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Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.
ModelicaFloChrt is a script/Perl process that extracts information from Modelica library html help files and generates flow charts of module connectivity in eps and pdf formats.
STOCHSIM is a stochastic simulator for biochemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. Simple spatial structures can be built.