Open Bioinformatics Foundation: Difference between revisions

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{{Use dmy dates|date=July 2020}}

The '''Open Bioinformatics Foundation''' is a [[non -profit]], volunteer -run organization focused on supporting [[open source programming]] in [[bioinformatics]].<ref name=obf-main>{{cite web|title=Open Bioinformatics Foundation|url=http://www.open-bio.org/wiki/Main_Page|accessdateaccess-date=1 September 2014}}</ref> The mission of the foundation is to support the development of open source toolkits for bioinformatics, organise developer-centric [[hackathon]] events and generally assist in the development and promotion of open source software development in the life sciences. The foundation also organises and runs the annual [[Bioinformatics Open Source Conference]], a satellite meeting of the [[Intelligent Systems for Molecular Biology]] conference.<ref name=obf-bosc>{{cite web|title=BOSC -– Open Bioinformatics Foundation|url=http://www.open-bio.org/wiki/BOSC|accessdateaccess-date=1 September 2014}}</ref> The foundation participates in the [[Google Summer of Code]], acting as an umbrella organisation for individual bioinformatics-related projects.<ref name=obf-gsoc>{{cite web|title=Google Summer of Code -– Open Bioinformatics Foundation|url=http://www.open-bio.org/wiki/Google_Summer_of_Code|accessdateaccess-date=1 September 2014}}</ref><ref name=google-obf>{{cite web|title=Open Bioinformatics Foundation|url=https://www.google-melange.com/gsoc/org2/google/gsoc2014/obf|website=www.google-melange.com|accessdateaccess-date=1 September 2014}}</ref>

The Open Bioinformatics Foundation was started in 2001, arising from the [[BioJava]], [[BioPerl]] and [[BioPython]] projects. A formal membership for the foundation was created in 2005.<ref name=obf-main /> In October 2012, the foundation began an association with [[Software in the Public Interest]] (SPI), a US-based non-profit which aids other organizations in the creation and distribution of [[free software|free]] and [[open-source software]]. The association with SPI allows financial donations to the foundation (these are 501(c)3 tax-exempt in the US).<ref name=obf-main /><ref name=spi-obf>{{cite web|title=obf|url=http://spi-inc.org/projects/obf/|website=http://spi-inc.org|accessdateaccess-date=1 September 2014}}</ref>

The foundation is governed by a Boardboard of Directorsdirectors, representing various Bio* projects. As of 20142019, the OBF President is HilmarPeter LappCock ([[National Evolutionary Synthesis Center|NESCentBioPython]]),.<ref representingname=obf-board-elections>{{cite BioPerlweb|title=Board Elections – Open Bioinformatics Foundation|url=https://www.open-bio.org/2020/01/14/obf-board-elections-december-2019/|access-date=15 December 2020}}</ref> Previous OBF Presidentspresidents include [[Ewan Birney]] and Hilmar Lapp ([[National Evolutionary Synthesis Center|NESCent]]), previous Board members include [[Steven E. Brenner]].<ref name=obf-board>{{cite web|title=Board -– Open Bioinformatics Foundation|url=http://www.open-bio.org/wiki/Board|accessdateaccess-date=1 September 2014}}</ref>

==Projects==

The foundation hosts servers for mailing lists, websites, and code repositories for a number of bioinformatics-related open source projects, including:<ref name=projects>{{cite web|title=Projects -– Open Bioinformatics Foundation|url=http://www.open-bio.org/wiki/Projects|accessdateaccess-date=1 September 2014}}</ref>

* [[BioJava]] -– Java toolkit

* [[BioDAS]] - XML Infrastructure for exchanging genome annotations<ref name=biodas-main>{{cite web|title=BioDAS|url=http://www.biodas.org/wiki/Main_Page|accessdate=1 September 2014}}</ref>

* [[BioMOBY]] -– Data and application execution through web services

* [[BioJava]] - Java toolkit

* [[BioRubyBioPerl]] -– RubyPerl toolkit

* [[BioMOBY]] - Data and application execution through web services

* [[BioPerlBioPython]] -– PerlPython toolkit

* [[BioPythonBioRuby]] -– PythonRuby toolkit

* BioPipe - Pipelines and workflow project for large-scale bioinformatics; now defunct<ref name=biopipe>{{cite web|title=Biopipe - BioPerl|url=http://www.bioperl.org/wiki/Biopipe|accessdate=1 September 2014}}</ref>

* [[BioPython]] - Python toolkit

* [[BioRuby]] - Ruby toolkit

* [[BioPHP]]

* [[EMBOSS]] -– Sequence analysis toolkit.

* [[BioSQL]] - [[RDBMS]] Database schema for storing sequences, annotations, taxa data.

* OBDA - a standard for sequence data access locally, remotely, and via [[RDBMS]]

* [[EMBOSS]] - Sequence analysis toolkit.

==See also==

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==External links==

* [http://www.open-bio.org Open Bioinformatics Foundation website]

{{Software in the Public Interest}}

[[Category:Bioinformatics organizations]]