Compartmental rule-based modeling of biochemical systems
Winter Simulation Conference
The Relevance of Topology in Parallel Simulation of Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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We present the Stochastic Simulator Compiler (SSC), a tool for exact stochastic simulations of well-mixed and spatially heterogeneous systems. SSC is the first tool to allow a readable high-level description with spatially heterogeneous simulation algorithms and complex geometries; this permits large systems to be expressed concisely. Meanwhile, direct native-code compilation allows SSC to generate very fast simulations. Availability: SSC currently runs on Linux and Mac OS X, and is freely available at http://web.mit.edu/irc/ssc/. Contact: mieszko@csail.mit.edu Supplementary information:Supplementary data are available at Bioinformatics online.