More than the sum of its parts. The IFB has a fundamental role in bringing to bear the pooling of the physical, operational, and human resources in order to answer users’ needs in services and support, disseminate technological innovations, tracking the cutting-edge developments in technology and research at national and international level (via ELIXIR), and developing the training required in this very fluid landscape.
The IFB’s modus operandi relies on a shared task force which regroups various experts from the IFB’s platforms, thus boosting the sharing of knowledge and expertise, the design of robust and innovative solutions, and the deployment of services. The value added by this synergistic federation of regional bioinformatics platforms is a critical feature of the IFB infrastructure.
Regional platforms provide services and technical support to scientific projects in their local life sciences community. They also provide training, develop tools for the life sciences community and share part of their IT infrastructure. The regional platforms are integrated into bioinformatics research laboratories and are therefore able to maintain an essential link between service provision and research activities.
The mission of the ABiMS platform is to assist researchers of the marine and, more broadly of the life sciences communities, in the analysis of their bioinformatic data as well as in the development of software and databases. It is also connected to the EMBRC infrastructure, is part of the IBiSA network via the regional BioGenOuest project, and is ISO 9001: 2015 certified. Through its numerous interactions with research units, ABiMS is involved in several projects with national and European impact, involving bioanalysis activities, software, and infrastructures development.
The Accessible Reproducible and Transparent bioinformatics platform of the Institut de Biologie Paris Seine provides support to biologists and medical doctors for functional genomics and precision medicine. It is implanted on the Jussieu campus of the faculty of sciences of Sorbonne Université and is also strongly involved in clinical research as a partner of the SIRIC Curamus that gathers efforts in cancerology from the 5 university hospitals of SU. ARTbio is running 2 public Galaxy servers, https://mississippi.fr and https://usegalaxy.sorbonne-universite.fr which provide environments for small RNA profiling and variant analyses, respectively. It also provides public servers for R analyses as well as for data storage. A third Galaxy server is dedicated to ARTbio user projects. ARTbio develops open source bioinformatics softwares, most of them available as Galaxy plugin tools (more than 48 tools available in https://github.com/ARTbio/tools-artbio. Beside accompaniments of user projects under contracts, ARTbio is maintaining its own research lines in order to develop top level expertise in three specific domains: small RNA biology and viral small RNAs, statistical and machine learning methods for single cell RNAseq analysis, and predisposition mutations in children and young adult acute myeloid leukemia (partner of the CONECT-AML INCA project). ARTbio has defined training in bioinformatic as a top priority in the incoming years. Thus, in addition to the organisation of regular training sessions, ARTbio is nowadays known for its companionship offer and is also leading the project STARTbio for a University Diploma in Bioinformatics at Sorbonne Université, based on a practical approach of analyses as well as heavy use of e-learning tools (videoconferences and executable tutorials)
The ATGC bioinformatics platform provides services for evolutionary, comparative, and functional genomics. It promotes the methodological developments from the Methods and Algorithms for Bioinformatics (MAB) team at LIRMM. These developments are disseminated to the scientific community as freely accessible services from the platform’s website. Most of the tools can be run directly online, via a dedicated web interface from which each user can load their own data. These interfaces have been designed to facilitate the usage of the tools and the analysis and the interpretation of results.
AuBi is the Clermont bioinformatics platform for life sciences (fundamental biology, microbiology, agronomy, environment, health and epidemiology). AuBi relies on the UCA (Clermont Auvergne university) Mesocentre to promote its computing facilities for data analysis, storage, training in bioinformatics, and web service hosting for research. The platform is committed to serving UCA teams and associated entities(public and private companies. Important skills are developed to support scientific projects in the field of large scale sequence analysis in genomics (assembling, annotation, variant analysis, DNAseq, ...), transcriptomics (RNAseq, ChiPseq, ...),epigenomic variations (BSseq), metagenomics, metatranscriptomics, metabolomics, molecular dynamics but also statistics and imaging.
The BIGEst platform brings together bioinformatics teams and services from the Strasbourg region: GMGM, IBMC, IBMP, ICube, IGBMC, IPHC and LGM. The platform offers expertise, bioinformatic tools and resources, as well as data mining algorithms focused on evolutionary and functional analyses in various application fields, including biomedical, plant, yeast, and bacterial studies.
