Bioinformatics, Data Management and Information Technology

WP leader: Johann Joets (UMR GV)

Partners involved: UMR GV, URGI, Biogemma

Context and objectives:

AMAIZING will produce and manipulate very large bodies of heterogeneous data including billions of sequence reads (WP3), genotyping (WP4) and phenotyping data points (WP5). These datasets will have to be conveniently stored, pre-processed and made available to the partners of the project and to the international community.

The WP2 aims at providing the partners with bioinformatics tools and Information Technology (IT) expertise, hardware services, scientific programming, database management, scientific software and database training to deal with this huge body of data.

WP2 will:

  • Offer the other WPs hardware resources, develop and manage databases and interfaces, develop data analysis tools
  • Provide conveniently dimensioned hardware services and solution to enhance existing software by adapting them to cluster computer (parallelization) or when possible to computer with 64 bits architecture, required to manage high memory (RAM).
  • Ensure population of databases (ThaliaDB, GnpIS,…) with data from work packages, exchange of data between producers, users and storage and integration centers, promotion of usage of standard format and ontology when possible, and collaboration with international data centers for data exchange according project rules.
  • Create a Information System dedicated to AMAIZING (AIS) data relied on the existing architecture and information system GnpIS of URGI, the ThaliaDB database from the UMR GV le Moulon and BioMercator and integrated with a web portal and a set of web services to implement breeders and geneticist customized queries.

Deliverables:

D2.1.1: Software and interfaces specification (URGI, M12)

D2.1.2: Training sessions on AIS (URGI, each year starting M36)

D2.2.1: Report on new hardware resources testing (le Moulon, M24)

D2.2.2: Release of optimized software for intensive computing (le Moulon, M24, M36, M48)

D2.3: Database feeding update (BGA, minor update every 6 months, major update every year)

D2.4.1: AIS web portal upgrades (including GnpIS databases and ThaliaDB updates, Web services releases, datamarts, Breeders and geneticist specific queries) (URGI One major update every year, one minor update every 6 months)

D2.4.2: BioMercator v5 release (Le Moulon, M36)