Open Bioinformatics Foundation: Difference between revisions

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The '''Open Bioinformatics Foundation''' is a [[non profit]], volunteer run organization focused on supporting [[open source]] [[programming]] in [[bioinformatics]].

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|access-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|access-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|access-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=google-melange.com|access-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=spi-inc.org|access-date=1 September 2014}}</ref>

The mission of the foundation is to support development of open source toolkits for bioinformatics, organize and run the [[Bioinformatics Open Source Conference]], and generally assist in the development and promotion of open source software development in the life sciences.

The foundation is governed by a board of directors, representing various Bio* projects. As of 2019, the OBF President is Peter Cock ([[BioPython]]).<ref name=obf-board-elections>{{cite web|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 presidents 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|access-date=1 September 2014}}</ref>

The foundation hosts servers for mailing lists, websites, and code repositories for the following open source projects:

* [[BioDAS]] (see: [http://www.biodas.org/]) - XML Infrastructure for exchanging genome annotations

==Projects==

* [[BioJava]] - Java toolkit

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|access-date=1 September 2014}}</ref>

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

* [[BioPerlBioJava]] -– PerlJava toolkit

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

* [http://www.gmod.org/biopipe BioPipe] - Pipelines and workflow project for creating bioinformatics protocol

* [[BioPythonBioPerl]] -– PythonPerl toolkit

* [[BioRubyBioPython]] -– RubyPython toolkit

* [[BioJavaBioRuby]] -– JavaRuby toolkit

* [[BioPHP]]

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

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

* OBDA (see: [http://obda.open-bio.org/]) - a standard for sequence data access locally, remotely, and via [[RDBMS]]

* [[EMBOSS]] - Sequence analysis toolkit.

==See also==

*[[List of open-source bioinformatics software]]

*[[Bioinformatics]]

*[[Generic Model Organism Database]]

*[[Bioinformatics.org]] [http://www.bioinformatics.org]

*[[Generic_Model_Organism_Database | GMOD]] [http://www.gmod.org]

*[http://www.bioinformatics.org/bioc-sharp/wiki/ BioC#] &mdash; Biolibrary for C#

==References==

== External links ==

{{reflist|2}}

* OBF [http://open-bio.org website]

* [http://www.bioinformatics.cc Bioinformatics News]

== External links ==

[[Category:Bioinformatics organizations]]

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

[[Category:Free and open source software organizations]]

{{Software in the Public Interest}}

{{science-org-stub}}

*[[Category:Bioinformatics organizations]]

[[Category:Free software project foundations]]