The “Biological Software and Databases” Group is in charge of the installation, maintenance and interfacing of biological software for researchers, as well as the release to a choice of international biological databanks. We ensure the concept of scientific databases that enable the placement of laboratory results online. The new interfaces of presentation of biological software operate since January 2008.

Software for biology:

All biological software available for the Institute is divided into 160 packets including about 750 programs. Installation, tests, release and maintenance of this software is the main part of our activities. We have built 270 standard Web interfaces that give the researchers user-friendly access to our software.

Individual development:

Local development and deployment service are available for researchers who need bioinformatics skills to achieve their projects, or to present their results using databases and Web tools. The study of the demand and the writting of specifications are proposed for each new project since 2008.

The Mobyle project:

This projet aims at giving a friendly portal sharing all our bioinformatics analysis software. This portal is available to the campus and outside, and is comparable to the services provided by the NCBI, the EBI or the SIB to the researchers worldwide.

In 2009-2010, Mobyle has been extended with two collaborations:

• MobyleNet : Mobyle bioinformatics portal Network with 9 french plat-forms of bioinformatics.

• BMID : a NIAID/NIH collaboration to create common user interface to publish tools on the Web

and improve their usability to scientists.

Biological databanks:

Biological databanks are updated with an automate developed here. It periodically searches the original banks and gives access to local copies. The important data volume remains the most difficult constraint to manage. The space used on disks for the whole formats represents 4.5 TB. Today 36 banks, including Embl, GenBank, RefSeq, Uniprot, Nrprot, Genpept, PDB, Interpro are available.

Databases:

New features were added to the server Genolist : the application “Find Target” searches for the presence or absence of genes of reference in one or several genomes. A tool “Bibliolist” was developed to curate, update or insert new bibliography into GenoList. Publications are automatically linked based on the gene name or gene description of organism to update. The results need to be validated by the annotator to be exported in GenoList.

We maintain and develop ARPAS, the software for the management of the collections of biological resources (CRBIP). This system is used by 28 collections of organisms at the campus. We are working on a project of a new version of this software for the CRBIP and other French BRCs of microorganisms.

Statistics:

The acquisition of skills in statistics for multiple correspondence analysis, functional analysis and hierarchical classification enabled a scientific collaboration with the Yersinia Research Unit and resulted in a publication.

Bioinformatics training courses:

A course of bio-informatics is taught in the “Genome Analysis” course of Master 2.

Contribution to “High-Throughput Sequencing” :

We are in charge of installation, development and scripting for the specific software required by NGS analysis.

The pipeline is set up by our group to be used by every researcher in the campus. Parallelization has been added to speed up the CPU bounded applications, using the cluster (elapsed time divided by 30).

Keywords: bioinformatics, biological software, databases

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