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Hardisty AR, Bacall F, Beard N, Balcázar-Vargas MP, Balech B, Barcza Z, Bourlat SJ, De Giovanni R, de Jong Y, De Leo F, Dobor L, Donvito G, Fellows D, Guerra AF, Ferreira N, Fetyukova Y, Fosso B, Giddy J, Goble C, Güntsch A, Haines R, Ernst VH, Hettling H, Hidy D, Horváth F, Ittzés D, Ittzés P, Jones A, Kottmann R, Kulawik R, Leidenberger S, Lyytikäinen-Saarenmaa P, Mathew C, Morrison N, Nenadic A, de la Hidalga AN, Obst M, Oostermeijer G, Paymal E, Pesole G, Pinto S, Poigné A, Fernandez FQ, Santamaria M, Saarenmaa H, Sipos G, Sylla KH, Tähtinen M, Vicario S, Vos RA, Williams AR, Yilmaz P. BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology. BMC Ecol 2016; 16:49. [PMID: 27765035 PMCID: PMC5073428 DOI: 10.1186/s12898-016-0103-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023] Open
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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Affiliation(s)
- Alex R Hardisty
- School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA, UK.
| | - Finn Bacall
- School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK
| | - Niall Beard
- School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK
| | - Maria-Paula Balcázar-Vargas
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090, Amsterdam, The Netherlands
| | - Bachir Balech
- Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), via Amendola 165/A, 70126, Bari, Italy
| | - Zoltán Barcza
- Department of Meteorology, Eötvös Loránd University, Pázmány sétány 1/A, Budapest, 1117, Hungary
| | - Sarah J Bourlat
- Department of Marine Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
| | - Renato De Giovanni
- Centro de Referência em Informação Ambiental, Avenida Dr. Romeu Tórtima, 388, Campinas, SP, 13084-791, Brazil
| | - Yde de Jong
- 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
| | - Francesca De Leo
- Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), via Amendola 165/A, 70126, Bari, Italy
| | - Laura Dobor
- Department of Meteorology, Eötvös Loránd University, Pázmány sétány 1/A, Budapest, 1117, Hungary
| | - Giacinto Donvito
- Institute of Nuclear Physics (INFN), Via E. Orabona 4, 70125, Bari, Italy
| | - Donal Fellows
- School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK
| | - Antonio Fernandez Guerra
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.,Jacobs University Bremen GmbH, Campus Ring 1, 28359, Bremen, Germany
| | - Nuno Ferreira
- Stichting EGI (EGI.eu), Science Park 140, 1098, Amsterdam, The Netherlands
| | - Yuliya Fetyukova
- SIB Labs, Joensuu Science Park, University of Eastern Finland, P.O. Box 111, 80101, Joensuu, Finland
| | - Bruno Fosso
- Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), via Amendola 165/A, 70126, Bari, Italy
| | - Jonathan Giddy
- School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA, UK
| | - Carole Goble
- School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK
| | - Anton Güntsch
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195, Berlin, Germany
| | - Robert Haines
- IT Services, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK
| | - Vera Hernández Ernst
- Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
| | - Hannes Hettling
- Naturalis Biodiversity Center, Postbus 9517, 2300, Leiden, The Netherlands
| | - Dóra Hidy
- MTA-SZIE Plant Ecology Research Group, Szent István University, Páter K. u.1., Gödöllő, 2103, Hungary
| | - Ferenc Horváth
- Institute of Ecology and Botany, Centre for Ecological Research, Hungarian Academy of Sciences, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Dóra Ittzés
- Institute of Ecology and Botany, Centre for Ecological Research, Hungarian Academy of Sciences, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Péter Ittzés
- Institute of Ecology and Botany, Centre for Ecological Research, Hungarian Academy of Sciences, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Andrew Jones
- School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA, UK
| | - Renzo Kottmann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Robert Kulawik
- Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
| | - Sonja Leidenberger
- Swedish Species Information Centre/ArtDatabanken, Swedish University of Agricultural Sciences, Bäcklösavägen 10, 750 07, Uppsala, Sweden
| | | | - Cherian Mathew
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195, Berlin, Germany
| | - Norman Morrison
- School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK
| | - Aleksandra Nenadic
- School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK
| | - Abraham Nieva de la Hidalga
- School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA, UK
| | - Matthias Obst
- Department of Marine Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
| | - Gerard Oostermeijer
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090, Amsterdam, The Netherlands
| | - Elisabeth Paymal
- Fondation pour la Recherche sur la Biodiversité (FRB), 195, rue Saint-Jacques, 75005, Paris, France
| | - Graziano Pesole
- 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
| | - Salvatore Pinto
- Stichting EGI (EGI.eu), Science Park 140, 1098, Amsterdam, The Netherlands
| | - Axel Poigné
- Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
| | - Francisco Quevedo Fernandez
- School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA, UK
| | - Monica Santamaria
- Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), via Amendola 165/A, 70126, Bari, Italy
| | - Hannu Saarenmaa
- SIB Labs, Joensuu Science Park, University of Eastern Finland, P.O. Box 111, 80101, Joensuu, Finland
| | - Gergely Sipos
- Stichting EGI (EGI.eu), Science Park 140, 1098, Amsterdam, The Netherlands
| | - Karl-Heinz Sylla
- Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
| | - Marko Tähtinen
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014, Helsinki, Finland
| | - Saverio Vicario
- Institute of Biomedical Technology (ITB), National Research Council (CNR), via Amendola 122/D, 70126, Bari, Italy
| | - Rutger Aldo Vos
- 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
| | - Alan R Williams
- School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK
| | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
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Canhos DAL, Sousa-Baena MS, de Souza S, Maia LC, Stehmann JR, Canhos VP, De Giovanni R, Bonacelli MBM, Los W, Peterson AT. The Importance of Biodiversity E-infrastructures for Megadiverse Countries. PLoS Biol 2015. [PMID: 26204382 PMCID: PMC4512726 DOI: 10.1371/journal.pbio.1002204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil’s speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2–4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish. This Community Page calls for new governance and funding models to ensure the sustainability of national e-infrastructures—important for global systems and crucial for local education, research, and policy.
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Affiliation(s)
- Dora A. L. Canhos
- Centro de Referência em Informação Ambiental (CRIA), Campinas, São Paulo, Brazil
- * E-mail:
| | | | - Sidnei de Souza
- Centro de Referência em Informação Ambiental (CRIA), Campinas, São Paulo, Brazil
| | - Leonor C. Maia
- Departamento de Micologia, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - João R. Stehmann
- Departamento de Botânica, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Vanderlei P. Canhos
- Centro de Referência em Informação Ambiental (CRIA), Campinas, São Paulo, Brazil
| | - Renato De Giovanni
- Centro de Referência em Informação Ambiental (CRIA), Campinas, São Paulo, Brazil
| | - Maria B. M. Bonacelli
- Departamento de Política Científica e Tecnológica (DPCT), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Wouter Los
- Zoological Museum, University of Amsterdam, Amsterdam, The Netherlands
| | - A. Townsend Peterson
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
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