The 2006 NESCent Phyloinformatics Hackathon: A Field Report

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Issue Date
2006
Author
Lapp, Hilmar
Bala, Sendu
Balhoff, James P.
Bouck, Amy
Goto, Naohisa
Holder, Mark T.
Holland, Richard
Holloway, Alisha K.
Katayama, Toshiaki
Lewis, Paul O.
Mackey, Aaron J.
Osborne, Brian I.
Piel, William H.
Kosakovsky Pond, Sergei L.
Poon, Art F. Y.
Qui, Wei-Gang
Stajich, Jason E.
Stoltzfus, Arlin
Thierer, Tobais
Vilella, Albert J.
Vos, Rutger A.
Zmasek, Christian M.
Zwickl, Derrick J.
Vision, Todd J.
Publisher
Oxford University Press
Type
Article
Article Version
Scholarly/refereed, publisher version
Published Version
http://www.la-press.com/the-2006-nescent-phyloinformatics-hackathon-a-field-report-article-a480
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(c) 2007 Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder MT, Holland R, Holloway A, Katayama T, Lewis PO et al. Copyright in this article, its metadata, and any supplementary data is held by its author or authors. It is published under the Creative Commons Attribution (CC-BY) licence. For further information go to: http://creativecommons.org/licenses/by/3.0/.
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Abstract
In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development.
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http://hdl.handle.net/1808/9211
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Citation
Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder MT, Holland R, Holloway A, Katayama T, Lewis PO et al.. 2007. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics. 3:357–366.

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(c) 2007 Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder MT, Holland R, Holloway A, Katayama T, Lewis PO et al. Copyright in this article, its metadata, and any supplementary data is held by its author or authors. It is published under the Creative Commons Attribution (CC-BY) licence. For further information go to: http://creativecommons.org/licenses/by/3.0/.
Except where otherwise noted, this item's license is described as: (c) 2007 Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder MT, Holland R, Holloway A, Katayama T, Lewis PO et al. Copyright in this article, its metadata, and any supplementary data is held by its author or authors. It is published under the Creative Commons Attribution (CC-BY) licence. For further information go to: http://creativecommons.org/licenses/by/3.0/.