Archive for the Platforms Category
Posted on septembre 25, 2010 by Vincent Lefort
The ReNaBi-Grand Sud regional center currently gathers four PFs located in the South part of France (IGS Marseille, CAZy Marseille, IMGT Montpellier, and ATGC Montpellier, Nice and Perpignan) with a staff of 42 people.
- ATGCbioinformatics platform involves several teams:
- CRBM (Montpellier)
- GET (Montpellier)
- IPMC (Nice)
- IRD (Montpellier)
- LGDP (Perpignan)
- LIRMM (Montpellier)
- South Green (Montpellier)
Biological models and applications
Each PF possesses its own specificity: ATGC covers evolutionary, comparative and functional genomics with an emphasis on algorithmics and software developments, and applications to tropical plants; CAZy attempts to cover all carbohydrate-active enzymes across all sequenced genomes; IMGT is the global reference in immunogenetics and immunoinformatics; IGS covers functional and structural genomics, with emphasis on intracellular pathogens and viruses. ReNaBi-GS thus has expertise in a large spectrum of fields, including Health, Agronomy, Evolution, and Ecology.
Databases and software tools
ATGC and IGS provide the community with original software tools, some widely used and cited. All PFs provide specialized databases, some being the international reference in their domain (e.g. IMGT, CAZy, or SouthGreen for the genomics of tropical plants). ReNaBi-GS is involved in many collaborative projects with biologists, e.g. from marine ecology (IGS) or the genomics of major pathogens such as Plasmodiums and Leishmania (ATGC). Our aim is to push forward existing methods and develop bioinformatics tools and databases with high international impact.
Project support and training
The ReNaBi-GS engineers can take care of different projects or requests from the biologist community, according to their area of expertise. For example, we help users to treat the millions of reads that are obtained through new generation sequencing, thanks to original programs and our computing facilities. We participate to the GRISBI project to share the computing resources with other ReNaBi nodes. We train students in various masters of bioinformatics, both at Montpellier and Marseille, and organize training sessions (e.g. on phylogeny) and regular bioinformatics seminars.
ReNaBi-GS services are internationally renowned and used worldwide. Some of our computer programs are highly cited (e.g. PhyML and T-Coffee, with 3,000 and 2,000 citations, respectively, cf. Web of Science) and our databases are widely accessed (e.g. IMGT, CAZy and SouthGreen, with 150,000, 150,000 and 50,000 requests per month, respectively).
Posted on février 12, 2010 by Pierre Tufféry
MobyleNet, built on the Mobyle bioinformatics portal environment, federates many bioinformatics platform, that will offer a distributed network of ressources.
The aims of MobyleNet are:
- Integrate into a single web portal framework (Mobyle) the services of the different nodes.
- Initiate a large application spectrum framework, covering complementary aspects of the bioinformatics.
- Making the services of the different sites interoperable.
- Build a confidence network over the specific skills of each platform, promoting quality management over the services.
More information available on MobyleNet
Posted on février 12, 2010 by Christophe Blanchet
The GRISBI Platform (Grid Support for Bioinformatics) is a joined initiative between six French bioinformatics platforms: PRABI Lyon, GenOuest Rennes and Roscoff, CBiB Bordeaux, BIPS Strasbourg, CIB Lille, MIGALE Jouy-en-Josas, to set up a grid infrastructure devoted to serving the Bioinformatics community at the national level. GRISBI is the infrastructure activity of the French RENABI network (Réseau National des plate-formes de Bioinformatique) that is coordinating the thirteen national Bioinformatics centers. GRISBI is financially supported by the RENABI Network and by the IBISA initiative (National coordination of the Infrastructures in Biology, Health and Agronomy). GRISBI has been labelled “IBISA ‘s National Platform” in 2008.
The main goal of GRISBI is to gather Bionformatics computing resources at the national level to make possible challenging bioinformatics applications dealing with large scale systems: comparative genomics and genome annotation, system biology, protein function prediction, molecular interaction like protein-protein or DNA-protein, … The six core centres will share and mutualize their existing resources with grid software components: storage and computing resources, but also database and software resources.
Web Site : www.grisbio.fr
Posted on février 2, 2010 by Christine Gaspin
The Sud-Ouest platform is a federation of different sites from Bordeaux and Toulouse:
Services provided to the community
The main activity of ReNaBi-SO focuses on development of tools (databases, softwares, web sites) in genomics, transcriptomics and metabolomics. All organisms are considered with some specificity per group. Biogemma has a recognized expertise in Crops Genomics. All the teams provide specialized biological data collections including bacteria (CBiB), Insertion Sequences in bacteria and archaea (IBCG/LMGM) data collection on aquaculture and farm animals (SIGENAE), plants (BIOGEMMA) and trees (GenoToul). Different software, tools and pipelines dedicated to quality control of NGS data (NG6), assembling, annotation of genomic and EST data data integration (Ensembl-contig browser) are also developed or extended with regard to the integration of new functionalities or new type of data. A major activity is to provide research programs in biology with resources, services and research support in bioinformatics. Those include computer power and storage facilities for large scale analysis, a direct access to the main biological databanks, formal and informal training sessions, bioinformatics developments and expertize in bioanalysis. Services are invoiced or offered through consultation and direct research collaborations mainly in the field of NGS data analysis. People have a good expertise on common tools and methods in the field of bioinformatics and practice in development of tools in this area.
