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
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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 GLU cell; Hippocampus CA1 interneuron oriens alveus GABA 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 GLU cell; Hippocampus CA1 interneuron oriens alveus GABA cell; GabaA; GabaB; Glutamate; Gaba; I Na,t; I K; I K,leak; I h; I K,Ca; I Calcium; Gaba; Glutamate;
'ca1' model code repository
Written by Marianne Bezaire, marianne.bezaire@gmail.com, www.mariannebezaire.com
In the lab of Ivan Soltesz, www.ivansolteszlab.org
Latest versions of this code are available online at:
Open Source Brain: http://www.opensourcebrain.org/projects/nc_ca1

Main code file: ../main.hoc
This file: Last updated on April 9, 2015

This file creates the instances of the CellCategoryInfo template, one
for each cell type, and loads in the information about each cell type
into each object.

It adjusts the number of each cell type based on the Scale parameter
of the model and also whether any cells are subject to cell death (for
modeling injuries to the network).

It reads in a particular cellnumbers dataset as specified in the
./datasets/cellnumbers_###.dat  where ### is the parameter NumData

objref f2												// Define object reference for the cellnumbers file

objref celltypestring[1], techstring[1], cellType[1]	// Define placeholder objects with a size of one, then
														//  redefine them with the correct size in the proc

double cellnumvar[1], cellLayerflag[1], cellArtflag[1], numCellTypes[1]	// Define placeholder doubles with a size
																		//  of one, then redefine them with the
																		//  correct size in the proc
objref pnmtmp, pctmp, nil
proc loadCellCategoryInfo() {local i, startpos			// This function will load celltype info into a CellCategoryInfo
														//  object (one object per cell type)
	f2 = new File()
	sprint(cmdstr, "../datasets/cellnumbers_%g.dat", NumData)	// Open the NumData dataset specified by the user (a
	f2.ropen(cmdstr)											//  3-digit number), which gives the number of cell
																//  types in the model, followed by one line for each
																//  cell type, which gives information about the type,
																//  number of cells, layer in which they are found, etc.
	numCellTypes = f2.scanvar			// Scan the first line, which contains a number giving the # of cell types

	// Define variables to temporarily hold data scanned from file
	objref celltypestring[numCellTypes], techstring[numCellTypes], cellType[numCellTypes]
	double cellnumvar[numCellTypes], cellLayerflag[numCellTypes], cellArtflag[numCellTypes]

	for i=0, numCellTypes-1 {				// For each cell type in the model
		celltypestring[i]= new String()
		techstring[i] = new String()
		f2.scanstr(celltypestring[i].s)				// Scan in the friendly cell name
		f2.scanstr(techstring[i].s)					// Scan in the technical cell name
		cellnumvar[i]=f2.scanvar					// Scan in the number of each cell type
		cellLayerflag[i]=f2.scanvar					// Scan the layer index (layers are defined by the user in the 
													//  LayerHeights parameter)
		cellArtflag[i]=f2.scanvar					// Scan in artificial flag, 1 = artificial cell, 0 = real cell
		cellnumvar[i]=int(cellnumvar[i]/Scale + .5)	// Scale down the number of cells in the model based on the Scale parameter
		// The 'if' condition below is where cells are flagged for cell death, as mentioned in the comments for the 
		//  PercentCellDeath parameter in the parameters.hoc file
		if (cellLayerflag[i]==0) {		// For cell types in a certain layer (in this example, layer index 0) are
										//  susceptible to death (because you are modeling an injury, for example)
										//  then use the PercentCellDeath parameter to calculate how many cells should
										//  survive.									
			cellnumvar[i] = int(cellnumvar[i] * ((100-PercentCellDeath)/100))
		if (cellnumvar[i]<1) {
			cellnumvar[i]=1 			// If all cells of a type are killed or 
										//  if the number of cells is scaled down
										//  to less than 1, ensure there is one
										//  cell of that type in the model.
	f2.close()	// Close the cellnumbers dataset file

	startpos=0	// Start the gid range at 0
	for i=0, numCellTypes-1 {
		cellType[i] = new CellCategoryInfo(i)	// Make one object for each cell type to store the info for that cell type
		// Set the properties of that cell type (the properties that were read in from the cellnumbers dataset file)
		cellType[i].setCellTypeParams(celltypestring[i].s, techstring[i].s, startpos, cellnumvar[i], cellLayerflag[i], cellArtflag[i])	
		// Initialize a placeholder vector that will store information about connectivity from other cell types to this cell type 
		cellType[i].numCons = new Vector(numCellTypes,0)
		cellType[i].setCellTypeDist				// Load the axonal distribution file
		startpos = startpos + cellnumvar[i]		// Increment the startGid for the next cell type's call to setCellTypeParams