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FERN - A Java Framework for Stochastic Simulation and Evaluation of Reaction Networks

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.

Although FERN consists of more than 100 classes and interfaces, most classes are basically just implementations of one of three major interfaces and abstract classes.
  • The interface Network provides the network structure of the model.
  • The abstract class Simulator performs simulations on a Network. It additionally calls the registered observers during the simulation run.
  • The abstract class Observer traces the simulation progress and creates the simulation output.

FERN is freely available under the GNU Lesser General Public License (LGPL).


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