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    IFB SUPPORTS THE TEAMS INVOLVED IN THE FIGHT AGAINST COVID-19

     

    To address the COVID-19 outbreak, the Institut Français de Bioinformatique (IFB) launches an action to identify the needs in computing and data analysis, and offers expertise and computing facilities to support the involved teams.

    Facilities

    • Skills in computing, statistical analysis, databases, data science and bioinformatics.  IFB federates 30 platforms of services spread over all the French regions, and gathering 400 experts in the different domains of bioinformatics.

    • A high-performance computing infrastructure. The National Network of Computing Resources (NNCR) regroups 22 000 computing cores and 115 Tb RAM on national and regional servers (HPC clusters andclouds, https://www.france-bioinformatique.fr/en/infrastructure-0), including very high memory servers (3 Tb RAM, powered with 48 à 256 cores per server).

    • Software environments suited to the needs of life and health sciences: bioinformatics tools, databases, packages, containers, virtual machines, workflows and a national Galaxy instance (https://usegalaxy.fr).

    • A community forum to share experience and provide mutual support between users and experts (https://community.france-bioinformatique.fr/).

    • Importantly, our actions include but are not restricted to our bioinformatics-specific skills. We interact with the teams involved in the fight against COVID-19, to identify their needs and provide concrete and efficient support.

    • Bioinformatics against COVID-19

    • Finally, IFB  is part of the international effort led by EBI to create a European COVID19 Data Portal (https://www.covid19dataportal.org/)

     

    In action

    We interact with the teams involved in the fight against COVID-19, to identify their needs and propose them a concrete and efficient support; We also make the link between the different COVID-19 targeting actions at the national and international level (ELIXIREBI).

     

    Contact us

    Simply send us an email : contact@groupes.france-bioinformatique.fr.

     

    Members

    IFB vs COVID-19 Task Force : Alban Gaignard, Christophe Antoniewski, Christophe Blanchet, Claudine Médigue, David Salgado, Hervé Ménager, Ivan Moszer, Jacques van Helden, Julien Seiler, Gildas Le Corguillé, Olivier Collin, Olivier Sand, Patrick Guterl, Sowmya Rajan, Victoria Dominguez Del Angel, Vincent Navratil

    Figure: Cracking COVID-19, by Alice van Helden, adapted from Alissa Eckert COVID-19 original (source: CDC)

     