Bilille is the Lille bioinformatics platform, which was founded in 2016 under the joint initiatives of the University of Lille, CNRS, Inserm, Institut Pasteur de Lille, CHU Lille, and Inria. It has expertise in bioinformatics, biostatistics and bioanalysis and offers a complete service to Lille research laboratories in biology and health.
BiRD is co-managed by the ITX and the LS2N, and employs six computational biologists. Thanks to the skills of this dedicated and highly qualified staff, BiRD advises, proposes and develops bioinformatic services based on high-throughput sequencing data. BiRD has expertise in large-scale data analysis and it has developed dedicated bioinformatics workflows that standardize the processing of raw data into biological significance. Training based on this expertise is proposed in data analysis and programming languages. The services are supported by a dedicated computing and storage infrastructure which is remotely accessible through several web services open to all scientists, regardless of their host institution.
The CBiB is a bioinformatics core facility that provides access to high-performance computing resources, biological data analysis, and programming expertise. The resources help scientists and private laboratories to answer their research needs in an efficient and cost-effective manner. Proposed are state-of-the-art technologies for working with clinical, translational, and basic science data, from acquisition and storage to analysis and sharing. Resources are secure and standards-compliant. From a few to several tens of thousands of samples, the Bioinformatics Centre provides complete DNA, RNA, metabolomics, proteomics as well as image data analysis and integration services.
Created in 2015, the C3BI includes five research units in Computational Biology, and the Hub of Bioinformatics and Biostatistics. The mission of the center is to develop methodological research in bioinformatics and biostatistics, give international visibility to the Institut Pasteur, offer support to experimental research units, and develop the computational and analysis skills of the campus. The platform activities comprise participation in research and analysis projects, on-site assignments within campus units and platforms, training and teaching sessions open to our partners, and provision of a number of resources to the national and international community.
The eBIO Bioinformatics platform created in December 2009 is at the heart of the University of Paris-Sud’s bioinformatics system. eBio is certified by IBIZA/Reseau National des Plateformes Bioinformatiques (RENABI) and is a member of the Alliance des Plateformes Bioinformatiques d’Ile de France (APLIBIO).
The platform is located in Toulouse, south of France. Its aim is to bring together material and human resources to provide life science research programmes with an access to state-of-the-art know-how and to high-level technologies. Over the years the team has built an expertise in diverse applications of sequence analysis. This has been used in software and pipeline developments as well as in data analysis projects including genome assembly (short/long reads), annotation (coding/non coding), (s)RNA-seq, methyl-seq data and variant analyses, metagenomics (metabarcoding/whole genome), and, more recently, data integration. Supported communities are those of agriculture, food, human health, ecology, and bioinformatics.
Hosted at INRIA-IRISA, the GenOuest facility offers an exhaustive bioinformatics environment with hardware and software infrastructure, public databases, software and workflows, together with the associated support. The technological portfolio relies on several computing resources (cluster, cloud, docker and a galaxy portal) and data management solutions (BioMAJ). Over the years GenOuest has invested in the development of data-centered tools. Further, thanks to the CeSGO project, GenOuest offers a set of collaborative tools to manage projects and scientific data in an optimal way. GenOuest also develops bioinformatics applications as well as training courses, and organises the technological transfer of new tools developed by research teams of the Institute.
The iCONICS platform develops and makes available software solutions and methodological expertise to meet three important needs for biomedical research: data curation, standardization, annotation, structuration, integration, and visualization (for data managers and software engineers), high-throughput omics data processing, including NGS data such as whole-exome and RNA-seq (for bioinformaticians), and finally, basic and advanced statistical analysis, especially integration of multimodal and high-dimensional data (for biostaticians). The platform thus supports scientific and clinical teams at every step of their research projects: from study design to data management, processing, analysis and interpretation, while considering a wide variety of data acquisition approaches (clinical, imaging, genomics, etc...)
