Usage notes for the cortical slice model described in Tomsett et al. 2014.

The parameter files for the model described by Tomsett et al. (2014) are included in the
main VERTEX download (in the bsfModel folder), and are also available on figshare. 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 be downloaded from figshare (link below).

If you have any trouble running the simulation or want further details on either the
simulation or the experimental data, please contact us using the contact form.

Figshare link: http://autap.se/figshare


Reference:

Tomsett RJ, Ainsworth M, Thiele A, Sanayei M, Chen X, Gieselmann MA, Whittington MA,
Cunningham MO, Kaiser M. (2014) Virtual Electrode Recording Tool for EXtracellular
potentials (VERTEX): comparing multi-electrode recordings from simulated and biological
mammalian cortical tissue, Brain Structure and Function. doi:10.1007/s00429-014-0793-x