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Cellicone is a project to develop an artificial life organism with the necessary components to make it comparable to biological life as we know it. This includes components ranging from proteins to cells to organs to limbs, and many steps between.
RGnome is a gtk based frontend for GNU R, which is a widely used language for statistical computing. It features a fully working R console and an editor with syntax highlighting.
NecJGui is an antennas design tool, interface for Numerical Electromagnetic Code. It allows easily making NEC input files, and viewing them in 3D. It also contains a version of the simulator, so it's complete IDE for full-wave EM simulation.
The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.