Open Bioinformatics Foundation

Open Bioinformatics Foundation
Name	Open Bioinformatics Foundation
Formation	2001
Type	Nonprofit
Purpose	Support open source bioinformatics software
Headquarters	International
Region served	Global

Contents

Open Bioinformatics Foundation is a nonprofit organization formed to support open source software development in computational biology and bioinformatics. Founded by contributors to community projects such as Biopython, BioPerl, BioRuby, the foundation has fostered collaboration among developers associated with projects like Galaxy (computational biology), Ensembl, UniProt, EMBL-EBI and NCBI. The foundation operates within a landscape that includes entities such as The Apache Software Foundation, Open Source Initiative, Software Carpentry, and academic institutions including Harvard University, University of Cambridge, Stanford University, Massachusetts Institute of Technology, and University of California, San Diego.

History

The organization traces roots to early 2000s discussions among developers behind BioPerl, Biopython, BioRuby and BioJava who met at gatherings like Bioinformatics Open Source Conference and community events in venues such as Cold Spring Harbor Laboratory, European Bioinformatics Institute and Max Planck Society. Early milestones included incorporation, the creation of mailing lists with participants from Sanger Institute, Wellcome Trust, National Institutes of Health, Lawrence Berkeley National Laboratory, and coordination with projects hosted by SourceForge and later GitHub. Influential collaborations involved contributors affiliated with University of Oxford, University College London, ETH Zurich, University of Tokyo, University of Toronto, Broad Institute, and Imperial College London. The foundation’s timeline intersects with initiatives such as Open Access, Creative Commons, GNU General Public License, and interoperability efforts exemplified by BioSchemas and standards from Global Alliance for Genomics and Health.

The foundation’s mission emphasizes stewardship of open source ecosystems shared by communities linked to European Molecular Biology Laboratory, National Center for Biotechnology Information, Wellcome Sanger Institute, Protein Data Bank, UniProt Consortium, Ensembl Genomes, and translational research groups at Johns Hopkins University, University of California, Berkeley, Karolinska Institute, Cold Spring Harbor Laboratory Press, and National Human Genome Research Institute. Activities include code hosting, mentorship programs modeled after Google Summer of Code, governance templates inspired by Apache License adopters, and community building at conferences such as ISMB, RECOMB, Gordon Research Conferences, FASEB, and EMBO symposia. The foundation supports interoperability with resources like KEGG, Reactome, PDB, RefSeq, and annotation projects associated with Gene Ontology and MGI.

Governance follows a volunteer board structure with officers drawn from contributors affiliated with institutions including European Bioinformatics Institute, Broad Institute, Cold Spring Harbor Laboratory, Sanger Institute, and universities like MIT, Stanford University, University of Cambridge and University of California, San Francisco. Membership comprises individual committers from projects such as Biopython, BioPerl, BioRuby, BioJava, BioJS, and users from biotech firms like Illumina, Thermo Fisher Scientific, Roche, Genentech, and startups incubated at Johns Hopkins Technology Ventures. The foundation’s policies reflect precedents set by organizations such as Mozilla Foundation, Linux Foundation, Apache Software Foundation, Open Source Initiative, and international standards bodies including ISO and W3C.

Hosted and incubated projects include language-specific toolkits like Biopython, BioPerl, BioRuby, BioJava, and visualization libraries related to BioJS plus workflow systems exemplified by Galaxy (computational biology), CWL (Common Workflow Language), Nextflow, and containerization practices using Docker and Singularity (software). Integration efforts connect to databases and resources such as UniProt, Ensembl, PDB, RefSeq, KEGG, Reactome, Gene Ontology Consortium, TreeBASE, and algorithmic libraries developed alongside groups at European Bioinformatics Institute and Sanger Institute. Projects often interoperate with formats and tools from SAMtools, HTSlib, BLAST, HMMER, MAFFT, Clustal Omega, BioConductor, Bioconductor, SeqAn, BEDTools, GATK, Picard (software), BWA, Minimap2, Cufflinks and visualization platforms used by UCSC Genome Browser, IGV, JBrowse, and workflow managers at Seven Bridges Genomics.

The foundation organizes and sponsors events such as Bioinformatics Open Source Conference, workshops at ISMB, tutorials at RECOMB, collaborative coding sprints at European Bioinformatics Institute, and training sessions inspired by Software Carpentry and Data Carpentry. Training collaborations have included educators and researchers from Harvard Medical School, Stanford Medicine, EMBO, Wellcome Trust Sanger Institute, Cold Spring Harbor Laboratory, National Institutes of Health, European Molecular Biology Laboratory, University of Cambridge, University of Oxford, and Johns Hopkins University. Community outreach leverages conference partnerships with Gordon Research Conferences, FASEB, EMBO, IEEE, and regional symposia organized by Society for Molecular Biology and Evolution and American Society for Microbiology.

Category:Bioinformatics organizations