Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux, and Mac Os X.
AMPHORA is an automated phylogenomic inference application for large-scale protein phylogenetic analysis. It has been applied to automated genome tree construction and metagenomic sequence phylotyping.
Biskit is a modular, object-oriented Python library for structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories.
Brian is a simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists.
GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. A browser-based version is here: http://gentledna.org/.
GIMIAS is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins.
A programmable audio generator intended as an aural aid to meditation, implementing the binaural beat principle as described in Gerald Oster's Oct. 1973 Scientific American article "Auditory Beats in the Brain."
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
ImageJ can display, edit, analyze, process, save, and print 8-bit color and grayscale, 16-bit integer, and 32-bit floating point images. It can read TIFF, PNG, GIF, JPEG, BMP, DICOM, FITS, and raw formats.
OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX, and Linux.
The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models can aid in understanding and potentially preventing the spread of such diseases.
The Virtual Cell is a unique computational environment for modeling and simulation of cell biology . It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists.