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;
TITLE sodium channel (voltage dependent, slightly higher threshold)

sodium channel (voltage dependent, slightly higher threshold)

Ions: na

Style: quasi-ohmic

From: modified from ch_Nav to have a slightly higher threshold, 
	  suitable for bistratified cells

2014 December (Marianne Bezaire): documented

#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'  */

	(mA) =(milliamp)
	(mV) =(millivolt)
	(uF) = (microfarad)
	(molar) = (1/liter)
	(nA) = (nanoamp)
	(mM) = (millimolar)
	(um) = (micron)
	FARADAY = 96520 (coul)
	R = 8.3134	(joule/degC)
	SUFFIX ch_Navbis
	RANGE g, gmax, minf, mtau, hinf, htau, ina, m, h
	RANGE myi
	ena  (mV)
	gmax (mho/cm2)   

	mAlphC = -0.2 (1)
	mAlphV = 38 (mV)
	mBetaC = 0.5 (1)
	mBetaV = 10 (mV)

	hAlphC = 0.23 (1)
	hAlphV = 62 (mV)
	hBetaC = 2 (1)
	hBetaV = 9.5 (mV)
	m h
	v (mV) 
	celsius (degC) : temperature - set in hoc; default is 6.3
	dt (ms) 

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

	SOLVE states
	g = gmax*m*m*m*h  
	ina = g*(v - ena)
	myi = ina
	m = minf
	h = hinf

PROCEDURE states() {	:Computes state variables m, h, and n 
	trates(v)			:      at the current v and dt.
	m = m + mexp*(minf-m)
	h = h + hexp*(hinf-h)
LOCAL q10	: declare outside a block so available to whole mechanism
PROCEDURE rates(v) {  :Computes rate and other constants at current v.
                      :Call once from HOC to initialize inf at resting v.
	LOCAL  alpha, beta, sum	: only available to block; must be first line in block

	q10 = 3^((celsius - 34)/10)

	:"m" sodium activation system - act and inact cross at -40
	alpha = mAlphC*vtrap((v+mAlphV),-5)
	beta = mBetaC*vtrap((v+mBetaV),5)
	sum = alpha+beta        
	mtau = 1/sum 
	minf = alpha/sum
	:"h" sodium inactivation system
	alpha = hAlphC/exp((v+hAlphV)/20)
	beta = hBetaC/(1+exp((v+hBetaV)/-10))
	sum = alpha+beta
	htau = 1/sum 
	hinf = alpha/sum 	
PROCEDURE trates(v) {  :Computes rate and other constants at current v.
                      :Call once from HOC to initialize inf at resting v.
	LOCAL tinc	: only available to block; must be first line in block
	TABLE minf, mexp, hinf, hexp, mtau, htau
	DEPEND dt, celsius, mAlphV, mAlphC, mBetaV, mBetaC, hAlphV, hAlphC, hBetaV, hBetaC
	FROM -100 TO 100 WITH 200
	rates(v)	: not consistently executed from here if usetable_hh == 1
				: so don't expect the tau values to be tracking along with
				: the inf values in hoc

	tinc = -dt * q10

	mexp = 1 - exp(tinc/mtau)
	hexp = 1 - exp(tinc/htau)
FUNCTION vtrap(x,y) {  :Traps for 0 in denominator of rate eqns.
	if (fabs(x/y) < 1e-6) {
		vtrap = y*(1 - x/y/2)
		vtrap = x/(exp(x/y) - 1)

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