Center of Informatics for Biology
Head : Michaël Pressigout
As part of the DSI (Information Systems Department
), the CIB (Center of Informatics for Biology) meets the IT needs of campus scientists through the development, provision and roll-out of tools or via its IT expertise and support.
The CIB has the following roles:
- offer all campus units IT developments (web interfaces, databases, development of tools, automation, scripts, parallelization & high-performance computing solutions). IT services are provided on a project basis in close association with the scientists
- offer technology watch services and propose themes for IT innovation; provide support, advice and expertise required for these activities
- organize bioinformatics training sessions; lead the campus bioinformatics community with a particular focus on IT
- offer biologists efficient tools and the databanks necessary for bioanalysis, install new tools as required
- cooperate with the various bioinformatics platforms both in France and worldwide. The CIB offers hosting on the Pasteur bioinformatics platform in association with the PFBaG platform. The Pasteur platform received official accreditation from the GIS-IBiSA (Scientific Interest Group-Infrastructure for Biology, Health and Agronomy) and is part of the APLIBIO – RENABI networks
- enhance tools developed by the Institut Pasteur
- provide the campus with IT experts to support research projects, particularly via temporary secondment
- maintain all Institut Pasteur information system services operational.
The bioinformatics tools on the Institut Pasteur platform are available, either via the mobyle
open access interface, or directly from a command line in Unix (access restricted to the Institut Pasteur community).
: this search engine enables you to search for a tool in full-text mode, by subject or operation type (EDAM categories), to view the banks available, to see the latest tools installed and to find out about tools developed at the Institut Pasteur.
Biological software portal
Scientists have access to a growing catalog of 230 packages including some 1,350 programs. New applications are added to meet the needs of biologists for their work. We have also built 280 web interfaces providing user-friendly access to the majority of locally installed software.
A scientific software development and deployment service is available to researchers who require bioinformatics expertise for their various projects or to present their findings using web techniques and databases. We recently incorporated an additional design and specification phase for all new projects.
This user-friendly portal provides access to bioinformatics software. The portal is open to both our campus and the external community and provides a service similar to the one that the NCBI, EBI and SIB offer scientists all over the world.
In 2009-2011, Mobyle was involved in two projects:
- MobyleNet: Mobyle bioinformatics portal Network, including 9 ReNaBi platforms in France.
- BMID: development of a shared user interface for publishing tools on the web and enhancing their use by scientists in partnership with NIAID/NIH.
Databanks are updated on a frequent basis. Local copies are made via access to the original databanks. The challenge lies in the sheer volume of data that needs to be processed. Total disk space for all formats amounts to 4.7 TB. There are currently 40 databanks available including Embl, GenBank, RefSeq, Uniprot, Nrprot, Genpept and Pdb.
A “BiblioList” tool was developed to clean up, update or integrate a new bibliographical reference in GenoList. Publications are automatically linked, either by the name of the gene, or by the description of the organism’s gene to be updated. The results must be validated by the annotator in order to be exported.
Software maintenance for the Institut Pasteur Biological Resource Center
We administer ARPAS, the software for managing collections of biological resources for the CRBIP. This system is used by 28 organism collections on campus. To improve availability and maintenance and to achieve ARPAS interoperability goals we launched a project to develop 2nd generation software called BRC-LIMS. This IBiSA-funded project is being developed by a vendor. We are managing the project for CRBIP and 10 Biological Resource Centers in France to renovate ARPAS and create a shared FBRCMi-catalog. Delivery is scheduled for May 2012.
A bioinformatics course is included in the 2nd year “Genome analysis” Masters program.
Contribution to high-throughput sequencing
We are in charge of installing and developing specific software required for NGS analysis. The pipeline is installed by our group for use by scientists on campus. Parallelization has been used to speed up applications requiring significant computing time on the cluster (thirtyfold reduction in time).
The GBrowse genome viewer was installed on the Genopole server to retrieve and display data produced at the Institut Pasteur. This tool enables scientists to discover, confirm or reannotate previously sequenced and annotated genomes. Focus can be placed on specific regions of the genome to identify genes of interest in order to develop new lines of attack and solutions against bacteria and viruses.
A cluster overhaul is currently underway to meet computing requirements for high-throughput sequencing, with greater design load, memory and input and output throughput capabilities.
Link to pasteur.fr website