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      BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

      research-article
      1 , , 2 , 2 , 3 , 4 , 5 , 6 , 7 , 3 , 8 , 4 , 5 , 9 , 2 , 10 , 11 , 12 , 8 , 4 , 1 , 2 , 13 , 14 , 15 , 16 , 17 , 18 , 18 , 18 , 1 , 10 , 15 , 19 , 20 , 13 , 2 , 2 , 1 , 6 , 3 , 21 , 4 , 22 , 12 , 15 , 1 , 4 , 8 , 12 , 15 , 23 , 24 , 3 , 16 , 2 , 10
      BMC Ecology
      BioMed Central
      Biodiversity science, Ecology, Computing software, Informatics, Workflows, Virtual laboratory, Biodiversity virtual e-laboratory, Data processing, Analysis, Automation

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          Abstract

          Background

          Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as “Web services”) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust “in silico” science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.

          Results

          BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible ‘virtual laboratory’, free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.

          Conclusions

          Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12898-016-0103-y) contains supplementary material, which is available to authorized users.

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          Most cited references50

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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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            Big data and the future of ecology

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              Correlative and mechanistic models of species distribution provide congruent forecasts under climate change

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                Author and article information

                Contributors
                hardistyar@cardiff.ac.uk
                finn.bacall@manchester.ac.uk
                niall.beard@manchester.ac.uk
                mpbalcazar@yahoo.com
                balechbachir@gmail.com
                zoltan.barcza@ttk.elte.hu
                sarah.bourlat@bioenv.gu.se
                renato@cria.org.br
                y.s.d.m.dejong@uva.nl
                f.deleo@ibbe.cnr.it
                doborl@nimbus.elte.hu
                giacinto.donvito@ba.infn.it
                donal.k.fellows@manchester.ac.uk
                afernand@mpi-bremen.de
                nunolf@gmail.com
                yuliya.fetyukova@uef.fi
                bruno.fosso@gmail.com
                jongiddy@gmail.com
                carole.goble@manchester.ac.uk
                a.guentsch@bgbm.org
                robert.haines@manchester.ac.uk
                vera_hernandez@web.de
                hannes.hettling@naturalis.nl
                dori.hidy@gmail.com
                horvath.ferenc@okologia.mta.hu
                dorakra@gmail.com
                ittzes@gmail.com
                jonesac@cardiff.ac.uk
                rkottman@mpi-bremen.de
                robkul@gmx.net
                sonja.leidenberger@slu.se
                paivi.lyytikainen-saarenmaa@helsinki.fi
                cherianm@gmail.com
                norman.morrison@elixir-europe.org
                a.nenadic@manchester.ac.uk
                nievadelahidalgaa@cardiff.ac.uk
                matthias.obst@marine.gu.se
                j.g.b.oostermeijer@uva.nl
                elisabeth@paymaldesign.com
                g.pesole@ibbe.cnr.it
                salvatore.pinto@esa.int
                apoigne@googlemail.com
                quevedofernandezf@cardiff.ac.uk
                m.santamaria@ibbe.cnr.it
                hannu.saarenmaa@uef.fi
                gergely.sipos@egi.eu
                karl-heinz.sylla@iais.fraunhofer.de
                marko.tahtinen@helsinki.fi
                saverio.vicario@gmail.com
                rutger.vos@naturalis.nl
                alan.r.williams@manchester.ac.uk
                pyilmaz@mpi-bremen.de
                Journal
                BMC Ecol
                BMC Ecol
                BMC Ecology
                BioMed Central (London )
                1472-6785
                20 October 2016
                20 October 2016
                2016
                : 16
                : 49
                Affiliations
                [1 ]School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA UK
                [2 ]School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL UK
                [3 ]Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090 Amsterdam, The Netherlands
                [4 ]Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), via Amendola 165/A, 70126 Bari, Italy
                [5 ]Department of Meteorology, Eötvös Loránd University, Pázmány sétány 1/A, Budapest, 1117 Hungary
                [6 ]Department of Marine Sciences, University of Gothenburg, Box 463, 405 30 Gothenburg, Sweden
                [7 ]Centro de Referência em Informação Ambiental, Avenida Dr. Romeu Tórtima, 388, Campinas, SP 13084-791 Brazil
                [8 ]SIB Labs, Joensuu Science Park, University of Eastern Finland, P.O. Box 111, 80101 Joensuu, Finland
                [9 ]Institute of Nuclear Physics (INFN), Via E. Orabona 4, 70125 Bari, Italy
                [10 ]Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
                [11 ]Jacobs University Bremen GmbH, Campus Ring 1, 28359 Bremen, Germany
                [12 ]Stichting EGI (EGI.eu), Science Park 140, 1098 Amsterdam, The Netherlands
                [13 ]Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195 Berlin, Germany
                [14 ]IT Services, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL UK
                [15 ]Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757 Sankt Augustin, Germany
                [16 ]Naturalis Biodiversity Center, Postbus 9517, 2300 Leiden, The Netherlands
                [17 ]MTA-SZIE Plant Ecology Research Group, Szent István University, Páter K. u.1., Gödöllő, 2103 Hungary
                [18 ]Institute of Ecology and Botany, Centre for Ecological Research, Hungarian Academy of Sciences, Alkotmány u. 2-4., Vácrátót, 2163 Hungary
                [19 ]Swedish Species Information Centre/ArtDatabanken, Swedish University of Agricultural Sciences, Bäcklösavägen 10, 750 07 Uppsala, Sweden
                [20 ]Department of Forest Sciences, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
                [21 ]Fondation pour la Recherche sur la Biodiversité (FRB), 195, rue Saint-Jacques, 75005 Paris, France
                [22 ]Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, via Orabona, 1514, 70126 Bari, Italy
                [23 ]Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014 Helsinki, Finland
                [24 ]Institute of Biomedical Technology (ITB), National Research Council (CNR), via Amendola 122/D, 70126 Bari, Italy
                Author information
                http://orcid.org/0000-0002-0767-4310
                Article
                103
                10.1186/s12898-016-0103-y
                5073428
                27765035
                89924b62-079f-490f-a8a3-a72cb9644a2b
                © The Author(s) 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 3 May 2016
                : 13 October 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100000780, European Commission;
                Award ID: 283359
                Award Recipient :
                Categories
                Software
                Custom metadata
                © The Author(s) 2016

                Ecology
                biodiversity science,ecology,computing software,informatics,workflows,virtual laboratory,biodiversity virtual e-laboratory,data processing,analysis,automation

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