Hippocampal CA3 network and circadian regulation (Stanley et al. 2013)

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This model produces the hippocampal CA3 neural network model used in the paper below. It has two modes of operation, a default mode and a circadian mode. In the circadian mode, parameters are swept through a range of values. This model can be quite easily adapted to produce theta and gamma oscillations, as certain parameter sweeps will reveal (see Figures). BASH scripts interact with GENESIS 2.3 to implement parameter sweeps. The model contains four cell types derived from prior papers. CA3 pyramidal are derived from Traub et al (1991); Basket, stratum oriens (O-LM), and Medial Septal GABAergic (MSG) interneurons are taken from Hajos et al (2004).
1 . Stanley DA, Talathi SS, Parekh MB, Cordiner DJ, Zhou J, Mareci TH, Ditto WL, Carney PR (2013) Phase shift in the 24-hour rhythm of hippocampal EEG spiking activity in a rat model of temporal lobe epilepsy. J Neurophysiol 110:1070-86 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Hippocampus; Medial Septum;
Cell Type(s): Hippocampus CA3 pyramidal GLU cell; Hippocampus CA3 interneuron basket GABA cell; Hippocampus CA3 stratum oriens lacunosum-moleculare interneuron; Hippocampus septum medial GABAergic neuron;
Channel(s): I Na,t; I A; I K; I h; I K,Ca; I Calcium;
Gap Junctions:
Receptor(s): GabaA; AMPA;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Epilepsy; Brain Rhythms; Circadian Rhythms;
Implementer(s): Stanley, David A ;
Search NeuronDB for information about:  Hippocampus CA3 pyramidal GLU cell; Hippocampus CA3 interneuron basket GABA cell; GabaA; AMPA; I Na,t; I A; I K; I h; I K,Ca; I Calcium; Gaba; Glutamate;
//Bash generated parameter file
int small_net = 0
int no_synapses = 0
int plot_on = 1
int include_NMDA = 0
int bc_gammanet = 0
float percent_msg_intact = 1.0
float percent_ACh_intact = 1.0
float pi = 3.1415926535
float EC_val = {1 + 0.25* {cos {2*{pi}/24*{6-12}}} }
float SCN_val = {1 + 0.20* {cos {2*{pi}/24*{6-0}}} }
float mel_val = {1 + 0.10* {cos {2*{pi}/24*{6-12}}} }
float ACh_val = {1 + 1.0* {cos {2*{pi}/24*{6-0}}} }
float Ca_val = {1 + 0.0* {cos {2*{pi}/24*{6-0}}} }
float EC_amp = 0.25
float SCN_amp = 0.20
float mel_amp = 0.10
float ACh_amp = 1.0
float Ca_amp = 0.0
float ACh_accom_amp = 0.0
float ACh_Esyn_amp = 0.0
float ACh_Isyn_amp = 0.0
float ACh_pyr_amp = 0.0
float ACh_bc_amp = 0.0
float ACh_olm_amp = 0.0
float pyr_inject0 = 500.0e-12
float bc_inject0 = 0.00e-11
float olm_inject0 = -1.0e-11
float msg_inject0 = 2.1e-11
float bc2pyr_GABA_A0 = 9.2e-9
float pyr2pyr_AMPA0 = 2.6e-9
float Gmax_pyr_bkgnd0 = 1.0e-9
str dataoutput_path = "./dataset_temp"
str expname_path = "0_test_fullnet_6am"
str circtime_path = "t0"
float sim_time = 1.0
int tindex = 1
//include main_script.g

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