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 Slower potassium channels (voltage dependent)

Slower potassium channels (voltage dependent)

Ions: k

Style: quasi-ohmic

From: Modified from Yuen and Durand, 1991 (squid axon) by Aradi and Holmes (2002)

2014 December (Marianne Bezaire): documented
2014 February (Marianne Bezaire): modified to fit the experimental data from Lu and Jonas
? ? ?: shifted by 65 mV as compared to the Aradi & Holmes paper, unsure why

#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_KvGroup
	RANGE g, gmax, ninf, ntau, ik
	RANGE myi
	v (mV) 
	celsius (degC) : temperature - set in hoc; default is 6.3
	dt (ms) 

	ek  (mV)
	gmax (mho/cm2)
ASSIGNED {		     
	g (mho/cm2)
	ik (mA/cm2)
	ntau (ms)
	myi (mA/cm2)

	SOLVE states
	g = gmax*n
	ik = g*(v-ek)
	myi =  ik

	n = ninf

PROCEDURE states() {	:Computes state variables m, h, and n 
	trates(v)	:      at the current v and dt.       
	n = n + nexp*(ninf-n)
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
	q10 = 3^((celsius - 34)/10)
	:"nf" fKDR activation system
	:alpha = a*(-(v+b))/(exp(-(v+b)/c)-1) : Lien and Jonas, 2003
	alpha = 0.0189324*vtrap(-(v-4.18371),6.42606) : Lien and Jonas, 2003
	beta = 0.015857*exp(-v/25.4834) : Lien and Jonas, 2003

	sum = alpha+beta        
	ntau = 1/sum
	ninf = 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
	TABLE ninf, nexp, ntau
	DEPEND dt, celsius
	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
	nexp = 1 - exp(tinc/ntau)
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)