Generic data-assimilation toolbox written in java, with native (c and fortran) libraries for high performance computing. Provides tools to couple to your own model and a wide range of algorithms, ranging from parameter calibration to Kalman filters.
Open Source home for the Virtual Cell platform (VCell). See http://vcell.org/ for details.
Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
Aquaria collects the source code needed to run the generation of the hssp / pssh databases and the visualisation of the content.
Eclim is a set of eclipse and vim plugins to integrate the two projects.
simple event-based plugin interface to open up hardwired software
News: since 2015 we continue all related developments within Collective Knowledge Framework: http://github.com/ctuning/ck/wiki Simple and universal event-based plugin framework and interface to open up hardwared black-box software (tools, application), make them interactive through external plugins, and connect them with other higher-level tools such as Collective Mind. For example, it is used to open up compilers (GCC, LLVM, Open64) for external tuning of optimization of internal heuristics, or to open up applications for online tuning and adaptation particularly on heterogeneous systems. It is based on successful Interactive Compilation Interface (ICI) which was added to mainline GCC >= 4.5. It supports C,C++,Fortran and Java. OpenME requires just one include file "openme.h" and 2 functions to register events or to have a call-back. The usage of this interface is briefly described in an open access publication available at http://arxiv.org/abs/1308.2410
A home for additional useful tasks and types for Ant (http://ant.apache.org).
OpenChem Workbench is an enterprise software suite designed for creating, saving, searching, and exchanging chemical data. It uses existing tools (NIST, Gaussian, CHEMKIN) and its own (easy molecule building, mechanism management, group additivity, etc.)
Proteus Cross Compiler system allows the generation and compilation of Java Code from llvm-gcc compatible languages (C/C++/fortran). The generated code will execute at up to 50% of native code.