Getting started with Building Workflows
BioVeL relies on Taverna, an open source and domain-independent Workflow Management System. Taverna is a suite of tools for design and execution of scientific workflows and aiding 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 (local or remote) only performs 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 towards 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 Web services that are specific to the interests of the biodiversity scientists community. This catalogue is related to and uses the same software as the BioCatalogue, which is a public, centralised, curated and monitored registry of life science Web services that can be used for building workflows. Both catalogues are community-oriented Web applications where service providers and community experts can register and curate services, and where users can discover them. Users can browse the catalogues and access their full search options for services, checking their status and availability. Services discovered in the catalogues can be utilised in Taverna workflows. Taverna Workbench as well has a plugin for searching for services directly from the Workbench.
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.
For any help with using BioVeL workflows, tools or services, please write to firstname.lastname@example.org.
For any other information, please write to email@example.com.
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