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The Bourne Commendation: Open Access Evangelist Wins 2009 Benjamin Franklin Award


By Kevin Davies

April 6, 2009 | Australian open-access evangelist Philip Bourne, a prolific computational biologist at the University of California San Diego (UCSD), has beaten out stiff competition to win the 2009 Benjamin Franklin Award.

The annual award, presented by the Bioinformatics Organization, is given to a scientist who epitomizes the open-source values espoused by the legendary inventor and statesman. Bourne will be presented with his award by Jeff Bizzaro, president of Bioinformatics.org, at the 2009 Bio-IT World Conference & Expo in Boston on Tuesday, April 28.

One of Bourne’s nominators said: “If Benjamin Franklin could observe not only his contributions, but Phil’s generous spirit, infectious energy, and passion for science, he would be proud to count Phil Bourne as a colleague of the highest esteem.”

Bourne was nominated for his numerous and varied contributions to both open access in bioinformatics and computational biology as well as his innovations with the Protein Data Bank (PDB). A past president of the International Society for Computational Biology (ISCB), Bourne is the founding editor-in-chief of PLoS Computational Biology, one of the open-access journals launched by the Public Library of Science. In just four years, the journal has become the highest impact factor journal in the niche of mathematical and computational biology. Bourne is also a co-founder (with PLoS) of the website SciVee.tv, which allows scientists across many disciplines to upload videos, lectures, presentations and posters. SciVee is one of four companies that Bourne has helped launch.

As co-director of the PDB, Bourne has transformed an under-utilized database into a major international resource. “He has been instrumental in establishing data standards for macromolecular structure data and for requiring that macromolecular structures deposited in the PDB are also published in a journal,” praised one of his award nominators. This policy “increases exposure of the structural data and enforces a certain level of data quality.” Another project is the BioLit project, which aims to integrate electronic literature directly with the PDB and similar resources by taking advantage of the increasing open accessibility of life sciences literature.

Bourne originally trained as a chemist, earning his PhD in chemistry in 1980 from the Flinders University in Australia. After a postdoctoral fellowship at Sheffield University in the UK, he moved to New York and later became director of the Cancer Center Computing Facility at Columbia University, where he helped establish a tumor registry and various applications and databases in support of patient care. Bourne is also a senior advisor to the life sciences at the San Diego Supercomputer Center (SDSC).

Bourne joins a distinguished group of honorees dating back to 2002. The other five finalists this year were: Warren DeLano (DeLano Scientific), developer of the PyMol molecular viewer application; evolutionary geneticist Jonathan Eisen (UC Davis); Don Gilbert (Indiana University), software/database developer; Heng Li (Welcome Trust Sanger Institute), chief developer of the Maq short-read aligner; and Steven Salzberg (University of Maryland), developer of tools such as MUMmer.

One of Bourne’s own videos on SciVee is on the topic of “ten simple rules for good presentations.” It should be interesting to watch the master in action when he presents his 2009 Benjamin Franklin lecture.

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