BioVeL relies on Taverna, an open source and domain-independent Workflow Management System (WMS). Taverna is a suite of tools used to design and execute scientific workflows and to aid in silico experimentation. BioVeL has chosen Taverna because of its comprehensive capabilities and its widespread adoption and take-up within scientific communities that increasingly recognise the need to carry out complex computerised analysis and experimental tasks.
Each service only perform a small well-defined task, thus necessitating that several of them are joined in a pipeline to model a useful experiment, or create a useful analysis. During the execution of a workflow, Taverna coordinates the operation of these many individual services. With Taverna, BioVeL does not replace other existing tools, but complements them toward a greater efficiency and makes them available in new contexts. As an example, the openModeller suite of tools for ecological niche modelling, developed by CRIA in Brazil is available as a standalone toolset. Through the BioVeL project, specific functionalities of the toolset are also available as Web Services, allowing them to be included as specific processing steps in a workflow, as illustrated with the horseshoe crab example.
To better address the needs of scientists and to make it easier to use, BioVeL has specifically developed the BioVeL Portal. Through a browser, without any preliminary installation, anyone can run BioVeL's workflows. BioVeL documentation explains how to use the Portal to run workflows as well as how to work directly from the Taverna Workbench.
BioVeL has developed the BiodiversityCatalogue, a curated catalogue of its workflows and Web services that are specific to the interests of the biodiversity scientists community. This catalogue is part of the BioCatalogue, which is a public, centralised, curated and monitored registry of life science Web services that can be used for building workflows. It is a community-oriented web site where service providers and community experts can register and curate services, and where users can discover them. Users can browse the catalogue and access its full search options for services, checking their status and availability.
To share workflow knowledge, BioVeL also provides a network of experts in the specific tools used in a workflow. This expertise is made available to researchers who engage in this type of data analysis without requiring them to have the expertise of each specific tool. With BioVeL, you have access to myExperiment, a social networking site, workflow repository and Virtual Research Environment (VRE) designed for people to share, discover and re-use workflows. myExperiment enables scientists to contribute to a pool of workflows that can be re-used and re-purposed by other scientists, promoting the building of communities and relationships, and facilitating collaborations. Therefore myExperiment reduces time-to-experiment, supports the sharing of expertise, and contributes to avoid reinvention. As with the BiodiversityCatalogue, BioVeL is developing a customised experience within myExperiment (the BioVeL Group) that closely matches the interests and needs of the biodiversity scientists community.
- MS11, "Ecosystem Functioning & Valuation Web Services and Workflows," Budapest, Hungary, June 6-7, 2013
- European Biodiversity Informatics Conference, Italy, September 3-6, 2013
- BioVeL Third Annual Meeting and General Assembly, Budapest, Hungary, September 30-October 4, 2013
- INTECOL 2013
London, UK, August
18-23, Booth E3