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Bionconductor - http://www.bioconductor.org/
The Bioconductor project produces an open source software framework that will assist biologists and statisticians working in bioinformatics, with primary emphasis on inference using DNA microarrays, built mostly using R. |
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The Systems Biology Markup Language - http://sbml.org/
Information on the SBML project which helps develop a variety of software packages for SBML, a computer-readable format for representing models of biochemical reaction networks in software. |
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Bioperl.org - http://www.bioperl.org
The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. The Bioperl server provides an online resource for modules, scripts, and web links. |
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http://www.acedb.org/ - http://www.acedb.org/
A hierarchical database system for displaying genomic data (originally C. elegans), suitable also for displaying other scientific data. |
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BioJava.org - http://biojava.org/
The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data. |
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The Scriptome - http://sysbio.harvard.edu/csb/resources/computational/scriptome
A set of software tools that filter, format, and merge data in tabular or common biological formats. Organized as a classified collection of Perl one-liners. |
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http://neobio.sourceforge.net - http://neobio.sourceforge.net
An open source library of Java bioinformatics algorithms. The current version consists mainly of sequence alignment algorithms such as Needleman- Wunsch and Smith-Waterman. |
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http://www.biophp.org - http://www.biophp.org
An open source project to develop PHP code and scripts for biocomputing. A wiki-like service allows collaboration between developers. |
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The Darwin Manual - http://www.inf.ethz.ch/personal/gonnet/DarwinManual/DarwinManual.html
Guide to running this programming language. Library contains programs to compute pairwise alignments, phylogenetic trees, multiple sequence alignments, and to make secondary structure predictions. |
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Cell Electrophysiology Simulation Environment (CESE) - http://cese.sourceforge.net/
A framework to perform electrophysiological simulations. Useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations. |
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BioQuery - http://www.bioquery.org/
Tools that searches multiple biomedical databases from your desktop. |
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High Throughput Screening Tools - http://www.htstools.com/
Analytical tools and SQL scripts that solve common problems in drug discovery. |
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http://bioinformatics.org/jSight/ - http://bioinformatics.org/jSight/
Extendable parallel system for automatic genome analysis. Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Features for converting between naming systems, sequence retrieval, E-PCR, gene prediction, similarity search, protein pattern search, and report formatting. Written in Java. |
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Brainwave Biosolutions - http://www.brainwave.in/
Bioinformatics Company focused on the development of data mining products, databases, visualization and analysis tools. |
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DW Computing - http://www.DWcomputing.com
Web design, computer sales, and custom programming, including bioinformatics. |