XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.
IU parallel fastDNAml is a program that infers evolutionary histories from genetic sequences, modified and extended from the serial version of fastDNAml to run in parallel on heterogeneous and widely distributed systems.
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sibsim is designed to simulate either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scaleable way. sibsim is based on XML, completely written in C++ and published under the GNU General Public License
ea-fold is a platform to perform protein folding simulations by means of evolutionary algorithms. The program implements a parallelized distributed evolutionary algorithms and a flexible force field.