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
- Access data relevant to COVID-19
- Make your data easier to find and share
- Find software and workflows to analyse your data
- Find computing resources to help you analyse datasets
- Contribute to ELIXIR’s work on COVID-19
- Find COVID-19 publications from ELIXIR
- Services offered by other European infrastructures
- Find out more
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
- Researchers can use ELIXIR’s Recommended Interoperability Resources to make their data COVID-19 data Findable, Accessible, Interoperable and Reusable (FAIR).
- 3DBionotes annotates biochemical and biomedical information onto structural models and includes examples relating to COVID-19.
- The FAIRSharing COVID-19 collection collates standards and databases relevant to COVID-19 including clinical trials, virology studies, public health and patient registries.
- BridgeDb is developing coronavirus gene and protein ID mapping databases in collaboration with Wikidata:WikiProject COVID-19.
Find software and workflows to analyse your data
- Find COVID-19-specific software and analysis tools via the ELIXIR tools registry.
- Follow the best practice in using the Galaxy workflow to analyse genomics and cheminformatics data related to COVID-19 and SARS-CoV-2.
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
- Join the COVID-19-BH-20 Biohackathon on 5-11 April 2020 and contribute with ELIXIR partners to projects such as FAIRification of SARS-CoV-2 data and the deployment of a Workflow Hub for COVID workflows and pipelines.
- Contribute to the development of the COVID-19 Disease Map, a repository of curated diagrams describing molecular mechanisms of SARS-CoV-2 and its interactions with the host immune system.
- Help us curate BioTools with the most suitable tools and software for COVID-19 research .
- Help curate the FAIRSharing COVID-19 collection with relevant standards and databases. Reach out through contact[at]fairsharing[dot]org.
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
- Access services offered by other life science research infrastructures, including samples, technologies for structural biology and support to vaccine development.