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We present DiSH-Sim, a simulator for large discrete models of biologicalsignal transduction pathways, capable of simulating networks with multi-valuedelements in both deterministic and stochastic manner. We focus on order ofupdate and thus incorporate information about timing, taking into account thatbiological processes are not synchronized and certain biochemical changes occurslower than others. Another feature of our simulator is the use of groupedrules to model multi-valued elements and delays. The DiSH-Sim is publiclyavailable and is being used to validate discrete cancer microenvironment andinfectious disease models. It is also incorporated within a large architecturethat includes natural language processing tools that read biological literatureto assemble logical models. This paper demonstrates the functionalities andease of use of DiSH-Sim, making it a very useful tool for discrete modeling.

DiSH Simulator: Capturing Dynamics of Cellular Signaling with Heterogeneous Knowledge