The 2006 NESCent Phyloinformatics Hackathon: A Field Report Export

@article{citeulike:3097456, 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.}, author = {Lapp, Hilmar and Bala, Sendu and Balhoff, James P. and Bouck, Amy and Goto, Naohisa and Holder, Mark and Holland, Richard and Holloway, Alisha and Katayama, Toshiaki and Lewis, Paul O. and Mackey, Aaron J. and Osborne, Brian I. and Piel, William H. and Sergei and Poon, Art F. Y. and Qiu, Wei-Gang and Stajich, Jason E. and Stoltzfus, Arlin and Thierer, Tobias and Vilella, Albert J. and Vos, Rutger A. and Zmasek, Christian M. and Zwickl, Derrick J. and Vision, Todd J.}, citeulike-article-id = {3097456}, journal = {Evolutionary Bioinformatics}, keywords = {algorithms, methods, programming}, pages = {287--296}, posted-at = {2008-08-08 07:37:01}, priority = {2}, title = {The 2006 NESCent Phyloinformatics Hackathon: A Field Report}, volume = {3}, year = {2007} }

TY - JOUR ID - citeulike:3097456 L3 - citeulike-article-id:3097456 N2 - 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. JF - Evolutionary Bioinformatics EP - 296 TI - The 2006 NESCent Phyloinformatics Hackathon: A Field Report VL - 3 SP - 287 KW - algorithms KW - methods KW - programming AU - Lapp, Hilmar AU - Bala, Sendu AU - Balhoff, James AU - Bouck, Amy AU - Goto, Naohisa AU - Holder, Mark AU - Holland, Richard AU - Holloway, Alisha AU - Katayama, Toshiaki AU - Lewis, Paul AU - Mackey, Aaron AU - Osborne, Brian AU - Piel, William AU - Sergei AU - Poon, Art AU - Qiu, Wei-Gang AU - Stajich, Jason AU - Stoltzfus, Arlin AU - Thierer, Tobias AU - Vilella, Albert AU - Vos, Rutger AU - Zmasek, Christian AU - Zwickl, Derrick AU - Vision, Todd PY - 2007/// ER -