Projects

Main projects

• BioJava
• BioPerl
• BioPipe
• BioPython
• BioRuby
• BioSQL
• DAS and their list of Global Sequence Identifiers
• MOBY
• EMBOSS
• OBDA (this website is out of date, a new one is being developed)

Affiliated projects

• Generic Genome Browser - part of GMOD
• Chado - The GMOD DB schema
• Pise - a tool to generate Web interfaces software for submitting jobs to these interfaces
• OpenBQS - Bibliographic query system
• BlipKit - Chris Mungall's Prolog toolkit for Bioinformatics and BioMedical Informatics
• BioMake & Skam - Task management tool, similar to makefiles

Other related projects

• BioPHP
• CGL - Comparative Genomics Library
• Wikiomics - Bioinformatics wiki

Ontologies and Definitions

• Cyclone - provides an open source Java API to the pathway tool BioCyc.
• GO-Perl - parsers and object model for OBO ontologies
• Chaos-XML - File format based on the sequence modules of the Chado relational schema
• Sequence Ontology
• Gene Ontology
• Obol