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;
TITLE sodium channel (voltage dependent, for axons)

sodium channel (voltage dependent, for axons)
Meant for axons, no slow inactivation.

Ions: na

Style: quasi-ohmic

From: M.Migliore Jul. 1997

2002 April (Michele Migliore): added sh to account for higher threshold
2014 December (Marianne Bezaire): documented

	SUFFIX ch_Navaxonp
	RANGE  gmax, myi, e, g
	GLOBAL minf, hinf, mtau, htau,thinf, qinf

	sh   = 15	 (mV)
	gmax = 0.010 (mho/cm2)	
	tha  =  -30	(mV)		: v 1/2 for act	
	qa   = 7.2	(mV)		: act slope (4.5)		
	Ra   = 0.4	(/ms)		: open (v)		
	Rb   = 0.124 	(/ms)		: close (v)		

	thi1  = -45	(mV)		: v 1/2 for inact 	
	thi2  = -45 (mV)		: v 1/2 for inact 	
	qd   = 1.5	(mV)	        : inact tau slope
	qg   = 1.5  (mV)
	mmin = 0.02	
	hmin = 0.5			
	q10 = 2
	Rg   = 0.01 (/ms)		: inact recov (v) 	
	Rd   = .03 	(/ms)		: inact (v)	

	thinf = -50 (mV)		: inact inf slope	
	qinf  = 4 	(mV)		: inact inf slope 

	ena		(mV)            : must be explicitly def. in hoc
	v 		(mV)

	(mA) = (milliamp)
	(mV) = (millivolt)
	(pS) = (picosiemens)
	(um) = (micron)

	ina 		(mA/cm2)
	myi 		(mA/cm2)
	g		(mho/cm2)
	minf 		hinf 		
	mtau (ms)	htau (ms) 	

STATE { m h}

	SOLVE states METHOD cnexp
	g = gmax*m*m*m*h
	ina = g * (v - ena)
	myi = ina


DERIVATIVE states {   
	m' = (minf-m)/mtau
	h' = (hinf-h)/htau

PROCEDURE trates(vm) {  
        LOCAL  a, b, qt
	a = trap0(vm,tha+sh,Ra,qa)
	b = trap0(-vm,-tha-sh,Rb,qa)
	mtau = 1/(a+b)/qt
        if (mtau<mmin) {mtau=mmin}
	minf = a/(a+b)

	a = trap0(vm,thi1+sh,Rd,qd)
	b = trap0(-vm,-thi2-sh,Rg,qg)
	htau =  1/(a+b)/qt
        if (htau<hmin) {htau=hmin}
	hinf = 1/(1+exp((vm-thinf-sh)/qinf))

FUNCTION trap0(v,th,a,q) {
	if (fabs(v-th) > 1e-6) {
	        trap0 = a * (v - th) / (1 - exp(-(v - th)/q))
	} else {
	        trap0 = a * q