Hippocampal CA1 NN with spontaneous theta, gamma: full scale & network clamp (Bezaire et al 2016)

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This model is a full-scale, biologically constrained rodent hippocampal CA1 network model that includes 9 cells types (pyramidal cells and 8 interneurons) with realistic proportions of each and realistic connectivity between the cells. In addition, the model receives realistic numbers of afferents from artificial cells representing hippocampal CA3 and entorhinal cortical layer III. The model is fully scaleable and parallelized so that it can be run at small scale on a personal computer or large scale on a supercomputer. The model network exhibits spontaneous theta and gamma rhythms without any rhythmic input. The model network can be perturbed in a variety of ways to better study the mechanisms of CA1 network dynamics. Also see online code at http://bitbucket.org/mbezaire/ca1 and further information at http://mariannebezaire.com/models/ca1
1 . Bezaire MJ, Raikov I, Burk K, Vyas D, Soltesz I (2016) Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent CA1 circuit. Elife [PubMed]
2 . Bezaire M, Raikov I, Burk K, Armstrong C, Soltesz I (2016) SimTracker tool and code template to design, manage and analyze neural network model simulations in parallel NEURON bioRxiv
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal cell; Hippocampus CA1 interneuron oriens alveus cell; Hippocampus CA1 basket cell; Hippocampus CA1 stratum radiatum interneuron; Hippocampus CA1 bistratified cell; Hippocampus CA1 axo-axonic cell; Hippocampus CA1 PV+ fast-firing interneuron;
Channel(s): I Na,t; I K; I K,leak; I h; I K,Ca; I Calcium;
Gap Junctions:
Receptor(s): GabaA; GabaB; Glutamate; Gaba;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; NEURON (web link to model);
Model Concept(s): Oscillations; Methods; Connectivity matrix; Laminar Connectivity; Gamma oscillations;
Implementer(s): Bezaire, Marianne [mariannejcase at gmail.com]; Raikov, Ivan [ivan.g.raikov at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell; Hippocampus CA1 interneuron oriens alveus cell; GabaA; GabaB; Glutamate; Gaba; I Na,t; I K; I K,leak; I h; I K,Ca; I Calcium; Gaba; Glutamate;
For more information, consult ModelDoc.pdf

loadstart = startsw()					// record the start time of the set up
{load_file("nrngui.hoc")}				// Standard definitions - NEURON library file

{load_file("netparmpi.hoc")}			// Contains the template that defines the properties of
										//  the ParallelNetManager class, which is used to set
										//   up a network that runs on parallel processors
{load_file("./setupfiles/ranstream.hoc")}	// Contains the template that defines a RandomStream
											//  class used to produce random numbers
											// 	for the cell noise (what type of noise?)
{load_file("./setupfiles/CellCategoryInfo.hoc")}	// Contains the template that defines a 
													//  CellCategoryInfo class used to store
													// 	celltype-specific parameters

{load_file("./setupfiles/SynStore.hoc")}	// Contains the template that defines a 
{load_file("./setupfiles/defaultvar.hoc")}	// Contains the proc definition for default_var proc

{load_file("./setupfiles/parameters.hoc")}	// Loads in operational and model parameters that can
											//  be changed at command line											

{load_file("./setupfiles/set_other_parameters.hoc")}// Loads in operational and model parameters
													//  that can't be changed at command line


{load_file("./setupfiles/load_cell_category_info.hoc")}	// Reads the 'cells2include.hoc' file and
														//  loads the information into one
														//  'CellCategoryInfo' object for each cell
														//  type (bio or art cells?). Info includes
														//  number of cells, gid ranges, type name 

{load_file("./setupfiles/load_cell_conns.hoc")}	// Load in the cell connectivity info
{load_file("./setupfiles/load_cell_syns.hoc")}	// Load in the cell connectivity info

strdef tempFileStr, cmd						// Define a string reference to store the name of the
										//  current cell template file

proc loadCellTemplates(){local i		// Proc to load the template that defines (each) cell class

	for i=0, numCellTypes-1 {			// Iterate over each cell type in cells2include (and art cells?)
		sprint(tempFileStr,"./cells/class_%s.hoc",cellType[i].technicalType)	// Concatenate the
																				//  path and file
		load_file(tempFileStr)			// Load the file with the template that defines the class
										//  for each cell type
loadCellTemplates()						// Run the newly defined proc

