ELIXIR support to COVID-19 research

ELIXIR provides a range of services that you can use for studying the SARS-CoV-2 coronavirus and the COVID-19 disease. This page will be updated frequently (last updated 7 April 2020). If you have questions about our COVID-19 related services, please contact Kathi at katharina.lauer[at]elixir-europe[dot]org.

Find a database to store your data

  • We encourage researchers to deposit their data in ELIXIR’s Deposition Databases. All raw and consensus viral sequence data should should be deposited in the European Nucleotide Archive (ENA).
  • EMBL-EBI has a dedicated page to assist deposition and sharing of SARS-CoV-2 data into other molecular databases. You can get support for submitting your data by emailing virus-dataflow[at]ebi.ac[dot]uk before submission.
  • If you already upload consensus sequence data to GISAID, we encourage you to also upload your data to the ENA. EMBL-EBI is looking at ways to assist in this process.

Access data relevant to COVID-19

  • A BridgeDB dataset includes human and SARS-related Coronavirus gene/protein mapping derived from Wikidata.
  • ViralZone includes pre-release access to SARS-CoV-2 proteome data as well as cross-links to complementary resources.
  • Cellosaurus includes frequently updated information on the cell lines useful for the study of SARS-CoV-2.
  • UniProtKB/Swiss-Prot contains information on SARS-CoV-2 protein sequences and how they function in a special early release.
  • Guide to Pharmacology contains curated information on SARS-CoV-2 targets and captures some of the pharmacological strategies being investigated to mitigate against COVID-19. New ligands are being posted to a pre-release blog.

Make your data easier to find and share

Find software and workflows to analyse your data

Find computing resources to help you analyse datasets

ELIXIR runs computing services that can be accessed by research projects. Many additional computing resources have been made available to support COVID-19 research projects and a number offer access to Docker Orchestrators, including Mesos and OpenStack access, Kubernetes/OKD and potentially GPUs where needed. For assistance please contact jonathan.tedds[at]elixir-europe[dot]org, ELIXIR’s Compute Platform Coordinator. Examples of compute resources include:

  • de.NBI cloud (ELIXIR Germany) provides priority access for projects relating to COVID-19.
  • CSC (ELIXIR Finland) has prioritised access to its cloud services for COVID-19 research.
  • e-INFRA CZ (ELIXIR Czech Republic) offers relaxed access conditions to supercomputer resources, storage services and distributed compute resources.
  • EMBL-EBI is contributing EMBASSY Cloud resources as detailed on the European Open Science Cloud, EOSC Marketplace.
  • A specific Galaxy COVID-19 instance for genomic analysis is available through Laniakea, ELIXIR Italy’s on-demand platform.
  • SIB (ELIXIR Switzerland) is providing a ready-to-use slurm workload manager with a scientific software stack via the ExPASy SIB Portal.
  • IFB (ELIXIR France) is providing a federated set of high performance compute and cloud resources including national and regional servers.

Contribute to ELIXIR’s work on COVID-19

Find COVID-19 publications from ELIXIR

  • Galaxy and HyPhy developments teams, Nekrutenko A, Pond SLK (2020). No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics. bioRxiv 2020.02.21.959973 (doi: https://doi.org/10.1101/2020.02.21.959973)
  • Brielle ES, Schneidman-Duhovny D, Linial M (2020). The SARS-CoV-2 exerts a distinctive strategy for interacting with the Angiotensin-Converting Enzyme 2 (ACE2) human receptor. bioRxiv 2020.03.10.986398 (doi: https://doi.org/10.1101/2020.03.10.9863988)
  • Vergoulis T, Kanellos I, Chatzopoulos S, Karidi DP Dalamagas T (2020). BIP4COVID19: Impact metrics and indicators for coronavirus related publications (Version 0.1) [Data set] Zenodo (doi: http://doi.org/10.5281/zenodo.3723282)

Services offered by other European infrastructures

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