Web Directory

» AceDB
   A hierarchical database system for displaying genomic data (originally C. elegans), suitable also for displaying other scientific data.
   http://www.acedb.org/

» AcePerl
   OO Interface to AceDB
   http://stein.cshl.org/AcePerl/

» Bielefeld University Bioinformatics Server
   BiBiServ supports Internet-based collaborative research, software development and distance education in bioinformatics.
   http://bibiserv.techfak.uni-bielefeld.de/

» BioJava.org
   The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
   http://biojava.org/

» BioLisp.org
   BioLisp.org is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences. We collect and disseminate Lisp biocomputing code, and gather pointers to Lisp and other Intelligent BioComputing methods.
   http://nostoc.stanford.edu/Docs/

» BioPHP
   An open source project to develop PHP code and scripts for biocomputing. A wiki-like service allows collaboration between developers.
   http://www.biophp.org

» BioPython
   The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
   http://www.biopython.org/

» BioQuery
   Tools that searches multiple biomedical databases from your desktop.
   http://www.bioquery.org/

» BioRuby
   BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language.
   http://bioruby.org/

» BioWarehouse Database Integration System
   Integrates multiple public bioinformatics databases into a single relational database system within a common bioinformatics schema.
   http://biowarehouse.ai.sri.com/

» Biochemical Algorithms Library
   C++ framework for rapid software prototyping in molecular modeling.
   http://www.bioinf.uni-sb.de/OK/BALL/

» Bionconductor
   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.
   http://www.bioconductor.org/

» Brainwave Biosolutions
   Bioinformatics Company focused on the development of data mining products, databases, visualization and analysis tools.
   http://www.brainwave.in/

» Cell Electrophysiology Simulation Environment (CESE)
   A framework to perform electrophysiological simulations. Useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
   http://cese.sourceforge.net/

» DW Computing
   Web design, computer sales, and custom programming, including bioinformatics.
   http://www.DWcomputing.com

» Daggoo
   Daggoo helps biologists create automated analyses workflows using existing web services. Includes a video of the project.
   http://www.daggoo.net

» Dynamite
   Code generator for writing dynamic programming programs.
   http://www.ebi.ac.uk/Dynamite/

» High Throughput Screening Tools
   Analytical tools and SQL scripts that solve common problems in drug discovery.
   http://www.htstools.com/

» InterMine
   A general-purpose object-oriented data warehouse system developed as part of the FlyMine project and made available as stand-alone open-source software.
   http://www.intermine.org

» MolTalk
   Software development for structural bioinformatics. Runs on Unix, Windows and MacOSX.
   http://www.moltalk.org/

» NCICB Core Infrastructure
   The National Cancer Institute's Center for Bioinformatics produces the caCORE infrastructure, an open-source enterprise architecture for cancer informatics.
   http://ncicb.nci.nih.gov/NCICB/infrastructure

» NeoBio
   An open source library of Java bioinformatics algorithms. The current version consists mainly of sequence alignment algorithms such as Needleman- Wunsch and Smith-Waterman.
   http://neobio.sourceforge.net

» PISE
   Given an abstract definition of a program's parameters, PISE can generate various types of interface from the configuration module.
   http://www.pasteur.fr/recherche/unites/sis/Pise/

» Pathway Tools
   Predict metabolic pathways from genomes and graphically depict pathways. Visualize gene expression data on a metabolic pathway map. Generate a metabolic wall chart. Includes a genome browser and support for transcriptional regulatory networks.
   http://bioinformatics.ai.sri.com/ptools/

» Phylogenetic Analysis Library
   PAL library is a Java toolkit for determining evolutionary trends.
   http://www.cebl.auckland.ac.nz/pal-project/

» Sight
   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, s
   http://bioinformatics.org/jSight/

» The BioSharp Project
   BioSharp is an open-source project to provide a framework for processing biological data using C# and other .net languages.
   http://biosharp.sourceforge.net/

» The Darwin Manual
   Guide to running this programming language. Library contains programs to compute pairwise alignments, phylogenetic trees, multiple sequence alignments, and to make secondary structure predictions.
   http://www.inf.ethz.ch/personal/gonnet/DarwinManual/DarwinManual.html

» The 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.
   http://sysbio.harvard.edu/csb/resources/computational/scriptome

» The Systems Biology Markup Language
   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.
   http://sbml.org/

» The XEMBL Project
   XEMBL provides access to the EMBL/GenBank/DDBJ Nucleotide Sequence Database, providing output in various XML standards.
   http://www.ebi.ac.uk/xembl/