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 Catégorie Demandeur Contact  task force  COVID-19
1Docking on the bigmem clusterInstallation 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.ComputeBaptiste MartinTask force NNCR Cluster
2In vitro screening for SARS-CoV-2 inhibitorsSupport 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.StatisticsFranck Touret, Bruno Coutard & Etienne DecrolyJacques van Helden
3VirHostNet SARS-CoV-2 releaseUpdate of the VirHostNet knowledge base (protein-protein interactions) dedicated to SARS-CoV-2 and to systems biology-based research against COVID-19.DatabasesVincent Navratil
4Analysis of SARS-CoV-2 envelope protein The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motifPublicationVincent Navratil
5COVIDScan: Thoracic CT scan results database of COVID suspected patientsThis 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.DatabasesPascal Béroud, Pole de radiologie et d'imagerie médicale du Grand Hôpital de l'Est FrancilienDavid Salgado
6VirHostSeq: 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.AnalysisVincent Navratil
7Viromedb: a complete viral genome databaseIn 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.DatabasesVincent Navratil
8Home 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.TrainingVictoria Dominguez Del Angel, Olivier Sand
9COVID-19 Workflows HubWorkflowHub 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). WorkflowsAlban Gaignard, Hervé Ménager
10SARS-CoV-2 originsAnalysis 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.PhylogenyEtienne Decroly (AFMB)Jacques van Helden
11Impact of COVID-19 on Human psychologyDeployment 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 neurosciencesGuillaume Gautreau (LabGEM)NNCR task force

Some other actions to support bioinformatics against COVID-19

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
magnifiercross linkedin facebook pinterest youtube rss twitter instagram facebook-blank rss-blank linkedin-blank pinterest youtube twitter instagram