    Ongoing and achieved IFB actions

    Nb Action Description Category Applicant Contact  task force  COVID-19
    1 Docking on the bigmem cluster Installation of a Java docking tool on the IFB-core-cluster, support for the use of the cluster, and access to the bigmem node for the screening of a molecular library in order to identify ligands potentially useful to fight SARS-CoV-2 infection. Compute Baptiste Martin Task force NNCR Cluster
    2 In vitro screening for SARS-CoV-2 inhibitors Support to Bruno Coutard's virology team for the statistical analysis of an in vitro screening with a library of 1520 antiviral molecules, in order to identify inhibitor of SARS-CoV-2 infection. Statistics Franck Touret, Bruno Coutard & Etienne Decroly Jacques van Helden
    3 VirHostNet SARS-CoV-2 release Update of the VirHostNet knowledge base (protein-protein interactions) dedicated to SARS-CoV-2 and to systems biology-based research against COVID-19. Databases Vincent Navratil, UCBL, PRABI-AMSB Vincent Navratil
    4 Analysis of SARS-CoV-2 envelope protein The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif Publication Vincent Navratil
    5 COVIDScan: Thoracic CT scan results database of COVID suspected patients This resource was developed to facilitate the creation of structured reports concerning thoracic scanners for patients suspected of COVID pneumonia. The tool can be integrated into Radiological Information Systems and allows the extraction of data. Databases Pascal Béroud, Pole de radiologie et d'imagerie médicale du Grand Hôpital de l'Est Francilien David Salgado
    6 VirHostSeq: dual RNA-seq metatranscriptome analysis of Covid-19 patients. In the context of the VibraFlu project (PIA ECOFECT) and in collaboration with Laurence Josset team at HCL, we have developed a bioinformatics pipeline called VirHostSeq for the analysis of dual RNA-seq transcriptome/metatranscriptomes. This pipeline is applied to real-time analysis of metatranscriptome of Covid-19 patients from HCL. Analysis Laurence Josset, Hopitaux civils de Lyon, Laboratoire Virpath Vincent Navratil
    7 Viromedb: a complete viral genome database In the context of the VibraFlu project (PIA ECOFECT) and in collaboration with Laurence Josset team at HCL, we have developed Viromedb a database of complete viral genome including SARS-CoV-2 referenced in GenBank and Refseq database. Databases Laurence Josset, Hopitaux civils de Lyon, Laboratoire Virpath Vincent Navratil
    8 Home Learning (lessons about COVID-19) This project, set up during the Virtual Biohackathon, aimed to develop beginner's lessons in bioinformatics around the Covid-19. Training Victoria Dominguez Del Angel, Olivier Sand
    9 COVID-19 Workflows Hub WorkflowHub is a European-wide registry of scientific workflows funded by EOSC-Life, which involves ELIXIR nodes: UK (lead), NL, BE, FR, DE and ES. COVID-19 Workflows Hub is a fast tracked instance resulting from the COVID-19 Biohackathon (from 5 to 11 April 2020). Workflows Alban Gaignard, Hervé Ménager
    10 SARS-CoV-2 origins Analysis of genomic and proteic sequences in various coronavirus strains in order to infer the evolutionary events at the origin of SARS-CoV-2, and to understand the mechanisms of virulence. Phylogeny Etienne Decroly (AFMB) Jacques van Helden
    11 Covidstress server: Impact of COVID-19 on Human psychology Deployment of a Shiny app enabling to visualise the results of a study about the impact of COVID-19 pandemy on Human psychology (stress, confidence, observance of sanitary rules), let by an international consortium of psychologists and neurobiologists. Psychology and neurosciences Guillaume Gautreau (LabGEM) NNCR task force
    12 Bioinformatics investigation about SARS-CoV-2 origins An French-taught introductory course to bioinformatics methods with practicals entirely based on questions and data related to the origins of SARS-CoV-2. The course is addressed to 2nd year students in sciences with a very basic background in biology. The bioinformatics approaches include: annotations of genomic and proteic sequences, pairwise alignments, profiles of percent identical proteins, similarity searches, multiple alignemnts, phylogeny inference. Training Jacques van Helden
    13 PIPprofileR: a web tool to generate profiles of percent identical positions A Shiny-based Web tool enabling to generate profiles of Percent Identical Positions (PIP), which are widely used to compare coronavirus genomes and etect recombinant regions. Tools Thomas Denecker
    14 Biomarker discovery in exhaled air Bioinformatic and biostatistical methods for the treatment and analysis of expired air by mass spectrometry and electronic nose developed by CEA in partnership with the Exhalomics platform of the Foch Hospital/University Versailles Saint-Quentin. In particular the ptairMS R package for processing PTR-TOF-MS spectrometry data, available on github. Tools, Signal Processing, Statistics Camille Roquencourt, Stanislas Grassin Delyle, Etienne Thévenot
    15 The great adventure of Science A series of four 1-hour sessions on the French radio France Culture about scientific approaches to the Covid-19 pandemic, opening wider questions about the world of science: publication, handling of uncertainty, public communication, competitiveness, political issues, frauds, power games, ... Public communication Jacques van Helden
    16 Development of an unversal quality control kit At the current stage only already commercialized RNA fragments are used, in order to ensure rapid product development; first evaluation of the corresponding quality tests was already performed at the CHU Bordeaux in September 2020. Next stage will concern the development of an universal quality control kit and will involve the analysis of possible RNA sequence combinatorics; the corresponding test kits will be validated at a national reference center Sequence analysis Alexis Groppi
    17 docking on grid Installing nodes for docking compute on biomed VO Compute Vincent Breton Antoine Mahul
    18 COVIDSIM-FR combining statistical analysis of hospital data and parcimonious non Markovian modelling for infering and simulatin the epidemic in France Epidemiosurveillance, anticipation tool, NPI simulator Mircea T. Sofonea info via SoutGreen / IRD
    19 Rt2-en estimating the reproduction number of COVID-19 epidemics in different countries and, for France, in regions and departments using incidence, hosptialisation, and mortality data. Analysis Samuel Alizon info via SoutGreen / IRD
    20French Covid-19 data modellingModelling some COVID-19 dataTool, simulatorMarc Lavielleinfo Victoria Dominguez Del Angel

    Some other actions to support bioinformatics against COVID-19 In France

    In France

    In Europe

    Internationally

    • RDA - Research Data Alliance - RDA COVID-19 Working Group - Urgent Call for Expert Contributions :
      The objective of this Working Group is to clearly define detailed guidelines on data sharing and re-use under the present COVID-19 circumstances to help researchers follow best practices to maximize the efficiency of their work. The guidelines will focus on the management of data originating from different data sources and the development of a system for data sharing in public health emergencies that supports scientific research (https://www.rd-alliance.org/rda-covid-19-working-group-urgent-call-expert-contributions).
    • Individual initiave (USA, Japan, Germany) - COVID-19 Biohackathon April 5-11 2020 :
      The goal of COVID-19-BH20 is to create a cohesive effort and work on tooling for COVID-19 analysis. The biohackathon will lead to more readily accessible data, protocols, detection kits, protein predictions etc. We will also push for policy change where it comes to non-public or hard to access data because we are facing such challenges! (https://github.com/virtual-biohackathons/covid-19-bh20)
    • Coronavirus Tools : http://evbc.uni-jena.de/tools/coronavirus-tools/
      IFB - Institut Français de Bioinformatique ♦ CNRS UMS 3601 ♦ IFB-Core, Génoscope - 2 rue Gaston Crémieux, 91057 - ÉVRY – CEDEX ANR-11-INBS-0013236
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