GenoToul proposes training sessions attended by a broad range of biologists and bioinformaticians ranging from beginners to more accustomed users. See.
Available skill covers sequence analysis from sequence assembling to genome and EST annotation and variability analysis.
Main scientific resources
Posted on février 2, 2010 by Maude Pupin
ReNaBi-Nord-Est currently gathers four PFs located in the North-East of France.
- Lille (CIB)
- Strasbourg (IGBMC)
- Vandoeuvre-lès-Nancy (MBI)
- Reims (MMP)
Biological models and applications.
Lille is involved in microbial bioinformatics. MBI, Strasbourg and Reims carry out activities regarding protein 3D modelling, possibly in complex with ligands or protein-protein interactions.
Databases and software tools.
ReNaBI-NE PFs are providing access to either their own software through websites (such as Hex for Protein docking, YASS for homology search, CARNAC for prediction of RNA 2D structure for sequence families, PipeAlign and MACSIMS for production and exploitation of high-grade multiple sequence alignment, IntelliGo for Semantic Similarity Measure). They develop and maintain the Norine database on nonribosomal peptides and the BioRegistry. Lille participates in the EGI and GRISBI initiatives.
Project support and training.
ReNaBi-NE PFs provide bioinformatics software and data to the community, but seldom support to projects. The IFB project will give them the opportunity to enlarge their provision of services. ReNaBi-NE PFs are involved in courses (for graduate students in biology or computer science), thematic days and workshops proposed on a yearly basis or selectively.
Tens of thousands tasks are run each month from all over the world on the different servers of ReNaBI-NE.
Posted on février 2, 2010 by Olivier Collin
The Grand-Ouest platform is a federation of different sites of Brittany and Pays de la Loire.
The ReNaBi-GO platform is a bioinformatics platform created in 2002 during the foundation process of Biogenouest. This platform is located in three different cities: Rennes, Nantes and Roscoff. In Rennes, ReNaBi-GO is hosted by the INRIA/IRISA with the GenOuest platform. In Nantes, Inserm hosts ReNaBi-GO with the BiRD platform and in Roscoff it is hosted by the CNRS and UPMC (Université Pierre et Marie Curie) with the ABiMS platform.
20 people are presently working on the platform: 8 persons in Rennes, 4 in Nantes and 8 in Roscoff. These engineers operate the different tasks of a bioinformatics facility: animation, system and database administration, software development, user support, spreading and teaching activities. The Rennes facility is certified according to the ISO 9001: 2000 standard since May 2008, the Nantes facility is certified since October 2008.
Altogether, the 3 sites provide a coherent resource for the community. Each site is characterized by a strong specific technological partnership: Rennes is linked to an INRIA research team focusing on algorithms and bioinformatics applications acceleration, Nantes is linked to a transcriptomic platform and Roscoff is linked to a sequencing facility. On a thematic side, each site possesses its own specificity: Rennes covers many aspects with an emphasis on sequence analysis and specialized architectures for computing, Nantes is focusing mostly on health and transcriptomics, and Roscoff is focusing on Marine sciences. Combining these different expertises ReNaBi-GO covers a large spectrum of scientific fields in Marine Biology, Agronomy, Health and Medicine.
Services provided to the community:
The platform proposes training sessions attended by a broad range of persons ranging from beginners to more accustomed users of bioinformatics tools. The subjects of the training sessions were programming languages, sequence analysis, motif discovery, phylogenetics and transcriptome analysis.
A complete catalog of the training can be seen on this site.
Main scientific resources
- Rasta Bacteria
- PLAST: parallel local alignment search tool for database comparison
- GASST :
ReNaBi-GO provides a complete bioinformatics infrastructure for the community. This includes computing power, storage but also a comprehensive list of software and databanks dedicated to biological data analysis. These resources are accessible anonymously through the different web servers (genouest.org, madtools.org) or after authentication on the cluster. Accounts are free.
Real time monitoring of GenOuest’s computing resources. Realt time monitoring of ABiMS computing resources.
Posted on février 2, 2010 by Ivan Moszer
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.
Posted on décembre 8, 2009 by Christine Oger
The PRABI is the Rhône-Alpes Bioinformatics Center, a RIO platform of the Rhône-Alpes Genopole. It gathers many research teams that develop new biological modeling using mathematics and computer sciences. The PRABI provides to the national and international community the computer tools that result from these researches. Moreover some « classical » tools of bioinformatics are also available. However it is not the aim of PRABI to compete with big international centers (as EBI, NCBI, …) on which a much larger collection of tools can be found.
The PRABI expects to be an exchange tool between biologists and bioinformatic researchers. This site aims at presenting the databases and computational tools available through the PRABI for biology and health research.
Rhone-Alpes BioInformatics Center
The Rhone-Alpes BioInformatics Center is a platform gathering 11 research teams spread on 4 different sites. the PRABI has research, service and training activities in a large number of bioinformatics and biostatistics fields.
Web site : PRABI
Posted on décembre 6, 2009 by admin
RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation. This service is provided by GenoToul.
The increasing number of ncRNA discovered since 2000 and the lack of user friendly tools for finding and annotating them, have made necessary to propose to biologists an in silico environment allowing structural and functional annotations of these molecules with regard to available protein genes annotation environments.
RNAspace home page
Web site : RNAspace