Fig 4. Running simulations.

(A) Relationships among various elements involved in running simulations with BioNet. The pre-built network (blue), is passed to the main Python script (pink) that loads custom user modules and runs BioNet/NEURON to produce the simulation output (purple). (B) The stages of the simulation executed by the main Python script. (C) Algorithm for distributing the cells over a parallel architecture. This simple example shows 10 cells distributed across 4 parallel processes (typically each parallel process corresponds to a CPU core). Cells are assigned to each process in turn (a “round-robin” assignment).