 0..1
rc.setrand(rs.r) // generate random connectivity
// open connections file
fc = new File(FCA1CONN)
fc.ropen()
conns.scanf(fc, gid-iCA1PC+1, nECL3180) // read incoming weights for cell gid
fc.close()
//print "conns.size = ", conns.size(), "gid-iCA1PC+1 = ", gid-iCA1PC+1
for j1 = 0, nECL3180-1 {
// only connection if physical connection exists
if (rc.x[j1] <= cp) {
//print " src ", j
src = cells.object(j1+iECL3180).stim
// high AMPA if weight is 1
if (conns.x[j1] == 1) {
// set up connection from source to target
// nc = pc.gid_connect(j1+iECL3180, syn)
//print "pattern CA1 cell ", gid-iCA1PC+1
nc = new NetCon(src, syn)
ncilist.append(nc)
nc.weight = ECL3180CA1PCCHWGT
nc.delay = ECL3180CA1PCDEL
} else {
// set up connection from source to target
// nc = pc.gid_connect(j1+iECL3180, syn)
nc = new NetCon(src, syn)
ncilist.append(nc)
nc.weight = ECL3180CA1PCCLWGT
nc.delay = ECL3180CA1PCDEL
}
}
}
for j2=0, nECL3360-1 {
// only connection if physical connection exists
if (rc.x[j2] <= cp) {
//print " src ", j
src = cells.object(j2+iECL3360).stim
// high AMPA if weight is 1
if (conns.x[j2] == 1) {
// set up connection from source to target
// nc = pc.gid_connect(j2+iECL3360, syn)
nc = new NetCon(src, syn)
ncilist.append(nc)
nc.weight = ECL3360CA1PCCHWGT
nc.delay = ECL3360CA1PCDEL
} else {
// set up connection from source to target
// nc = pc.gid_connect(j2+iECL3360, syn)
nc = new NetCon(src, syn)
ncilist.append(nc)
nc.weight = ECL3360CA1PCCLWGT
nc.delay = ECL3360CA1PCDEL
}
}
}
}
}
}
}
// Target cells receive "convergence" number of inputs from
// the pool of source cells (only one input per source cell at most)
// ("convergence" not reached if no. of sources < convergence)
// connectcells(number of targets, first target cell,
// number of source cells, first source cell,
// convergence, first synapse,
// last synapse, connection delay, weight)
// appends the NetCons to a List called nclist
objref f
strdef fn
proc connectCA3PCtoCA1PC() {local i, j, k, gid, nsyn, r localobj syn, nc, rs, u, rr, vca1pc, ca1pc, conns, fp
// initialize the pseudorandom number generator
u = new Vector($3) // for sampling without replacement
conns = new Vector(nca1pcell)
jj = 0
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid >= $2 && gid < $2+$1) { // appropriate CA1-PC target cell
// open CA1-PC active cells file
fp = new File(FCA1CONN)
fp.ropen()
conns.scanf(fp, gid-iCA1PC+1, nca1pcell) // read pattern
fp.close()
// print "conns.size = ", conns.size(), "gid-iCA1PC+1 = ", gid-iCA1PC+1
if (conns.x[jj] == 1) {
// print "jj = ", jj, "pattern ca1 cell = ", conns.x[jj]
//if (gid == ca1pc.x[jj]) {
//f.printf("%d\n", 1)
//print "pattern ca1-pc = ", i - iCA1PC
print "jj = ", jj, "i = ", i, ", gid = ", gid, ", pattern ca1 cell = ", conns.x[jj]
//print "i = ", i, "gid = ", gid, "pattern ca1pc.x[jj] = ", ca1pc.x[jj]
rs = ranlist.object(i) // RandomStream for cells.object(i)
rs.start()
rs.r.discunif($4, $4+$3-1) // return source cell index
u.fill(0) // u.x[i]==1 means spike source i has already been chosen
nsyn = 0
while (nsyn < $5 && nsyn < $3) {
r = rs.repick()
// no self-connection and only one connection from any source
if (r != gidvec.x[i]) if (u.x[r-$4] == 0) {
// target synapses
for j = $6, $7 {
// set up connection from source to target
syn = cells.object(i).pre_list.object(j)
nc = pc.gid_connect(r, syn)
nclist.append(nc)
nc.delay = CA3PC2CA1PCd
nc.weight = CA3PC2CA1PCCHw
}
u.x[r-$4] = 1
nsyn += 1
}
}
//jj = jj + 1
} else {
//print "jj = ", jj, "non-pattern ca1 cell = ", conns.x[jj]
//f.printf("%d\n", 0)
//print "non-pattern ca1-pc = ", i - iCA1PC
rs = ranlist.object(i) // RandomStream for cells.object(i)
rs.start()
rs.r.discunif($4, $4+$3-1) // return source cell index
u.fill(0) // u.x[i]==1 means spike source i has already been chosen
nsyn = 0
while (nsyn < $5 && nsyn < $3) {
r = rs.repick()
// no self-connection and only one connection from any source
if (r != gidvec.x[i]) if (u.x[r-$4] == 0) {
// target synapses
for j = $6, $7 {
// set up connection from source to target
syn = cells.object(i).pre_list.object(j)
nc = pc.gid_connect(r, syn)
nclist.append(nc)
nc.delay = CA3PC2CA1PCd
nc.weight = CA3PC2CA1PCCLw
}
u.x[r-$4] = 1
nsyn += 1
}
}
}
jj = jj + 1
}
}
//fp.close()
}
// stimcells(number of targets, first target cell, mean amplitude, variance, duration)
// tonic stimulation to cells to give spontaneous firing
proc stimcells() {local i, gid, r localobj stim, rs
for i=0, cells.count-1 {
gid = gidvec.x[i] // id of cell
if (gid >= $2 && gid < $1+$2) { // appropriate target cell
rs = ranlist.object(i) // the RandomStream that corresponds to
// cells.object(i)
rs.start()
r = rs.r.normal($3, $4) // return stimulation current
cells.object(i).soma stim = new IClamp(0.5)
stim.del = 0
stim.dur = $5
stim.amp = r
stimlist.append(stim)
}
}
}
//mknet() // go ahead and create the net!
mknet(FDGCONN, 1) // go ahead and create the net!
print" DONE "