The platform is organised around three major areas: data management (the structuring of data originating from robots), tool development (web applications, databases, pipelines), and support for research projects in an oncogenomic contexte. There now exists a set of conventional pipelines to analyze WES, WGS, ChIP-Seq, RNA-Seq, TGS, and microarray oncoscan/cytoscan data.
The platform’s expertise is versatile and encompasses many aspects of high-throughput data in biology and in clinics: management, processing, integration, and statistical and functional analysis. Covered are fundamental, translational, and clinical research, including clinical trials. For all these domains, the platform also develops appropriate methods, implements tools and automated pipelines. These are packaged and released publicly or granted on-line access. Software optimisation for high-performance computing is also part of the platform’s know-how. Finally, it has developed an experience in training biologists, clinicians, and bioinformaticians in all of the above-mentioned fields.
The MBI platform stands for “Modelling of Biomolecules and their Interactions”. It is essentially a research platform offering services in a framework of scientific collaborative projects. The main activities concern 3D modelling of proteins in interaction with ligands, of proteins, RNA or DNA, as well as the functional annotation of biomolecules. Available tools include molecular dynamic simulation (NAMD) software and very fast rigid docking and shape comparison programs, all which are run on hybrid clusters of CPUs and GPUs. Data science expertise, including in symbolic data mining, machine learning, and complex graph analysis, is also available for bioinformatics and biomedical applications.
The LABGeM team from the CEA/Genoscope has developed MicroScope, a web-based platform for prokaryotic genome analysis and expert functional annotation. MicroScope combines tools and graphical interfaces to study genomes in a comparative and metabolic context. This platform provides data from thousands of genome projects and from post-genomic experiments thus allowing users to expand their understanding of gene function. Expert annotations are continuously gathered in the MicroScope database and so contribute to the improvement of the quality of microbial genome annotations. MicroScope can be used as a community resource for comparative analysis and annotation of publicly available genomes, but also as a private resource with restricted access rights on genomic data.
The Migale bioinformatics platform is a team of the INRA MaIAGE research unit (Applied Mathematics and Computer Science, from Genome to the Environment). Since 2003, it provides four type of services to the life sciences community: an open infrastructure dedicated to life sciences data analysis (500 Tb, 1000 equivalent CPUs), dissemination of expertise in bioinformatics (the annual “Bioinformatic by practice” training session), design and development of bioinformatics applications (genome browser and databases), and data analysis in genomics, metagenomics and metatranscriptomics.
The MMG-GBIT IFB platform is linked to the Bioinformatics & Genetics research team of Inserm U1251. It benefits from this strong interaction and provides users with the team’s expertise in human genetics, rare diseases, and oncogenetics as well as NGS data analysis. It provides international reference systems to help collect, annotate, filter, and interpret human genetics data in relation to diseases. These tools, databases, registries and observatories have already received millions of worldwide queries. In addition, training is also provided as well as assisting researchers, from design to analysis, in any bioinformatics or tool development projects related to human genetics.
Orphanet is a knowledge base on rare diseases and orphan drugs. It aims to survey and generate data on rare diseases so as to improve the diagnosis, care, and treatment of patients. The Orphanet website provides high-quality information on rare diseases and ensures equal access for researchers to the knowledge base and to the Orphanet Rare Disease Ontology. Orphanet also maintains the Orphanet rare disease nomenclature (ORPHA number) which is essential in enhancing the visibility of rare diseases in health and research information systems, thus acting as an interoperability vector.
The Synergie-Lyon-Cancer (SLC) Bioinformatics Facility was founded in 2009 by Pr. Gilles Thomas to promote the exploitation of massive amounts of data being generated from large scale genomic projects in the field of Cancer Research. It is hosted at the Centre Léon Bérard in Lyon. The staff currently includes ten people under the supervision of Alain Viari. The facility has focused its efforts on the management and analysis of large volumes of NGS data, mostly whole genome sequencing (WGS). It also developed a strong expertise in transcriptomic analysis using various NGS techniques.
The PACA Bioinfo services focus on microbial genomics, metagenomics, comparative genomics, and molecular phylogeny. It provides the community with various free access online tools proposed without prior registration. The platform also collaborates with genomic or metagenomic projects for which it constitutes the main bioinformatic support, in particular with teams of the Mediterranean Institute of Microbiology in Marseille. Significant progress has resulted from the genomic analyses of giant viruses, two sponges, and metagenomes from ancient frozen soils (permafrost). The platform also provides generic statistical tools for comparing large datasets of counts (ACD-tools) as encountered in classical or metagenome-based ecological studies.
