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-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 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
- 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.
- 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.
- 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.
- Human Protein Atlas provides data on human host proteins that interact with SARS-CoV-2.
- The FAIRDOM Hub hosts the outputs of the Disease Map Consortium resource, a repository of known molecular host-pathogen interactions specific to SARS-CoV2.
- 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.
- 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.
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 a COVID-19 tool.
- 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.
- DisGeNET, the database of gene-disease associations, now has a COVID-19 data collection.
Find software and workflows to analyse your data
- The ELIXIR tools registry contains COVID-19-specific software and analysis tools.
- Use COVID-19 Workflows Hub to find cheminformatics workflows, such as the virtual screening of the SARS-CoV-2 main protease.
- The Galaxy Europe server mirrors locally many COVID-19 datasets, allowing for faster analysis.
- Follow the best practice in using the Galaxy workflow to analyse genomics and cheminformatics data related to COVID-19 and SARS-CoV-2.
- Join the Galaxy-ELIXIR webinar series to learn how to use the Galaxy platform and public computational resources to analyse COVID-19 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.
- 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
- Join the BioHackathon Europe on 9-13 November 2020 and contribute with ELIXIR partners to COVID-related projects.
- 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
- 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, K.B. (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).
- 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)
- Navratil V, Lionnard L, Longhi S, Combet C, Aouacheria A (2020). The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif. bioRxiv 2020.04.09.033522 (https://doi.org/10.1101/2020.04.09.033522)
- 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)
- 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
- Access services offered by other life science research infrastructures, including samples, technologies for structural biology and support to vaccine development.