Using registries to integrate bioinformatics tools and services into workbench environments

The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them. The descriptions are, however, hard and expensive to create and maintain, because they are volatile and require an exhaustive knowledge of the described resource, its applicability to biological research, and the data model and syntax used to describe it. We present here the Workbench Integration Enabler, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry

Bioinformatics applications discovery and composition with the Mobyle suite and MobyleNet

International audienceGiven the sheer number of existing analysis tools and data sources, defining and running bioinformatics analyses is often challenging. We present here the Mobyle framework, a web-based environment to access such resources. It enables the use of local and remote bioinformatics services, seamlessly integrated within a homogeneous and web-accessible environment that focuses on usability. This framework offers the possibility of integrating a wide range of services that span from the traditional server-side command-line based programs to workflows and client-based visualization tools. By abstracting whenever possible the user from the details of syntactic compatibility and providing multiple classification tools, Mobyle provides an efficient web-based solution to run and chain bioinformatics analyses. The MobyleNet project promotes an organization that federates a network of small resources that shares its expertise within a community that spans various complementary domains of bioinformatics. Its most tangible expected result is the integration of the bioinformatics tools of the different nodes, providing interoperability, user assistance and quality management between its members