Lapp, ISCB Software Sharing Symposium
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Transcript of Lapp, ISCB Software Sharing Symposium
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Hilmar LappOpen Bioinformatics Foundation
(and NESCent) ISCB Session on Software Sharing
ISMB 2008
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About myself• Biologist by training
• BioPerl core developer since 1999
• Lead developer of Bioperl-db, BioSQL
• O|B|F Board of Directors since 2001
• Bioinformatics & computational biology at Novartis (Vienna, San Diego)1997-2006
• Asst. Director for Informatics at NESCent (Durham, NC) since 2006
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O|B|F
• Open Bioinformatics Foundationhttp://open-bio.org
• Incorporated in 2001 as a Not-For-Profit
• Founded primarily to handle HW needs of the Bio* projects, and to run BOSC
• Run by Board of Directors
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O|B|F Mission
Further the cause of the Bio* projects and generally Open Source software by providing infrastructural hardware and software support to hosted projects, and by running BOSC as a forum for Open Source developers.
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O|B|F Infrastucture
• Mailing lists
• Version control server (cvs and svn)
• Anonymous web-browsable cvs or svn
• Web sites, wikis
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• Started ~1995
• 975 modules in core
• >600,000 lines
• Genome Biol paper (2002) cited > 500x
• Leadership baton passed multiple times
• 10s of committers
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• to use
• to re-use, repurpose, or modify
• to redistribute, modified or not
Free as in speech=
Freedom
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OSI-compliant license
• to use
• to re-use, repurpose, or modify
• to redistribute, modified or not
Free as in speech=
Freedom
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• to interact
• to collaborate
• to create & to contribute
Free as in speech=
Culture conducive
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Open Development
• to interact
• to collaborate
• to create & to contribute
Free as in speech=
Culture conducive
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Comparative Methods in R Hackathon, Dec 2007
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• 8 participating R packages
• Ade4, Ape, apTreeshape, Geiger, Laser, OUCH, PaleoTS, Picante
• Before the hackathon
• 1/8 were using version control (but none public)
• 1/8 had a mailing list
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Building Projects & Community
• Phylobase
• Picante
• R-phylo.org
• R-SIG-phylo
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• Goal: support FOSS projects to recruit new developers
• Students are paired with mentors
• Mentors are affiliated with a mentoring organization
• Global program: both students and mentors work remotely
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• 11 students (projects) (2 female)
• 5 started a new project
• 7 projects remain active
• 2 manuscripts pub-lished, 2 more in prep.
• 4 got noticed by research community
Phyloinformatics Summer of Code 2007
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Acknowledgments• Open Bioinformatics
Foundation
• Ewan Birney,Steven Brenner,Chris Dagdigian,Andrew Dalke,Kam Dahlquist,Darin London,Jason Stajich
• Fellow Bio* developers
• BioHackathon sponsors:
• DBCLS/CBRC (2008),NESCent (2006),Apple (2003),Electric Genetics (2002),O’Reilly (2002)
• National Evolutionary Synthesis Center (NESCent) fellows