PISKaS: Parallel Implementation of a Spatial Kappa Simulator. PISKaS is a stochastic simulator for rule-based models written in an expanded version of Kappa-Language, which we call Spatial Kappa (see the wiki of this repository). PISKaS is directly based on (and forked from) the repository of the simulation software KaSim v3.5. The main new features of PISKaS are: Models must be written in Spatial Kappa (wiki/usage). Simulations will run using an MPI framework, where every compartment or cell (subcompartments defined with an array notation) use an independent core of the computing architecture. To run a spatial simulation you need to use the mpirun tool of your MPI framework, and give as ”number-of-cores” parameter (-n X), where X is the amount of compartments or cells of your model. You need to specify the synchronization step for your simulation using the PISKaS argument -sync-t. This argument defines the time step to synchronize compartments; a small value gives a slow but accurate simulation and a large value, a fast but unaccurate simulation. It is recomended to first read the pdf of KaSim reference manual (available here) to learn about stochastic simulation and Kappa-Language.

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  1. von Stechow, Louise (ed.); Delgado, Alberto Santos (ed.): Computational cell biology. Methods and protocols (2018)