FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java. It includes state of the art algorithms for stochastic simulation and a powerful visualization system based on gnuplot and Cytoscape.FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level.
Institut für Informatik, Ludwig-Maximilians-Universität München
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Florian Erhard, Caroline C. Friedel, Ralf Zimmer.
FERN – a Java framework for stochastic simulation and evaluation of reaction networks.
BMC Bioinformatics, vol 9, no. 1, pp. 356, 2008.