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1National Evolutionary Synthesis Center, 2024 W. Main St., Suite A200, Durham NC 27705, U.S.A. 2Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 0XY, United Kingdom. 3Department of Biology, CB 3280, University of North Carolina, Chapel Hill, NC 27599. 4Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan. 5School of Computational Science, 150-F Dirac Science Library, Florida State University, Tallahassee, Florida 32306-4120, U.S.A. 6EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom. 7Section of Evolution and Ecology, Center for Population Biology, 3347 Storer Hall, University of California, Davis, CA 95616, U.S.A. 8Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan. 9Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269-3043, U.S.A. 10GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA 19426, U.S.A. 11ZBio LLC, Nyack, NY 10960, U.S.A. 12Peabody Museum of Natural History, Yale University, 170 Whitney Ave., New Haven CT 06511, U.S.A. 13University of California, San Diego, Division of Comparative Pathology and Antiviral Research Center, 150 West Washington Street, San Diego, CA 92103. 14Department of Biological Sciences, Hunter College, City University of New York, 695 Park Ave, New York, NY 10021, U.S.A. 15Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A. 16Biochemical Science Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8310, Gaithersburg, MD, 20899-8310. 17Biomatters Ltd, Level 6, 220 Queen St, Auckland, New Zealand. 18Department of Zoology, University of British Columbia, #2370-6270 University Blvd., Vancouver, B.C. V6T 1Z4, Canada. 19Burnham Institute for Medical Research, La Jolla, CA 92037, U.S.A. 20Department of Biology, Duke University, P.O. Box 90338, Durham, NC 27708, U.S.A.
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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Talking on behalf of my co-author, we found the whole process of submitting our paper very smooth and transparent. It was the first time that we could follow the process step-by-step. In addition we found that the reviewers were open- and broad-minded, giving us very constructive comments and advice. All of this has become rather rare in most journals at present. We are grateful to the journal to give us the opportunity to ...