| Contributors: |
Institute for Bioscience and Biotechnology Research (IBBR), Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA; National Evolutionary Synthesis Center, 2024 W. Main St, Durham, NC, 27705, USA; The iPlant Collaborative and EEB Department, University of Arizona, 1657 E Helen St, Tucson, AZ, 85721, USA; Digital Enterprise Research Institute, National University of Ireland, University Road, Galway, Ireland; Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331-3803, USA; Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA; Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309-0334, USA; Department of Computer Science, New Mexico State University, MSC CS, Box 30001, Las Cruces, NM, 88003, USA; NCB Naturalis, Einsteinweg 2, Leiden, 2333 CC, the Netherlands; Arnold Arboretum of Harvard University, Boston, MA, 02130, USA; Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, PO Box 443051, Moscow, ID, 83844-3051, USA; University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA; Department of Ecology & Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN, 37996, USA; Department of Computer Science, University of Texas at Austin, Austin, TX, 78701, USA; Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA; UC Davis Genome Center, One Shields Ave, Davis, CA, 95618, USA; Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA; University of Texas at Austin, BEACON, Austin, TX, USA; Biology Department, Duke University, Biological Sciences Building, 125 Science Drive, Durham, NC, 27708, USA; Biodiversity Synthesis Center, Field Museum of Natural History, 1400 S Lakeshore Dr, Chicago, IL, 60605, USA; Department of Ecology and Evolutionary Biology, South University of California Los Angeles, 621 Charles E. Young Dr, Los Angeles, CA, 90095, USA; U.C. Berkeley Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA; Paperpile, 34 Houghton Street, Somerville, MA, 02143, USA |
| Description: |
BACKGROUND:Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces.RESULTS:With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components ; (2) proof-of-concept pruners and controllers ; (3) a meta-API for taxonomic name resolution services ; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying ; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes ; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org webcite), and a server image.CONCLUSIONS:Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user ... |