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.
Skills in computing, statistical analysis, databases, data science and bioinformatics. IFB federates 36 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 and clouds), 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.
A community forum to share experience and provide mutual support between users and experts.
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.
Finally, IFB is part of the international effort led by EBI to create a European COVID19 Data Portal
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).
Simply send us an email : contact@groupes.france-bioinformatique.fr.
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)
| 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 | COVIDistress 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 |
| 20 | French Covid-19 data modelling | Modelling some COVID-19 data | Tool, simulator | Marc Lavielle | info Victoria Dominguez Del Angel |
| 21 | COVIDici | Visualization of the main COVID-19 screening and clinical data in France at the departmental and regional levels, along with 7-days predictions based on a discrete-time compartmental model | Visualization, prevision | Samuel Alizon | Mircea Sofonea |
| 22 | COVimpact | Estimates the hospital burden by age group that would be generated by a future wave of the Covid epidemic19 as a function of immune parameters and the size of the wave. | Simulator, prevision | Samuel Alizon | Mircea Sofonea | 23 | EMERGEN-Bioinfo digital platform | Since Jan 2021, the French government launched the EMERGEN project to deploy a national infrastructure of genomic surveillance and research for COVID-19 and other emerging infectious diseases. The French Institute of Bioinformatics develops a bioinformatics platform that includes a compute and storage cluster facility, a specialised Galaxy server and a database to collect, analyse, manage and give access to the data produced by the EMERGEN consortium. | Compute & Storage facility | Jacques van Helden & David Salgado | Jacques van Helden & David Salgado |
| 24 | EMERGEN-DB | A database to collect, manage, analyse and give access to the data produced by the EMERGEN consortium in charge of genomic surveillance and research about COVID-19. The database is equipped with human-friendly and application-programmatic interfaces (API). It includes data brokering functionalities to enable curating the metadata and submitting them to international repositories such as GISAID and ENA | Database | Thomas Denecker | Thomas Denecker | 25 | covid19.usegalaxy.fr | A Galaxy server equipped with specialised tools for the analysis of COVID-19 data. The server is used to automate the analysis of SARS-CoV-2 genomic sequences produced by the EMERGEN consortium. | Webserver | Gildas Le Corguillé & Naira Naouar | Gildas Le Corguillé & Naira Naouar |
