The Biodiversity Virtual e-Laboratory (BioVeL) project set out to provide a seamlessly connected environment to make it easier for biodiversity scientists to carry out in silico analysis of biodiversity data and to pursue in silico experiments based on composing and executing sequences of complex digital data manipulations and modelling tasks. Founded on a “Commons” of services and workflows and the infrastructure for running them, it is accessed through repositories, catalogues, and portals, and used in software applications. The work has been guided by: i) three topical science areas of societal importance: ecosystem functionality, CO2 sequestration, invasive species management; and ii) an international network of expertise and “pals”, bringing together the science and ICT communities. We engaged senior and young scientists, service providers and platform developers.
We successfully delivered a pilot operational platform used for real scientific endeavour and take-up by early adopters and community platforms. We overcame significant technical challenges and have begun to tackle the social challenges of introducing the ideas to the wider scientific community. The maturity and readiness of the community and the technology remains a challenge. The BioVeL results are to be sustained and adopted by several LifeWatch national initiatives, EU projects (e.g., EU-BON, Scratchpads) and other RIs (e.g., ELIXIR-UK). Several follow-on projects using the e-Lab have already been established or proposals submitted.
We seeded the BioVeL e-Lab with a commons for taxonomy and data refinement, ecological niche modelling, population modelling, ecosystem modelling, phylogenetics, metagenomics, mapping and visualisation: i) 36 analysis services are registered in our BioDiversityCatalogue along with 38 third party services; ii) 48 common, parameterisable workflows are deposited in our customised myExperiment Repository space, and executable in our own Portal and third party applications. We operate the e-Lab with a computational platform for workflow execution using the Taverna software suite and third party, general services (e.g., R, OpenRefine). Major improvements in the Taverna platform contributed to its extensibility, scalability and sustainability, and to its absorption into the Apache Foundation. Innovations in workflow design, deployment and application embedding support a spectrum of users from experts to novices; a breadth of workflows from pre-cooked to bespoke; and a range of experiments from big data processing to multi-sweep modelling. Our e-Lab can be packaged as an instance (“BioVeL-in-a-Box”) for independent installation and control.
Beneficiaries range from resource providers (e.g., GBIF) through specialist portal hosts (e.g., Swedish LifeWatch) and infrastructure providers (e.g., Scratchpads) to policy makers and scientists who have thus far worked on 27 scientific studies, resulting in 22 publications. Our Portal already has 204 registered users, with 30-35 active per month. Expert users benefit from our Biodiversity workflow workbench. We have supported users with a helpdesk and 18 training events. We have reached out to users by tapping into communities and other FP7 projects, promotion at 118 meetings and conferences, and through 11 workshops. We have sought a multiplier effect.
Our BioVel eLab has been shown to enable new research opportunities by processing at scale (i.e., doing the same thing over and over again) and/or dealing with data at scale (i.e., processing over very large amounts of data) and by effectively accomplishing routine tasks of processing and preparing data, as well as analysis. BioVeL tools shield researchers from the complexities of access to public data resources and services. The transparent, standardised analytical approaches support policy and management contexts, and the ability to review and “tweak” workflows supports teaching and re-use. An international panel of experts has positively evaluated the project in late 2014. It is perceived globally as a leader in its field and a promising approach to modern biodiversity informatics. One of the most critical processes that must be stimulated now is enlightenment and adoption.
Here you can find the full Project Final Report.
19 February 2015
At the final review of the project by the EC, one of the reviewers said: “Incredible work done with a community that is not unified. Remarkable work. It opens for new development in a near future. Hope for success. Good project. Happy that you have been financed three plus years ago.”Tweets by @bioveleu