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

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Accession:187604
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
Reference:
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
Citations  Citation Browser
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;
Gene(s):
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; 
NEURON {
  SUFFIX nothing
}

: gmin - the starting gid for this type of cell
FUNCTION get_x_pos(gid, gmin, BinNumX, BinNumYZ, binSizeX) {
	LOCAL CellNum, tmp
	CellNum=gid - gmin+1
	tmp = floor((CellNum-1)/BinNumYZ)
	get_x_pos =  fmod(tmp,BinNumX)*binSizeX+binSizeX/2.0
	:printf("---get_x_pos=%f\n", get_x_pos)
}

FUNCTION get_y_pos(gid, gmin, BinNumY, BinNumZ, binSizeY) {
	LOCAL CellNum, tmp, pos
	CellNum=gid - gmin+1
	tmp = floor((CellNum-1)/BinNumZ)
	get_y_pos =  fmod(tmp,BinNumY)*binSizeY+binSizeY/2.0
}

FUNCTION get_z_pos(gid, gmin, BinNumZ, binSizeZ, ZHeight) {
	LOCAL CellNum, pos
	CellNum=gid - gmin+1
	get_z_pos = fmod((CellNum-1),BinNumZ)*binSizeZ+binSizeZ/2+ZHeight
}


COMMENT
VERBATIM
static double get_x_pos (int gid, int gmin, int BinNumX, int BinNumYZ, int binSizeX) {
	double pos;
	int CellNum, tmp;
	CellNum=gid - gmin+1;
	tmp = floor((CellNum-1)/BinNumYZ);
	pos =  (tmp%BinNumX)*binSizeX+binSizeX/2.0;
	return pos;
}
ENDVERBATIM

VERBATIM
static double get_y_pos (int gid, int gmin, int BinNumY, int BinNumZ, int binSizeY) {
	double pos;
	int CellNum, tmp;
	CellNum=gid - gmin+1;
	tmp = floor((CellNum-1)/BinNumZ);
	pos =  (tmp%BinNumY)*binSizeY+binSizeY/2.0;
	return pos;
}
ENDVERBATIM

VERBATIM
static double get_z_pos (int gid, int gmin, int BinNumZ, int binSizeZ, int ZHeight) {
	double pos;
	int CellNum;
	CellNum=gid - gmin+1;
	pos = ((CellNum-1)%BinNumZ)*binSizeZ+binSizeZ/2+ZHeight;
	return pos;
}
ENDVERBATIM
ENDCOMMENT