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The 2006 NESCent Phyloinformatics Hackathon: A Field Report

Publication ,  Journal Article
Lapp, H; Bala, S; Balhoff, JP; Bouck, A; Goto, N; Holder, M; Holland, R; Holloway, A; Katayama, T; Lewis, PO; Mackey, AJ; Osborne, BI ...
Published in: Evolutionary bioinformatics online
January 2007

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.

Duke Scholars

Published In

Evolutionary bioinformatics online

EISSN

1176-9343

ISSN

1176-9343

Publication Date

January 2007

Volume

3

Start / End Page

287 / 296

Related Subject Headings

  • Bioinformatics
  • 3105 Genetics
  • 3102 Bioinformatics and computational biology
  • 0802 Computation Theory and Mathematics
  • 0601 Biochemistry and Cell Biology
  • 0502 Environmental Science and Management
 

Citation

APA
Chicago
ICMJE
MLA
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Lapp, H., Bala, S., Balhoff, J. P., Bouck, A., Goto, N., Holder, M., … Vision, T. J. (2007). The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics Online, 3, 287–296.
Lapp, Hilmar, Sendu Bala, James P. Balhoff, Amy Bouck, Naohisa Goto, Mark Holder, Richard Holland, et al. “The 2006 NESCent Phyloinformatics Hackathon: A Field Report.” Evolutionary Bioinformatics Online 3 (January 2007): 287–96.
Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, et al. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary bioinformatics online. 2007 Jan;3:287–96.
Lapp, Hilmar, et al. “The 2006 NESCent Phyloinformatics Hackathon: A Field Report.” Evolutionary Bioinformatics Online, vol. 3, Jan. 2007, pp. 287–96.
Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis PO, Mackey AJ, Osborne BI, Piel WH, Kosakovsky Pond SL, Poon AFY, Qiu W-G, Stajich JE, Stoltzfus A, Thierer T, Vilella AJ, Vos RA, Zmasek CM, Zwickl DJ, Vision TJ. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary bioinformatics online. 2007 Jan;3:287–296.

Published In

Evolutionary bioinformatics online

EISSN

1176-9343

ISSN

1176-9343

Publication Date

January 2007

Volume

3

Start / End Page

287 / 296

Related Subject Headings

  • Bioinformatics
  • 3105 Genetics
  • 3102 Bioinformatics and computational biology
  • 0802 Computation Theory and Mathematics
  • 0601 Biochemistry and Cell Biology
  • 0502 Environmental Science and Management