whole-brain model by OIST, RIKEN and UEC, Japan.

Previous to a simulation, check that the folder log is empty. The gdf files containing the spikes of the different populations will be stored at log.

This version can run on a desktop PC, we recommend at least using 10 threads for this simulation (the running time is 30 min. approximately for 1s of biological time). Please check the file simParams.py for changing the main simulation settings:

dt: time bin (we recommend 0.1 ms)

nbcpu: the number of threads (at least 10).

simDuration: 1500.0 ms (the simulation will add 500ms for initial settings, then it is needed at least 500ms for network stabilization. The last 1000.ms corresponds to resting state).

regions: to activate/deactivate regions.

To start a simulation run from command line: python stim_all_model.py

For running on HPC clusters, please include the command above within a job (i.e SLURM), and adjust nbcpu accordingly (you may change to 1 if any issue on HPC, and manage the computational resources directly from the job file).

NEST versions (2.16 ~ 2.20)

Python version: 3.0 ~

If this work was used in your research, we ask kindly to refer our work. Thank you !.