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/

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/

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/

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 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

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/

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

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 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/

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/

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

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/

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

InterMine
- InterMine is an 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

Boulder.pm
- Simple but powerful data exchange language, suitable for serializing biological data objects.
- http://www.broad.mit.edu/genome_software/other/boulder.html

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

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

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

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

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

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

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

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

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/

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/

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

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

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