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

BMC Ecology

Software

Anton Güntsch¹  Cherian Mathew¹  Renato De Giovanni²  Päivi Lyytikäinen-Saarenmaa³  Matthias Obst⁴  Sarah J. Bourlat⁴  Zoltán Barcza⁵  Laura Dobor⁵  Marko Tähtinen⁶  Elisabeth Paymal⁷  Robert Kulawik⁸  Axel Poigné⁸  Vera Hernández Ernst⁸  Karl-Heinz Sylla⁸  Robert Haines⁹  Gerard Oostermeijer^1,10  Maria-Paula Balcázar-Vargas^1,10  Rutger Aldo Vos^1,11  Yde de Jong^1,12  Saverio Vicario^1,13  Bachir Balech^1,14  Francesca De Leo^1,14  Bruno Fosso^1,14  Monica Santamaria^1,14  Graziano Pesole^1,15  Dóra Ittzés^1,16  Ferenc Horváth^1,16  Péter Ittzés^1,16  Giacinto Donvito^1,17  Dóra Hidy^1,18  Pelin Yilmaz^1,19  Renzo Kottmann^1,19  Antonio Fernandez Guerra^2,20  Hannes Hettling^2,21  Hannu Saarenmaa^2,22  Yuliya Fetyukova^2,22  Francisco Quevedo Fernandez^2,23  Jonathan Giddy^2,23  Andrew Jones^2,23  Alex R. Hardisty^2,23  Abraham Nieva de la Hidalga^2,23  Donal Fellows^2,24  Finn Bacall^2,24  Aleksandra Nenadic^2,24  Alan R. Williams^2,24  Norman Morrison^2,24  Carole Goble^2,24  Niall Beard^2,24  Gergely Sipos^2,25  Nuno Ferreira^2,25  Salvatore Pinto^2,25  Sonja Leidenberger^2,26 

[1] Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195, Berlin, Germany;Centro de Referência em Informação Ambiental, Avenida Dr. Romeu Tórtima, 388, 13084-791, Campinas, SP, Brazil;Department of Forest Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland;Department of Marine Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden;Department of Meteorology, Eötvös Loránd University, Pázmány sétány 1/A, 1117, Budapest, Hungary;Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014, Helsinki, Finland;Fondation pour la Recherche sur la Biodiversité (FRB), 195, rue Saint-Jacques, 75005, Paris, France;Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757, Sankt Augustin, Germany;IT Services, University of Manchester, Kilburn Building, Oxford Road, M13 9PL, Manchester, UK;Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090, Amsterdam, The Netherlands;Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090, Amsterdam, The Netherlands;Naturalis Biodiversity Center, Postbus 9517, 2300, Leiden, The Netherlands;Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090, Amsterdam, The Netherlands;SIB Labs, Joensuu Science Park, University of Eastern Finland, P.O. Box 111, 80101, Joensuu, Finland;Institute of Biomedical Technology (ITB), National Research Council (CNR), via Amendola 122/D, 70126, Bari, Italy;Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), via Amendola 165/A, 70126, Bari, Italy;Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), via Amendola 165/A, 70126, Bari, Italy;Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, via Orabona, 1514, 70126, Bari, Italy;Institute of Ecology and Botany, Centre for Ecological Research, Hungarian Academy of Sciences, Alkotmány u. 2-4., 2163, Vácrátót, Hungary;Institute of Nuclear Physics (INFN), Via E. Orabona 4, 70125, Bari, Italy;MTA-SZIE Plant Ecology Research Group, Szent István University, Páter K. u.1., 2103, Gödöllő, Hungary;Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany;Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany;Jacobs University Bremen GmbH, Campus Ring 1, 28359, Bremen, Germany;Naturalis Biodiversity Center, Postbus 9517, 2300, Leiden, The Netherlands;SIB Labs, Joensuu Science Park, University of Eastern Finland, P.O. Box 111, 80101, Joensuu, Finland;School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, CF24 3AA, Cardiff, UK;School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, M13 9PL, Manchester, UK;Stichting EGI (EGI.eu), Science Park 140, 1098, Amsterdam, The Netherlands;Swedish Species Information Centre/ArtDatabanken, Swedish University of Agricultural Sciences, Bäcklösavägen 10, 750 07, Uppsala, Sweden;

关键词: Biodiversity science;    Ecology;    Computing software;    Informatics;    Workflows;    Virtual laboratory;    Biodiversity virtual e-laboratory;    Data processing;    Analysis;    Automation;   

DOI  :  10.1186/s12898-016-0103-y

 received in 2016-05-03, accepted in 2016-10-13,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundMaking 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.ResultsBioVeL 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© The Author(s) 2016