Large-scale model of neocortical slice in vitro exhibiting persistent gamma (Tomsett et al. 2014)
Usage notes for the cortical slice model described in Tomsett et al. 2014. Requires the VERTEX simulator for Matlab: www.vertexsimulator.org
These are the parameter files for the model described by Tomsett et al. (2014). The parameters are set to run the full model as described in the paper, using VERTEX in parallel mode with 12 labs, to run the simulation for 2400 ms. To run the model, first make sure you have added the VERTEX simulator to your Matlab path as described in Tutorial 0 at vertexsimulator.org. You should also compile the MEX file as described in that tutorial to allow more than one connection from a presynaptic to a postsynaptic neuron. then run the script bsf_model_run.m - this will load the parameters from the other .m files, initialise the network, and run the simulation. You can modify parameters either in the other parameter files, or in the bsf_model_run.m file (for example, if you want to change the number of labs or the location to save results). Results can then be loaded and analysed as described in the tutorials.
NB: the results will be qualitatively, but not quantitatively, the same as in the paper, because the random number generator control code was not implemented at that time.
The model contains approximately 175,000 neurons, each with several compartments, so the memory requirements are quite large. Including the overheads for running on 12 Matlab workers, the simulation uses about 30 GB RAM on our Intel Xeon based Linux server (Matlab 2012b).
We have also uploaded the raw experimental data used for comparison in figure 9 of the paper, along with a script to generate a similar gamma power map to that shown in figure 9a. The data can also be downloaded from figshare.
If you have any trouble running the simulation or want further details on either the simulation or the experimental data, please contact me!