Hilmar LappOpen Bioinformatics Foundation

(and NESCent) ISCB Session on Software Sharing

ISMB 2008

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

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

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.

O|B|F Infrastucture

• Mailing lists

• Version control server (cvs and svn)

• Anonymous web-browsable cvs or svn

• Web sites, wikis

• Started ~1995

• 975 modules in core

• >600,000 lines

• Genome Biol paper (2002) cited > 500x

• Leadership baton passed multiple times

• 10s of committers

• to use

• to re-use, repurpose, or modify

• to redistribute, modified or not

Free as in speech=

Freedom

OSI-compliant license

• to use

• to re-use, repurpose, or modify

• to redistribute, modified or not

Free as in speech=

Freedom

• to interact

• to collaborate

• to create & to contribute

Free as in speech=

Culture conducive

Open Development

• to interact

• to collaborate

• to create & to contribute

Free as in speech=

Culture conducive

Comparative Methods in R Hackathon, Dec 2007

• 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

Building Projects & Community

• Phylobase

• Picante

• R-phylo.org

• R-SIG-phylo

• 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

• 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

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