Open Bioinformatics Foundation

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The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.[1] 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.[2] The foundation participates in the Google Summer of Code, acting as an umbrella organisation for individual bioinformatics-related projects.[3][4]

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.[1] 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 and open-source software. The association with SPI allows financial donations to the foundation (these are 501(c)3 tax-exempt in the US).[1][5]

The foundation is governed by a Board of Directors, representing various Bio* projects. As of 2014, the OBF President is Hilmar Lapp (NESCent), representing BioPerl. Previous OBF Presidents include Ewan Birney and previous Board members include Steven E. Brenner.[6]

Projects[edit]

The foundation hosts servers for mailing lists, websites, and code repositories for a number of bioinformatics-related open source projects, including:[7]

  • BioDAS - XML Infrastructure for exchanging genome annotations[8]
  • BioJava - Java toolkit
  • BioMOBY - Data and application execution through web services
  • BioPerl - Perl toolkit
  • BioPipe - Pipelines and workflow project for large-scale bioinformatics; now defunct[9]
  • BioPython - Python toolkit
  • BioRuby - Ruby toolkit
  • BioPHP
  • 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[edit]

References[edit]

  1. ^ a b c "Open Bioinformatics Foundation". Retrieved 1 September 2014. 
  2. ^ "BOSC - Open Bioinformatics Foundation". Retrieved 1 September 2014. 
  3. ^ "Google Summer of Code - Open Bioinformatics Foundation". Retrieved 1 September 2014. 
  4. ^ "Open Bioinformatics Foundation". www.google-melange.com. Retrieved 1 September 2014. 
  5. ^ "obf". http://spi-inc.org. Retrieved 1 September 2014. 
  6. ^ "Board - Open Bioinformatics Foundation". Retrieved 1 September 2014. 
  7. ^ "Projects - Open Bioinformatics Foundation". Retrieved 1 September 2014. 
  8. ^ "BioDAS". Retrieved 1 September 2014. 
  9. ^ "Biopipe - BioPerl". Retrieved 1 September 2014. 

External links[edit]