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

Hardisty, Alex R. ORCID:, Bacall, Finn, Beard, Niall, Balcázar‑Vargas, Maria-Paula, Balech, Bachir, Barcza, Zoltán, Bourlat, Sarah J., De Giovanni, Renato, de Jong, Yde, De Leo, Francesca, Dobor, Laura, Donvito, Giacinto, Fellows, Donal, Fernandez Guerra, Antonio, Ferreira, Nuno, Fetyukova, Yuliya, Fosso, Bruno, Giddy, Jonathan, Goble, Carole, Guntsch, Anton, Haines, Robert, Hernandez Ernst, Vera, Hettling, Hannes, Hiddy, Dora, Horvath, Ferenc, Ittzes, Dora, Ittzes, Peter, Jones, Andrew, Kottmann, Renzo, Kulawik, Robert, Leidenberger, Sonja, Lyytikäinen‑Saarenmaa, Paivi, Mathew, Cherian, Morrison, Norman, Nenadic, Aleksandra, Nieva De La Hidalga, Abraham ORCID:, Obst, Matthias, Oostermeijer, Gerard, Paymal, Elisabeth, Pesole, Graziano, Pinto, Salvatore, Poigne, Axel, Quevedo Fernandez, Francisco, Santamaria, Monica, Saarenmaa, Hannu, Sipos, Gergely, Sylla, Karl-Heinz, Tahtinen, Marko, Vicario, Saverio, Aldo Vos, Rutger, Williams, Alan R. and Yilmaz, Pelin 2016. BioVeL: A virtual laboratory for data analysis and modelling in biodiversity science and ecology. BMC Ecology 16 , 49. 10.1186/s12898-016-0103-y

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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 sixty 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.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Chemistry
Computer Science & Informatics
Subjects: G Geography. Anthropology. Recreation > GE Environmental Sciences
Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Q Science > QA Mathematics > QA76 Computer software
Q Science > QH Natural history
Uncontrolled Keywords: Biodiversity science, ecology, computing software, informatics, workflows, virtual laboratory, Biodiversity virtual e-laboratory, data processing, analysis, automation
Additional Information: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, 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 ( applies to the data made available in this article, unless otherwise stated.
Publisher: BioMed Central
ISSN: 1472-6785
Funders: EC Horizon 2020
Date of First Compliant Deposit: 8 November 2016
Date of Acceptance: 13 October 2016
Last Modified: 24 May 2023 17:37

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