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
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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.
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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).
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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).
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A community forum to share experience and provide mutual support between users and experts (https://community.france-bioinformatique.fr/).
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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.
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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 (ELIXIR, EBI).
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 | Requester | Contact for COVID-19 task force |
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| 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 | |
| 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 | 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 developped 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 | 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 developped Viromedb a database of complete viral genome including SARS-CoV-2 referenced in GenBank and Refseq database. | Databases | Vincent Navratil | |
| 8 | Home Learning 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 origin | 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 | Jacques van Helden |
| 11 | 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 psychologi (stress, confidence, observance of sanitary rules), let by an international consortium of psychologists and neurobiologists. | Psychology and neurosciences | Guillaume Gautreau (LabGEM) | NNCR task force |
Some other actions to support bioinformatics against COVID-19
In France
- ANR is launching a call for projects with an accelerated evaluation and selection process on COVID-19. With an initial budget of 3 M€ and focused on four priorities identified by the WHO, this Flash call aims to rapidly support the scientific communities mobilized on COVID-19 (https://anr.fr/en/call-for-proposals-details/call/flash-call-covid-19/).
- Real-time, reproducible and fair share systems biology research against Covid-19. http://virhostnet.prabi.fr/
- The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif. https://www.biorxiv.org/content/10.1101/2020.04.09.033522v1
In Europe
- Best practices for the analysis of SARS-CoV-2 data - Genomics and Cheminformatics :
The goal of this resource is to provide publicly accessible infrastructure and workflows for SARS-CoV-2 data analyses. (https://covid19.galaxyproject.org/) - ELIXIR support for SARS-CoV-2 research :
As the ESFRI Research Infrastructure for life science data, ELIXIR Nodes provide a range of services that can be used by researchers and consortia working on SARS-CoV-2 research. (https://elixir-europe.org/covid-19-resources) - COVID-19 Molecular Structure and Therapeutics Hub https://covid.bioexcel.eu/
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/
