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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.
The 3D Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical image data. Follow the link for more info: http://slicer.org