Overview: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).

GitHub link: https://github.com/davestanley/HippocampalCA3Net/

Original paper: Stanley, DA, Talathi, SS, Parekh, MB, Cordiner,
D, 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(5):1070-86. doi:
10.1152/jn.00911.2012.

References:
Hajos M, Hoffmann WE, Orban G, Kiss T, and Erdi P. Modulation of
septo- hippocampal Theta activity by GABAA receptors: an experimental
and computational approach. Neuroscience 126: 599-610, 2004.
Traub RD, Wong RK, Miles R, and Michelson H. A model of a CA3
hippocampal pyramidal neuron incorporating voltage-clamp data on
intrinsic conductances. J Neurophysiol 66: 635-650, 1991.

Please address questions to David Stanley (Boston University).


Running the default model:
1) Unzip downloaded file (if necessary)
2) Make sure that the genesis binary is in your current path
3) Change directory into simfiles and type genesis main_default.g
4) Data analysis scripts are located in matlab_plotting/extract_data.
The file analyse_script.m will automatically load and plot simulation
data in Matlab.

Running the circadian model:
The simfiles folder also contains a script called ssh_script.sh. This
is used for setting up batch simulations to conduct parameter sweeps.
Some parameters in the model depend on time (see Methods, Stanley 2013)
this script enables one to sweep through different times of day.

For additional help customizing the model and automatic processing of
batch simulations, please contact the authors.



Figure 1: Full Model, Raster Plot (analyse_script.m).




Figure 2: Sample Simulation Output (main_default.g).




Figure 3: Network Structure.




Figure 4: Network Connectivity. Expressed in terms of synaptic
convergence (# presynaptic cells contacting each postynaptic cell).