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      The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects

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          Abstract

          Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called “genome projects”. The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure.

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          A whole-genome assembly of Drosophila.

          We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.
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            The Human Genome Project: lessons from large-scale biology.

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              The iPlant Collaborative: Cyberinfrastructure for Plant Biology

              The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.
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                Author and article information

                Journal
                F1000Res
                F1000Res
                F1000Research
                F1000Research
                F1000Research (London, UK )
                2046-1402
                5 January 2016
                2016
                : 5
                : 18
                Affiliations
                [1 ]Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW 2753, Australia
                [1 ]Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
                [1 ]Department of Zoology, University of Cambridge, Cambridge, UK
                [1 ]Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
                Author notes

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: Dr Papanicolaou and I are colleagues who have both been involved in Heliconius genomics for many years and were both part of the Heliconius Genome Consortium.

                Competing interests: No competing interests were disclosed.

                Article
                10.12688/f1000research.7559.1
                4798206
                27006757
                b1976c41-8fe6-48b6-88c5-a92f329fb614
                Copyright: © 2016 Papanicolaou A

                This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 10 December 2015
                Funding
                The author is supported by the Hawkesbury Institute for the Environment (Western Sydney University); no grants were involved in supporting this work.
                Categories
                Opinion Article
                Articles
                Bioinformatics
                Genomics

                genome sequencing,bioinformatics education,opinion in bioinformatics,insect genomics,biocuration

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