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What is StochKit?
Traditional ordinary differential equation-based approaches to simulation of chemical reacting systems fail to capture the randomness inherent in such systems at scales common in intracellular biochemical processes.
We present STOCHKIT, an efficient, extensible stochastic simulation framework developed in the C++ language that aims to make stochastic simulation accessible to practicing biologists and chemists, while remaining open to extension via new stochastic and multiscale algorithms.
The beta version contains the popular Gillespie SSA algorithm, explicit tau-leaping, implicit tau-leaping and trapezoidal tau-leaping methods. METHODS We also provide some basic tools to solve a question of great concern to developers of accelerated stochastic algorithms---how can we verify the accuracy of a stochastic solver, given the inherently random nature of stochastic simulation? The Kolmogorov distance and histogram distance for quantifying differences in statistical distribution shapes are provided in MATLAB languages. STRUCTURE PROCESS This manual provides a detailed introduction to the software.
STOCHKIT is available for free to anyone for research use. If you are interested in incorporating any of the STOCHKIT software into commercial applications, please contact Professor Petzold at: petzold@engineering.ucsb.edu
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