FERN is a fast, extensible and comprehensive framework for the stochastic simulation and analysis of chemical reaction networks. A chemical reaction network is composed of several molecular species coupled by reaction channels. The goal of stochastic simulation algorithms (SSAs) is to simulate a trajectory of the species ’ populations by a Monte Carlo Markov Chain. Starting from a vector of initial amounts for each species, the SSA updates these values by firing reaction channels accordingly to a distribution given by their propensities. Additionally it calculates the time between two firings and hence provides a time scale for the events. For a broader view about the theory of SSAs please refer to [2, 4, 8]. This guide is intended to be a complete description of the basic FERN package. The documentation for the Cytoscape plugin is separately available a
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