KaSim in Haskell
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Graph for Scala is intended to provide basic graph functionality seamlessly fitting into the Scala Collection Library. Like the well known members of scala.collection, Graph for Scala is an in-memory graph library aiming at editing and traversing graphs, finding cycles etc. in a user-friendly way.
Graph rewriting library for Scala
The module integration simulator MOIS. Use for large-scale modelling as it allows a module-based model specification.
Command line stochastic simulator for kappa models. Documentation can be found in the man/ directory