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 Hyperpolarization-activated, CN-gated channel (voltage dependent)

Hyperpolarization-activated, CN-gated channel (voltage dependent)

Ions: non-specific

Style: quasi-ohmic

From: Chen et al (2001), distal dendrite, control h channel
(modeling by Ildiko Aradi, iaradi@uci.edu)

2014 December (Marianne Bezaire): documented, only slow tau used, fake
ion switched to a non-specific current

#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)
	RANGE gmax, g, i, e
	RANGE hinf
	RANGE slow_tau :, fast_tau
	RANGE myi
	gmax  (mho/cm2)
	e (mV)
	v (mV) 
	celsius (degC)
	dt (ms)    
	g (mho/cm2)
 	i (mA/cm2)
 	:fast_tau (ms)
 	slow_tau (ms) 
 	myi (mA/cm2)

	SOLVE states METHOD cnexp
	g = gmax*h*h
	i = g*(v - e)
	myi = i
INITIAL { : called from hoc to calculate hinf at resting potential
	h = hinf

DERIVATIVE states {	:computes h at current v and dt 
	h' = (hinf-h)/slow_tau :  + (hinf-h)/fast_tau
PROCEDURE trates(v) {  :Computes rate and other constants at current v.
	TABLE hinf, slow_tau : , fast_tau
	DEPEND celsius 
	FROM -120 TO 100 WITH 220
    :q10 = 3^((celsius - 6.3)/10)
    q10 = 3^((celsius - 34)/10)
	hinf =  1 / (1 + exp( (v+91)/10 ))

	:"hyf" FAST CONTROL Hype activation system
	:fast_tau = (14.9 + 14.1 / (1+exp(-(v+95.2)/0.5)))/q10

	:"hys" SLOW CONTROL Hype activation system
	slow_tau = (80*1.5 + .75*172.7 / (1+exp(-(v+59.3)/-0.83)))/q10



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