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      Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

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          Abstract

          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), 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 demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.

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          Most cited references30

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          Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

          Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
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            The delayed rise of present-day mammals.

            Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals.
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              TimeTree: a public knowledge-base of divergence times among organisms.

              Biologists and other scientists routinely need to know times of divergence between species and to construct phylogenies calibrated to time (timetrees). Published studies reporting time estimates from molecular data have been increasing rapidly, but the data have been largely inaccessible to the greater community of scientists because of their complexity. TimeTree brings these data together in a consistent format and uses a hierarchical structure, corresponding to the tree of life, to maximize their utility. Results are presented and summarized, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature. TimeTree is available at http://www.timetree.net
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                Author and article information

                Journal
                BMC Bioinformatics
                BMC Bioinformatics
                BMC Bioinformatics
                BioMed Central
                1471-2105
                2013
                13 May 2013
                : 14
                : 158
                Affiliations
                [1 ]Institute for Bioscience and Biotechnology Research (IBBR), Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
                [2 ]National Evolutionary Synthesis Center, 2024 W. Main St, Durham, NC, 27705, USA
                [3 ]The iPlant Collaborative and EEB Department, University of Arizona, 1657 E Helen St, Tucson, AZ, 85721, USA
                [4 ]Digital Enterprise Research Institute, National University of Ireland, University Road, Galway, Ireland
                [5 ]Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331-3803, USA
                [6 ]Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
                [7 ]Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309-0334, USA
                [8 ]Department of Computer Science, New Mexico State University, MSC CS, Box 30001, Las Cruces, NM, 88003, USA
                [9 ]NCB Naturalis, Einsteinweg 2, Leiden, 2333 CC, the Netherlands
                [10 ]Arnold Arboretum of Harvard University, Boston, MA, 02130, USA
                [11 ]Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, PO Box 443051, Moscow, ID, 83844-3051, USA
                [12 ]University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
                [13 ]Department of Ecology & Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN, 37996, USA
                [14 ]Department of Computer Science, University of Texas at Austin, Austin, TX, 78701, USA
                [15 ]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
                [16 ]UC Davis Genome Center, One Shields Ave, Davis, CA, 95618, USA
                [17 ]Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
                [18 ]University of Texas at Austin, BEACON, Austin, TX, USA
                [19 ]Biology Department, Duke University, Biological Sciences Building, 125 Science Drive, Durham, NC, 27708, USA
                [20 ]Biodiversity Synthesis Center, Field Museum of Natural History, 1400 S Lakeshore Dr, Chicago, IL, 60605, USA
                [21 ]Department of Ecology and Evolutionary Biology, South University of California Los Angeles, 621 Charles E. Young Dr, Los Angeles, CA, 90095, USA
                [22 ]U.C. Berkeley Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA
                [23 ]Paperpile, 34 Houghton Street, Somerville, MA, 02143, USA
                Article
                1471-2105-14-158
                10.1186/1471-2105-14-158
                3669619
                23668630
                abd4ccbf-ebd4-42c3-9ffc-fb4f5f801fc3
                Copyright ©2013 Stoltzfus et al.; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 January 2013
                : 30 April 2013
                Categories
                Software

                Bioinformatics & Computational biology
                phylogeny,taxonomy,hackathon,web services,data reuse,tree of life

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