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
References:
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 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;
TITLE calcium-activated potassium channel (non-voltage-dependent)

COMMENT
Ca2+ activated K+ channel (not voltage dependent)

From:  original said for granule cells, but used in all the cell types

Updates:
2014 December (Marianne Bezaire): documented
ENDCOMMENT


VERBATIM
#include <stdlib.h> /* 	Include this library so that the following
						(innocuous) warning does not appear:
						 In function '_thread_cleanup':
						 warning: incompatible implicit declaration of 
						          built-in function 'free'  */
ENDVERBATIM

UNITS {
        (molar) = (1/liter)
        (mM)    = (millimolar)
	(mA)	= (milliamp)
	(mV)	= (millivolt)
}

NEURON {
	SUFFIX ch_KCaS
	USEION k READ ek WRITE ik VALENCE 1
	USEION ca READ cai VALENCE 2
	RANGE g, gmax, qinf, qtau, ik
	RANGE myi
    THREADSAFE
}

INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}

PARAMETER {
      celsius (degC) : temperature - set in hoc; default is 6.3
	v		(mV)
	dt		(ms)
	gmax  (mho/cm2)
	ek	(mV)
	cai (mM)
}

STATE { q }

ASSIGNED {
	ik (mA/cm2) 
	g (mho/cm2) 
	qinf 
	qtau (ms) 
	qexp
	myi (mA/cm2)
}


BREAKPOINT {          :Computes i=g*q^2*(v-ek)
	SOLVE state
    g = gmax * q*q
	ik = g * (v-ek)
	myi = ik
}

UNITSOFF
: verbatim blocks are not thread safe (perhaps related, this mechanism cannot be used with cvode)
INITIAL {
	q=qinf
	rate(cai)
}

PROCEDURE state() {  :Computes state variable q at current v and dt.
	:cai = ncai + lcai + tcai
	rate(cai)
	q = q + (qinf-q) * qexp
}

LOCAL q10
PROCEDURE rate(cai) {  :Computes rate and other constants at current v.
	LOCAL alpha, beta, tinc
	q10 = 3^((celsius - 34)/10) : set to 1 for the cutsuridis model?
		:"q" activation system
alpha = 1.25e1 * cai * cai
beta = 0.00025 

	qtau = 1 /(alpha + beta)/q10
	qinf = alpha * qtau
	tinc = -dt
	qexp = 1 - exp(tinc/qtau)
}

UNITSON

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