proc calcNetSize(){local i				// Calculate the final network size (after any cell death)
	cellType[0].numCells = 1
	cellType[0].updateGidRange(0)	// Update the gid range for each
	totalCells = 0						// Initialize totalCells (which counts the number of 'real'
										//  cells) so we can add to it iteratively in the 'for' loop
	ncell = cellType[0].numCells		// Initialize ncell (which counts all 'real' and 'artificial'
										//  cells) so we can add to it iteratively in the 'for' loop
	for i=1,numCellTypes-1 {			// Run the following code for 'real' cell types only - need a different way of singling out real cells?	
		cellType[i].numCells = 1
		cellType[i].updateGidRange(cellType[i-1].cellEndGid+1)	// Update the gid range for each
																//  cell type
		totalCells = totalCells + cellType[i].numCells			// Update the total number of cells
																//   after sclerosis, not including
																//   artificial cells
		ncell = ncell + cellType[i].numCells 					// Update the total number of cells
																//   after sclerosis, including
																//   artificial cells

proc calcBinSize(){local NumGCells

	for i=0, numCellTypes-1 {		// Using the specified dimensions of the network (in um) and
									//  the total number of cells of each type, set the number
									//  of bins in X, Y, Z dimensions such that the cells will be
									//  evenly distributed throughout the allotted volume
									// just changed this so even the stim cells will be allotted, as now we have some
									// stimulation protocols that incorporate stim cell position
									// For the z length, use the height of the layer in which the
									// cell somata are found for this cell type

objref pnm, pc, nc, nil
proc parallelizer() {
	pnm = new ParallelNetManager(ncell)	// Set up a parallel net manager for all the cells
	pc = pnm.pc
	pnm.round_robin()					// Incorporate all processors - cells 0 through ncell-1
										//	are distributed throughout the hosts
										//	(cell 0 goes to host 0, cell 1 to host 1, etc)

iterator pcitr() {local i2, startgid	// Create iterator for use as a standard 'for' loop
										//  throughout given # cells usage:
										//  for pcitr(&i1, &i2, &gid, it_start, it_end) {do stuff}
										//  it_start and it_end let you define range over
										//  which to iterate
										//  i1 is the index of the cell on the cell list for that host
										//  i2 is the index of that cell for that cell type on that host
	numcycles = int($4/pc.nhost)
	extra = $4%pc.nhost
	if (extra>pc.id) {addcycle=1}
	i1 = numcycles+addcycle // the index into the cell # on this host.
	i2 = 0 // the index of the cell in that cell type's list on that host
	if (startgid<=$5) {
		for (i3=startgid; i3 <= $5; i3 += pc.nhost) {	// Just iterate through the cells on
														//  this host(this simple statement
														//  iterates through all the cells on
														//  this host and only these cells because 
														//  the roundrobin call made earlier dealt
														//  the cells among the processors in an
														//  orderly manner (like a deck of cards)
				$&1 = i1
				$&2 = i2
				$&3 = i3
				i1 += 1
				i2 += 1

objref  strobj
strobj = new StringFunctions()
strdef direx
if (strcmp(UID,"0")==0 && pc.id==0) {
	type = unix_mac_pc() // 1 if unix, 2 if mac, 3 if mswin, or 4 if mac osx darwin
	if (type<3) {
		{system("uuidgen", direx)} // unix or mac
		strobj.left(direx, strobj.len(direx)-1)
	} else {
		{system("cscript //NoLogo setupfiles/uuid.vbs", direx)} // pc
	UID = direx

loadtime = startsw() - loadstart		// Calculate the set up time (now - recorded start time) in seconds
if (pc.id == 0) {printf("\nTIME HOST 0: %g seconds (set up)\n************\n", loadtime)}
createstart = startsw()					// Record the start time of the cell creation


objref cells, ransynlist, ranstimlist, raninitlist, ranwgtlist, ranlfplist
cells = new List()						
ransynlist = new List()
ranstimlist = new List()
raninitlist = new List()
ranwgtlist = new List()
ranlfplist = new List()
{load_file("./setupfiles/create_cells_pos.hoc")}	// Creates each cell on its assigned host
													//  and sets its position using the algorithm
													//  defined above
objref cell
for pcitr(&i, &ij, &gid, 0, ncell-1) {
	if (pc.gid_exists(gid)) {
		cell = pc.gid2cell(gid)

strdef cmd

createtime = startsw() - createstart	// Calculate time taken to create the cells
if (pc.id == 0) {printf("\nTIME HOST 0: %g seconds (created cells)\n************\n", createtime)}
connectstart = startsw()				// Grab start time of cell connection

oldtimeout = pc.timeout(0)

V. Launch ModelView
//objref m
//m = new ModelView(0)

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