APLIBIO

Posted on février 2, 2010 by

The APLIBIO regional center currently brings together 8 PFs located in Paris and in the Paris area with a staff of 80 people:

Biological models and applications. APLIBIO focuses its activities mainly on the following types of organism: microorganisms (e.g. infectious diseases at eBio and Pasteur, or environmental metagenomics at MicroScope and MIGALE), plants and their bioagressors such as fungi (URGI), and human (genetic diseases at GENATLAS, cancers at Curie). A specific activity is dedicated to protein structural analysis and chemoinformatics (RPBS and MIGALE).

Databases and software tools. All PFs are providing biological data collections, often combining heterogeneous data (genome sequences, expression data, biodiversity, genetic information, protein structures, etc.). Internationally recognized examples of such collections include the human gene and disease database GENATLAS, the plant genomics information system GnpIS or the microbial database GenoList. Elaborated software platforms are also developed, such as state-of-the-art annotation environments like MaGe and AGMIAL, or integrated web portals like Mobyle. These cutting-edge services are driven by specialized information technology developments (e.g. data integration, automated pipelines, text mining, database interoperability, human-computer interaction, etc.).

Project support and training. One major activity of most PFs is to provide collaborators with skills and know-how required for the projects they submit, usually involving large-scale data analyses. Amongst others, these services include specialized assistance for genome (re-)annotation, developments for the analysis and visualization of “next-generation sequencing” (NGS) data, or biostatistics expertise for clinicians interpreting tumour reports. In addition, a number of trainings, thematic tutorials and workshops are organized by the various PFs of the regional center.

Indicators. APLIBIO is involved in ca. 60 projects each year, submitted by biologist collaborators, 40% of whom are located outside the Paris area. With 3 million tasks and 800,000 queries per month, the computing and database servers are accessed worldwide. Detailed figures about the APLIBIO resources and productions are available below.

Services provided to the community

APLIBIO services cover database and software hosting, access to computing facilities, data integration and database design, software engineering, project support and training.

The platform offers access to a scientific computation infrastructure devoted to data analysis in the fields of genomics, proteomics and small molecules. Computing capacities at each site range from 80-core to 400-core systems. The grand total of the platform equipment sums up to 1,660 cores and 571 TB of disk storage. The infrastructure hosts a variety of online tools and databases, either installed from external distributions or developed by local bioinformatics labs. Several sites make available and maintain or mirror dozens of data collections (e.g. 51 at MIGALE, 36 at Pasteur) and hundreds of bioinformatics software tools (e.g. 500 at MIGALE, 700 at Pasteur, 40 RPBS-specific tools), accessible through integration portals (like Mobyle – developed by Pasteur and RPBS) that provide researchers with unified interfaces for launching and chaining programs.

A growing number of users expresses the need of automating the processing and analysis of their data: to this end, APLIBIO designs and develops specific databases, processing pipelines and other analysis tools and interfaces required for data integration (e.g. eBio proposes several original programs for RNA analysis, URGI has a specific expertise in developing pipelines for plants and fungi). Thus, APLIBIO services include several in-house developed specialized information systems that have hundreds of registered users and enjoy an international exposure (e.g. GENATLAS – database of genes and diseases, MicroScope and GenoList – microbial genome databases, GnpIS – plant and bioagressor genomics and genetics database). A large fraction of this activity is dedicated to NGS data analysis, especially in the frame of transversal working groups established this year.

A major service consists in supporting activity and projects of biologists and “omics” platforms (large-scale sequencing, microarray transcriptomics, mass spectrometry proteomics, cell phenotyping), in several application domains: among others, microbial genome (re)annotation and comparative analysis (eBio, MicroScope, MIGALE, Pasteur), biostatistics expertise for cancer research (Curie), RNA analysis (eBio), protein structure/function analysis and prediction (MIGALE, RPBS), therapeutic compound identification (RPBS), etc.

Finally, the platform is disseminating knowledge and know-how in bioinformatics and biostatistics by participating in many university courses (masters) and organizing hands-on tutorials and other training sessions in several contexts (at individual sites, in European projects, in workshops, etc.). For instance, Curie contributes to “ateliers Inserm”, and MIGALE has trained more than 500 people in the last 5 years, through a dozen different modules going from basic courses on Linux usage to courses on phylogeny methods or microbial genome annotation techniques.

 

 

 

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