Software Development

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/

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

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/

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/

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://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

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/

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/

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/

CLEML: Carbon Labeling Experiment Markup Language
CLEML open format for representing and exchanging 13C metabolic flux analysis models.
http://sg.ustc.edu.cn/MFA/cleml/

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

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

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

EST2uni
A tool to analyze a set of ESTs. Cleans, clusters and annotates the sequences and prepares a web site to browse the results in a complete automatic way.
http://www.melogen.upv.es/genomica/web_estpipe/index.php

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

JCell
A Java based framework to reconstruct genetic interactions from microarray data.
http://www-ra.informatik.uni-tuebingen.de/software/JCell/

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

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/

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

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

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, sequence retrieval, E-PCR, gene prediction, similarity search, protein pattern search, and report formatting. Written in Java.
http://bioinformatics.org/jSight/

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/