ELIXIR support to COVID-19 research

Map of Europe
Use our interactive map to find out what each country in ELIXIR is doing in response to COVID-19.

ELIXIR provides a range of services that you can use for studying the SARS-CoV-2 coronavirus and the COVID-19 disease. If you have questions about our COVID related services, please contact Kathi at katharina.lauer [at] elixir-europe.org.

Find a database to store your data

COVID Data Portal
The European Commission and the EBI have launched the European COVID-19 Data Portal. This brings together relevant datasets for sharing and analysis in an effort to accelerate coronavirus research.
  • We encourage researchers to deposit their data in ELIXIR’s Deposition Databases. All raw and consensus viral sequence data 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.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

  • BioExcel-CV19 is a platform designed to provide web-access to atomistic-MD trajectories for macromolecules involved in the COVID-19 disease.
  • A BridgeDB dataset includes human and SARS-related Coronavirus gene/protein mapping derived from Wikidata.
  • Cellosaurus includes frequently updated information on the cell lines useful for the study of SARS-CoV-2.
  • CoV-AbDab: the Coronavirus Antibody Database is a database of coronavirus-binding antibody sequences and structures.
  • CovidMine is an InterMine dedicated to COVID-19/SARS-CoV-2 data. It integrates confirmed Covid-19 cases, deaths, Sars-CoV-2 reference genome and nucleotide sequences from isolates deposited in Genbank.
  • Covid Viral Beacon is a tool for those interested in the SARS-CoV-2 variability, mainly at genomic scale, but also related changes such as at amino acid level along with other metadata.
  • The FAIRDOM Hub hosts the outputs of the Disease Map Consortium resource, a repository of known molecular host-pathogen interactions specific to SARS-CoV2.
  • 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.
  • Human Protein Atlas provides data on human host proteins that interact with SARS-CoV-2.
  • PhylomeDB now has a Coronavirus Phylomes page, containing a full phylogenomic analysis of 60 coronaviruses genomes, including SARS-Cov2, SARS and MERS. You can browse and download gene phylogenetic trees and multiple sequence alignments.
  • UniProtKB/Swiss-Prot contains information on SARS-CoV-2 protein sequences and how they function in a special early release.
  • ViralZone includes pre-release access to SARS-CoV-2 proteome data as well as cross-links to complementary resources.

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.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.
  • The European Galaxy server is an open, web-based platform for data intensive research and provides access to compute and storage resources. There are more than 2,500 different scientific tools, specific COVID-19 training materials, and workflows to guide users through COVID-19 data analysis.
  • 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

  • Alexander SPH, Armstrong J, Davenport AP, et al. (2020) A rational roadmap for SARS-CoV-2/COVID-19 pharmacotherapeutic research and development. IUPHAR Review 29 [published online ahead of print, 2020 May 1]. Br J Pharmacol. 10.1111/bph.15094. (https://doi.org/10.1111/bph.15094)
  • Blomberg, N, Lauer, KB (2020). Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic. Eur J Hum Genet 28, 719–723. https://doi.org/10.1038/s41431-020-0637-5
  • Brielle ES, Schneidman-Duhovny D, Linial M (2020). The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor. Viruses 12 (5) 2020 (https://doi.org/10.1101/2020.03.10.986398).
  • Kemenesi G, Zeghbib S, Somogyi BA, et al (2020). Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix. bioRxiv; . (doi: https://doi.org/10.1101/2020.05.06.080119).
  • Lam SD, Bordin N, Waman VP, Scholes HM, Ashford P, Sen H, van Dorp L, Rauer C, Dawson NL, Pang CSM, Abbasian M, Sillitoe I, Edwards SJL, Fraternali F, Lees JG, Santini JM & Orengo (2020) SARS‑CoV‑2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals. Nature Scientific Reports 10:16471 (doi: https://doi.org/10.1038/s41598-020-71936-5)
  • Manevski D, Gorenjec NR, Kejžar N, Blagus R (2020) Modeling COVID-19 pandemic using Bayesian analysis with application to Slovene data. Mathematical Biosciences, Volume 329 (https://doi.org/10.1016/j.mbs.2020.108466).
  • Milad M, Fuchs J, Maier W, Weigang S, Díaz i Pedrosa N, Weiss L, Lother A, Nekrutenko A, Ruzsics Z, Panning M, Kochs G, Gilsbach R, Grüning B (2020) The landscape of SARS-CoV-2 RNA modifications. bioRxiv 2020.07.18.204362 (doi: https://doi.org/10.1101/2020.07.18.204362)
  • Nekrutenko A, Pond SLK (2020). Galaxy and HyPhy developments teams. No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics. bioRxiv 2020.02.21.959973 (https://doi.org/10.1101/2020.02.21.959973)
  • Ostaszewski, M, Mazein, A, Gillespie, ME et al. (2020). COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data 7, 136. (https://doi.org/10.1038/s41597-020-0477-8)
  • Picardi E, Mansi L, Pesole G. A-to-I RNA editing in SARS-COV-2: real or artifact? (2020) bioRxiv. (doi: https://doi.org/10.1101/2020.07.27.223172).
  • Sicari D, Chatziioannou A, Koutsandreas T, Sitia R, Chevet E. (2020) Role of the early secretory pathway in SARS-CoV-2 infection. The Journal of Cell Biology Sep;219(9). (https://doi.org/10.1083/jcb.202006005).
  • Tagliamonte MS, Abid N, Ostrov DA, et al. (2020) Recombination and purifying selection preserves covariant movements of mosaic SARS-CoV-2 protein S. bioRxiv. (doi: https://doi.org/10.1101/2020.03.30.015685).
  • 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 (https://doi.org/10.5281/zenodo.3723282)

Services offered by other European infrastructures

Find out more

  • If you have questions about COVID-19 related ELIXIR services please contact Kathi at katharina.lauer [at] elixir-europe.org.
  • For other bioinformatics services, including training materials, please see the main ELIXIR Service page.