WP1. Distributed national environment of services in bioinformatics
WP1 describes the deployment of a distributed national environment of services in bioinformatics, relying on a network of physical infrastructure (computing and storage) equipped with a software environment (middleware, tools), ensuring access to biological data, and supported by a mutualised task force.
WP1 is organised around 7 actions.
National Network of Computational Resources (NNCR) (Action 1.1)
Leadership: Julien Seiler & Christophe Blanchet
Development and evolution of a physical infrastructure adapted to the needs of biologists for data analysis, and providing bioinformaticians with a suitable environment for the development and deployment of novel resources. This infrastructure will be distributed over the IFB core and severala few regional platforms, and will be installed and maintained collectively by a task force available on the platforms.
Software and data environment: middleware, tools and workflows (Action 1.2)
Leadership: Gildas Le Corguilé & Jacques van Helden
The physical infrastructure will combine two middleware with complementary features and applications: cluster and cloud. Tools will be available via various interfaces suited for diverse users: web sites, stand-alone applications with graphical user interfaces (via a Virtual Desktop), command lines, application programmatic interfaces, Web services. To ensure the reproducibility of complex analyses, workflow management systems will be available on both Web (Galaxy) and command-line (Snakemake) interfaces.
Support to databases (Action 1.3)
Leadership: Claudine Médigue & Guy Perrière
IFB will open its infrastructure to deploy thematic databases developed by French researchers and to maintain mirrors of reference public databases. It will offer a targeted support to some strategic database projects, especially those having a high added value resulting from expert-based curation. It will also accompany these projects to comply with the requirements to obtain the label of “ELIXIR Core Data Resources”.
Catalogue of French resources in bioinformatics (Action 1.4)
Leadership: Hervé Ménager & Jacques van Helden
IFB will ensure the visibility and accessibility of bioinformatics resources (tools, databases, individual expertise, platforms and training material), which will be synchronized with related international catalogues (e.g. ELIXIR bio.tools, TeSS). This catalogue will also contribute to readily identify the most adapted resources and their availability to support end-user needs (which tool does what and where is it installed? who is knowledgeable for a given question?).
Access to end-users (Action 1.5)
Leadership: Christine Gaspin & Erwan Corre
IFB will define homogeneous conditions of access and usage of the computing resources across all the nodes of the NNCR. This will enable to balance the usage between NNCR nodes depending on their respective load. By default, users will be granted to use a fixed quota free of charge, and have the possibility to request extra resources charged according to a predefined pricing (see WP5, economic model), or exceptional resources (huge memory, storage or computation) based on a case-by-case evaluation.
Sharing of services with other national research support infrastructures (Action 1.6)
Leadership: Christophe Bruley & Jean-françois Dufayard
Several other national research infrastructures strongly depend on bioinformatics to ensure their own missions. Following the meeting of July 11, IFB started a survey of the needs expressed by other infrastructures. The preliminary answers highlighted expectations about specific expertise, technologies (Virtual machines, interoperability), training, and convergent expression of issues to cope with the increasing requirement for very large data storage and analytic power. This process will be pursued in order to define collective solutions to fulfill these requirements.
Consulting and orientation desk (Action 1.7)
Leadership: Vincent Lefort & Ivan Moszer
The desk will answer the requests from end-users by identifying the human relevant expertise and computer resources on the French territory (based on the above described catalogue), estimate their availability, and follow the treatment of their demand. It will also offer an expertise to the evaluation of requirements in bioinformatics upstream to the conception of research projects.
