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parFE is fully-parallel high-performance finite element code targeted to the modeling of trabecular bones in humans. It employs scalable multigrid solvers for efficient solutions on massively parallel computers.

MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/

MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/

Biologic Institute's Stylus simulation software suite. (See the SVN repository for source code.)

Common code developed by researchers in the Edwards Bioinformatics Group at SDSU. This code is free for everyone to use. It is our base code that we provide on an as-is basis. Please let us know if you use the code or have questions/comments

""" E-Cell's source code repository has moved to GitHub! https://github.com/ecell The development of E-Cell now continues on GitHub. The Subversion repository was abandoned. """ E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components driven by multiple algorithms with different timescales to coexist in a model.

Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/

Parallel IBDWS is an upgrade from IBDWS that utilizes parallel processing. Also, the incorporation of DNA sequence data has been added since the last code release

openevo is a project started to find out about behaviour of evolutionary generated machine code. It implements a certain set of CPU instruction codes and a few interrupts for interaction with the runtime environment.

The Molecular Modeling Templates, MMT is a C++ class library for molecular simulation applications. MMT serves as a code basis that can be easily extended and modified to perform Monte Carlo and molecular dynamics simulations.

Virtual machine/emulator; "holding pen" for self-replicating programs written in custom RISC assembly-like language, evolving via random point mutations and periodic fitness-based cullings. Inspired (like Avida) by Thomas Ray's alife simulator, Tierra

PubMed Central browser. Source code: http://github.com/dualword/dualword-pmc/