The Bioinformatics and Biostatistics Hub is the service part of the Computational Biology Department. The Hub team involves 50 biostatistics and bioinformatics experts. The mission of the platform is to develop methodological research in bioinformatics and biostatistics, give visibility in this field to the Institut Pasteur on an international level, offer support to experimental research units, and develop the computational and analysis skills of the campus. The platform activities comprise participation in research and analysis projects, on-site assignments within campus units and platforms, training and teaching sessions open to our partners, and the provision of a number of resources to the national and international community. The Hub team and all the Department have a long standing experience in the development of web sites (e.g. NGPhylogeny.fr), intensive and parallel computations using both GPU and Big Mems, health data management.
The PRABI-AMSB (for Analysis and Modelling of Biological Systems) platform proposes bioinformatic services for biologists who need assistance with specific tools or in-depth expertise for more important projects. The expertise available at PRABI-AMSB covers the following areas: expression data (RNA-seq), interaction data (ChIP-seq, Tap-tag/MS, Yeast Two Hybrid screens), metagenomics and metatranscriptomics, comparative genomics and phylogeny, genome assembly and annotation, and systems biology (metabolic, protein interaction and regulatory networks).
The PRABI-Lyon-Grenoble is a consortium of eight research teams involved in bioinformatics in Lyon and Grenoble. Therefore, the expertise available at PRABI-Lyon-Grenoble covers a broad range of domains: molecular phylogeny and evolution, metabolic networks, biostatistics for medicine, multivariate statistics in ecology, plants population genetics, expression data, high-dimension statistics, proteomics, comparative genomics, transposable elements, and systems biology (metabolic, protein interaction and regulatory networks). As the PRABI-Lyon-Grenoble is a consortium of research teams, it is involved in many training and teaching activities (from first year students to professionals).
RPBS is a platform dedicated to structural bioinformatics. It proposes: the development of structural bioinformatics methods/protocols, service hosting and on-line deployment of services, training and consulting, and calculation hosting through PAAS.
South Green is a bioinformatics platform dedicated to the genomics of tropical and Mediterranean plants and related pathogens. It federates bioinformaticians from different units and institutes of Montpellier (Bioversity, CIRAD, INRAE, and IRD) with a multidisciplinary expertise in data integration, software development, sequencing data analyses, and high-performance computing. South Green ensures the development of novel information systems such as GreenPhyl, SNiPlay, Gigwa, or AgroLD, and offers bioinformatic pipelines through Galaxy and TOGGLe workflow managers. The platform has built a strong expertise in the development of Genome Hubs and integrated information systems, which deployed for several plants and currently being extended to pathogens.
TAGC is a mixed research & services Inserm units specialised in the development and application of omics approaches to various biological systems. The laboratory includes a sequencing facility (TGML, a member of France Génomique) and a strong team of bioinformaticians who develop and give public access to bioinformatics resources (software tools and databases) in domains ranging from the analysis of single protein and DNA sequences to large-scale analysis and integration of omics data, with a specific focus on genome variations, genetic and epigenetic regulation, and network analysis.
The main missions of the platform are to contribute to the management, compatible with open science, of patrimonial data produced by INRAE and its partners, and to propose tools and suitable environments (including training) for data analysis to researchers. The main activities of the platform during the last five years were: plants and fungi data integration in the GnpIS information System, giving access to computing resources and analysis tools, analysis support, and user training (use of GnpIS, annotation, SNP calling, …)
ISfinder is a public database and international reference center for prokaryotic IS and a research tool. The project is divided into two major types of activity, intimately connected to the ISfinder database. The first concerns the improvement of ISfinder itself and the development of tools necessary to exploit the information included in the database. The second, as a direct consequence, involves detailed analysis of the information in the database. ISfinder activity involves database analysis, facilitating IS classification, identification of new families, and provision of information concerning their genomic impact (e.g. effects linked to the choice of target site).