Bioinformatics Links Directory : Bio-* Programming Tools

This section contains links that include information on software development tools, such as BioJava and BioPerl. Other application programming interfaces (API) which are specifically designed for processing biological data are also listed here.

BioPipe - (Found July 2, 2008 )

The biopipe is a workflow framework that seeks to address some of the complexity involved in carrying out large scale bioinformatics analysis. It has been designed to work intimately with the bioperl package.
http://biopipe.org/

BioPHP - (Found July 2, 2008 )

Open Source PHP code for bioinformatics. Includes functions and minitools (copy and paste one page scripts for basic tasks in bioinformatics. A wiki-like service allows modification and improvement of code.
http://www.biophp.org/

BioPerl course - (Found July 2, 2008 )

Great tutorial for those interested in the bioperl group of modules.
http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/

BioPerl - (Found July 2, 2008 )

The BioPerl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.
http://www.bioperl.org/

BioPax - (Found July 2, 2008 )

The BioPAX web site provides information about a collaborative effort to create a data exchange format for biological pathways.
http://www.biopax.org/

BioMoby - (Found July 2, 2008 )

BioMOBY is an international research project involving biological data hosts, biological data service providers, and coders whose aim is to explore various methodologies for biological data representation, distribution, and discovery.
http://biomoby.org/

BioJava - (Found July 2, 2008 )

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

BioDAS - (Found July 2, 2008 )

This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data.
http://biodas.org/

Systems Biology Markup Language (SBML) - (Found July 2, 2008 )

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and many other areas in systems biology.
http://www.sbml.org/