Platform

Platform services cover database design, software engineering, software hosting, data integration and training. Software developments are made in the frame of projects, in which the platform is explicitly involved as a partner.
The platform offers services to manage confidentiality of the data before publication and data release. Users of our projects, can also have space and the possibility to run analysis tools and pipelines.
As main specificity, the platform develops and maintains a modular and interoperable information system for plant and pest genomics called GnpIS, composed of databases, databanks and sequence analysis tools. It enables scientists to mine genomic and genetic data, to extract valuable information on genes of agronomical interest and on genome structure and evolution.

GnpIS store data from several species such as grape, wheat, maize, Arabidopsis, rice, poplar (apple, in progress) but also some insects and fungi.

It has been selected by several genome consortiums to be an international data warehouse for the wheat and grape species as well as several fungi.

As second specificity, the platform has a strong expertise in developping pipelines for plants and fungi such as annotation pipelines for genes and transposable elements.
The platform, in the frame of its projects in partnership (ANR, IBISA, INRA GAP fundings) is currently improving its databases (GnpIS) to manage data concerning meta analysis of QTLs, or genetic association data. it is also developping some pipelines to deal with NGS data.
In particular: an in-house analysis pipeline, MapHits, for SNP detection and visualization that is integrated in Galaxy tool. This integration in production on our cluster is in progress for large scale analysis.
Another in-house tool: S-Mart for RNA-Seq analysis. It is done in strong collaboration and synergy with the unit research team.
A GMOD gene report is also in development to complete GnpGenome and gbrowse viewers.

For more information on these services, tools and their availability, please contact us .