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Jamberoo (former JMolEditor) is a library of algorithms for structural Computational Chemistry implemented in the Java programming language. The Jamberoo classes can be integrated into other Java applications.

Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform. Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results. ...

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.