Encoding and retrieval in a model of the hippocampal CA1 microcircuit (Cutsuridis et al. 2009)

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Accession:123815
This NEURON code implements a small network model (100 pyramidal cells and 4 types of inhibitory interneuron) of storage and recall of patterns in the CA1 region of the mammalian hippocampus. Patterns of PC activity are stored either by a predefined weight matrix generated by Hebbian learning, or by STDP at CA3 Schaffer collateral AMPA synapses.
Reference:
1 . Cutsuridis V, Cobb S, Graham BP (2010) Encoding and retrieval in a model of the hippocampal CA1 microcircuit. Hippocampus 20:423-46 [PubMed]
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 basket cell;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Pattern Recognition; Activity Patterns; Temporal Pattern Generation; Learning; STDP; Connectivity matrix; Storage/recall;
Implementer(s): Graham, Bruce [B.Graham at cs.stir.ac.uk]; Cutsuridis, Vassilis [vcutsuridis at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; GabaA; AMPA; NMDA;
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Hipp_paper_code
Results
Weights
readme.txt
ANsyn.mod *
bgka.mod *
burststim2.mod *
cad.mod *
cagk.mod *
cal.mod *
calH.mod *
car.mod *
cat.mod *
ccanl.mod *
gskch.mod *
h.mod *
hha_old.mod *
hha2.mod *
hNa.mod *
IA.mod *
ichan2.mod *
Ih.mod *
kad.mod *
kap.mod *
Kaxon.mod *
kca.mod *
Kdend.mod *
km.mod *
Ksoma.mod *
LcaMig.mod *
my_exp2syn.mod *
Naaxon.mod *
Nadend.mod *
Nasoma.mod *
nca.mod *
nmda.mod *
regn_stim.mod *
somacar.mod *
STDPE2Syn.mod *
axoaxonic_cell17S.hoc *
basket_cell17S.hoc *
bistratified_cell13S.hoc *
burst_cell.hoc *
HAM_SR.ses
HAM_StoRec_par.hoc
HAM_StoRec_ser.hoc
mosinit.hoc
olm_cell2.hoc
pyramidal_cell_14Vb.hoc
ranstream.hoc *
stim_cell.hoc *
                            
COMMENT
km.mod
Potassium channel, Hodgkin-Huxley style kinetics
Based on I-M (muscarinic K channel)
Slow, noninactivating
Author: Zach Mainen, Salk Institute, 1995, zach@salk.edu
	
ENDCOMMENT

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

NEURON {
	SUFFIX km
	USEION k READ ek WRITE ik
	RANGE n, gk, gbar
	RANGE ninf, ntau
	GLOBAL Ra, Rb
	GLOBAL q10, temp, tadj, vmin, vmax
}

UNITS {
	(mA) = (milliamp)
	(mV) = (millivolt)
	(pS) = (picosiemens)
	(um) = (micron)
} 

PARAMETER {
	v 		(mV)
	dt		(ms)
	gbar = 10   	(pS/um2)	: 0.03 mho/cm2
	tha  = -30	(mV)		: v 1/2 for inf
	qa   = 9	(mV)		: inf slope		
	Ra   = 0.001	(/ms)		: max act rate  (slow)
	Rb   = 0.001	(/ms)		: max deact rate  (slow)
	celsius		(degC)
	temp = 23	(degC)		: original temp 	
	q10  = 2.3			: temperature sensitivity
	vmin = -120	(mV)
	vmax = 100	(mV)
} 


ASSIGNED {
	a		(/ms)
	b		(/ms)
	ik 		(mA/cm2)
	gk		(pS/um2)
	ek		(mV)
	ninf
	ntau (ms)	
	tadj
}
 

STATE { n }

INITIAL { 
	trates(v)
	n = ninf
}

BREAKPOINT {
        SOLVE states
	gk = tadj*gbar*n
	ik = (1e-4) * gk * (v - ek)
} 

LOCAL nexp

PROCEDURE states() {   : Computes state variable n 
        trates(v)      : at the current v and dt.
        n = n + nexp*(ninf-n)
        VERBATIM
        return 0;
        ENDVERBATIM
}

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
	DEPEND dt, celsius, temp, Ra, Rb, tha, qa
	
	FROM vmin TO vmax WITH 199

	rates(v): not consistently executed from here if usetable_hh == 1
        tadj = q10^((celsius - temp)/10)  :temperature adjastment
        tinc = -dt * tadj
        nexp = 1 - exp(tinc/ntau)
}


PROCEDURE rates(v) {  :Computes rate and other constants at current v.
                      :Call once from HOC to initialize inf at resting v.

        a = Ra * (v - tha) / (1 - exp(-(v - tha)/qa))
        b = -Rb * (v - tha) / (1 - exp((v - tha)/qa))
        ntau = 1/(a+b)
	ninf = a*ntau
}


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