GenOuest BioInformatics Platform

Mobyle portal upgraded to 1.5

Olivier Sallou — Thu, 16 May 2013 08:38:46 +0000

The Mobyle portal has been upgraded to its latest version.
It provides new functions as well as a workflow editor integrated with the portal tools.

With the worflow editor you can build complex operation with the provided tools and save your results in your workspace.

Galaxy on GenOuest

Olivier Sallou — Fri, 05 Apr 2013 13:07:47 +0000

The platform hosts a Galaxy instance. All you need to use it is an account on the platform.
Connect to http://galaxy.genouest.org using your platform credentials, and that’s it.

This instance has a dedicated storage space, provides many tools and a workflow creation tool.

RapsoDyn

Coline THOMAS — Mon, 25 Mar 2013 12:10:17 +0000

RapsoDyn is a 8 years project funded by French Investment for the future (Investissement d’avenir, bioressources), call 2011 and is coordinated by Nathalie Nesi, UMR IGEPP, Inra Rennes.

This project’s name stand for “Optimisation of the RAPeSeed Oil content anD Yield under low Nitrogen input”. It aim to help and speed up selection of adapted B. napus variety, through genetic and genomic approaches.

GenOuest member involved: Coline Thomas

Hadoopizer

Anthony Bretaudeau — Tue, 19 Feb 2013 08:11:15 +0000

A project that aims at providing a private cloud environment for the analysis of bioinformatics data. This environment is available on a dedicated website: http://genocloud.genouest.org.
This project gave birth to Hadoopizer which is a generic tool for the parallelisation of bioinformatics analysis in the cloud using the MapReduce paradigm (Hadoop).

GenOuest member involved: Anthony Bretaudeau

Dr Motifs

Anthony Bretaudeau — Tue, 19 Feb 2013 08:01:07 +0000

Dr Motifs is a bioinformatics project launched by the GenOuest bioinformatics platform (Rennes, France) in March 2010. This project is funded by IBiSA.

Dr Motifs stands for “Découverte et Recherche de Motifs” in French. If you don’t speak French, this means “Patterns discovery and matching” in English.
The aim of this project is to provide a complete platform for the study of motifs in biological data like nucleic or proteic sequences.
A more complete description of the project and its goal is available here.

Dr Motifs website: www.drmotifs.org
GenOuest member involved: Anthony Bretaudeau

The e-Biogenouest project : towards an e-Science approach in the Western France life sciences

Yvan LeBras — Mon, 14 Jan 2013 08:51:53 +0000

A Biogenouest unifying project funded by the Brittany and Pays de la Loire French regions, started in May 2012.

Its goal is to evaluate development possibility of the Information and communication technologies (ICT, TIC in French) use in life sciences in western France. It consists of a test phase that will lead to the writing of a masterplan targeting the development of infrastructure and tools needed to develop an e-Science approach in the Western France.

GenOuest member involved: coordination : Olivier Collin / animation : Yvan Le Bras
e-Biogenouest HUB: http://www.e-biogenouest.org/

WorkPackage 2.3

Sivasangari Nandy — Mon, 07 Jan 2013 15:32:37 +0000

A France Genomics project, started in late october 2012.
Similar to WorkPackage 2.2, this project focuses on assembling tools.

It will also offer a website where users will be able to choose the fittest software according to their project’s specificity.

Partner teams: GenScale (INRIA – IRISA), IG (CEA), Pasteur Institute, Sigenae (INRA)
GenOuest member involved: Sivasangari Nandy and Renaud Jullien

MapDeCoDe (workpackage 2.2)

Sivasangari Nandy — Mon, 07 Jan 2013 14:46:14 +0000

A France Genomic project, started in late october 2012.
Its goal is to identify and evaluate as many mapping tools as possible. We will investigate novel metrics and exhaustive test sets in order to grade them according to their biological applications and data specifities, memory requirements, execution time.

The result will be a freely accessible website where biologists will be able to find the best suited software for their mapping needs.

Partner teams: MIG (INRA), Bonsai (Lille 1, CNRS, INRIA), GenScale (INRIA – IRISA), IG (CEA)
GenOuest member involved: Sivasangari Nandy and Renaud Jullien

EMME project (Experimental Metadata Management Environment)

Cyril MONJEAUD — Tue, 04 Dec 2012 13:35:46 +0000

EMME, started in November 2011, is an IBISA project. It aims at facilitating the data integration and exchange among different entities of Biogenouest.
EMME suggests the use of tools developed by the ISA team to manage experimental metadata and BioInvIndex (BII) submission. Thus, information and data from each experiment will be more easily available.

EMME portal : http://emme.genouest.org/
GenOuest member involved : Cyril Monjeaud

ADT Inria Biosciences Resources

Claudia Heriveau — Thu, 29 Nov 2012 14:59:15 +0000

This projet, started in november 2011, aims at promoting bioinformatics software and resources developed by INRIA teams and their partners. A web portal will be deployed to allow users to test the software online. A tool is also developed to enhance the search of a specific resource using different criteria.

website : http://cherivea.genouest.org/IBR/