Find out what ELIXIR members are doing to support the fight against COVID-19 in their countries. For a list of services ELIXIR is providing for COVID-19 research see the ELIXIR support to COVID-19 page.
- Developed a tool to simplify the submission of Sars-CoV-2 viral sequencing data to the European Nucleotide Archive.
- Integration of COVID-19 specific data in the TCRex (epitope) and DynaMine (protein structure predictions) Node Services.
- Actively involved in setting up best practices for the analysis of SARS-CoV-2 data through Galaxy using publicly accessible infrastructure and workflows. Find out more in the dedicated ELIXIR webinar series.
- The Node contributes to the COVID-19-specific instance for EOSC-Life's WorkflowHub.
ELIXIR Czech Republic×
- Helping the Institute of Health Information and Statistics of the Czech Republic to create an epidemiological model of the pandemic.
- Involved in the research team established by IDEA at CERGE-EI to model the epidemiological situation in the Czech Republic.
- Offering computing resources to the testing centre at Palacký University, which hosts EATRIS-CZ, for processing large amounts of test data.
- See also the ELIXIR Czech website.
- Information available soon.
- Developed data collection services and modelling tools for hospitals to track the spread of COVID-19. See the special pages on the University of Tartu website.
- Supporting National COVID-19 monitoring study with data management and analytics.
- Implemented Galaxy workflows and providing compute capacity for analysing local SARS-CoV-2 sequences along with Estonian Scientific Computing Infrastructure.
- Established a feature in the software registry bio.tools to allow scientists to search for the most suitable software for COVID-19-related work.
- Prioritising access to national cloud and computing facilities for COVID-19 research projects.
- Mobilised resources for the virtual COVID-19 BioHackathon.
- Formed a COVID-19 Task Force with national experts in bioinformatics and infrastructure provision.
- Created a website listing the national computing infrastructures and workflows. See the IFB website.
- de.NBI/ ELIXIR-DE participate in various research projects fighting the pandemic -see the de.NBI website.
- Establishment of a task force for COVID-19 human omics data management.
- Participation in developing the COVID-19 disease map.
- Prioritised access to its computing facilities for COVID-19 research projects - more information
- COVID-19 activities using the European Galaxy server.
- Offering data expertise to community-driven efforts like the Research Data Alliance COVID-19 Working Group.
- Developed a timeline map to track the spreading of the disease to predict the outcome of the outbreak in each country.
- Collaborating in EBI’s Data Hubs.
- Developing COVIDoutcome, a portal to link mutation and outcome.
- Collecting virus and blood samples from patients to investigate immune system response (n=20,000).
- Offering training in genomics for bench scientists who do not have access to labs amid COVID-19 closures.
- Mobilised the national compute resources to support virtual the COVID-19 BioHackathon and for on-demand Galaxy workflow support. See the Laniakea website. Release of CorGAT, a Galaxy based workflow with custom tools and utilities for the annotation of genomic variants.
- Webinars and tutorials about Open Science and COVID-19 in collaboration with OpenAIRE, RDA, EOSC-Pillar and EOSC-Life. “Ask Me Anything” event for younger people and high-school students.
- Intrinsically disordered proteins of SARS-CoV-2 have been manually curated and added to DisProt, see the dedicated blog post. Curation in the MINT database of molecular interactions involving proteins from SARS-CoV2, SARS and other members of the Coronaviridae family. Signor 2.0 database collected and annotated information on cellular pathways that are modulated by SARS-COV-2 infection.
- Microbiome investigation on COVID-19 positive swab samples by applying a meta-transcriptomic approach.
- Setup the Dutch Data Support Programme, as part of the national Health-RI initiative and maintains a list of national services and activities.
- ELIXIR-NL partners participate in several VODAN projects, including the generation of a semantic model for the WHO CRF.
- Works with all academic partners and national funding organisation projects to coordinate the data management/stewardship for all COVID-19 projects, including a.o. the organisation of Webinars for support and community building and Metadata For Machine Workshops in order to deliver Metadata standards for Dutch COVID-19 projects.
- Building a National COVID Health data portal for FAIR access to (meta)data, starting with the standardised clinical data collected with the ISARIC WHO eCRF.
- Organising the implementation of a National COVID-19 citizen control registry & Data governance, including a generic Policy for Access to and Sharing of COVID-19 Data, based on common Data Sharing Agreements.
- Launched a viral portal.
- Developed Galaxy workflows for pre-processing raw Illumina data and analysing SARS-CoV-2 sequences.
- Offering data management support to projects that applied for emergency funding.
- Developed a Detection and Therapeutics Oligo Database for SARS-CoV-2.
- Offering data management expertise to COVID-19 projects.
- Providing compute capacity to Galaxy Europe.
- Developing a COVID-19 registry of patient data to enable online data collection and provide (some) compute resources for national and international research.
- Created a website that gathers all the efforts of ELIXIR Spain and TransBioNet members. See the Spanish National Bioinformatics Institute (INB) website.
- Collaborative work on COVID-19 Viral Beacon, a platform allowing researchers to browse SARS-CoV-2 variability at the genome, amino acid, structural and motif level.
- ELIXIR-ES RIR resources including the COVID-19 customization of the text mining resource DisGeNET to identify mentions of genes, diseases, variants and phenotypes, COVID-19 and SARS-CoV-2 virus, and the 3DBIONOTES-COVID19 tool that brings together structural and functional information on SARS-CoV-2 proteome.
- Availability of CoV-Hipathia, a web tool implementing mechanistic analysis of COVID-19-related pathways from gene expression data. CoV-Hipathia together with DisGeNet are part of COVID-19 Disease Maps, the collaborative effort led by UNILU to create, update and extend a Disease Map focused on COVID-19.
- Planning the collection of human sequences (e.g. proteomics, serology) to store it securely in a local instance of the European Genome phenome Archive (EGA).
- Launched a COVID-19 portal.
- Running databases and tools for COVID-19 research.
- Created a dedicated webpage to compile all related resources. See the SIB website.
- Centralizing and analysing, on its Swiss Pathogen Surveillance Platform SPSP, all SARS-CoV-2 sequenced data from Switzerland, to be shared with ENA and GISAID and to support the work of the national COVID-dedicated task force (pending funding approval).
- Developed outreach resources for schools (in French) and lay audiences (in English and French) to understand the biology of the coronavirus.
- Providing resources such as Guide to Pharmacology and FAIRSharing, with COVID-specific overlays.
- Led work to develop COVID-19 workflows in Workflow Hub.
- Running FAIRDOM-SEEK platform, which is used by the COVID-19 Disease Map.
- Created CoV-AbDab: the Coronavirus Antibody Database.
- See the ELIXIR UK website.
The EBI and the European Commission have launched the European COVID-19 Data Portal. This enables the rapid collection and sharing of relevant data, in an effort to accelerate coronavirus research.