The global Coronavirus (COVID-19) pandemic has led to many organisations and individual bioinformaticians creating a plethora of data visualisation tools, dashboards and phylogeny maps in an attempt to share accurate data, speed up research efforts, and ultimately find solutions to this public health crisis.
Such efforts, however, would not be possible without a robust global data infrastructure. Thankfully, raw data sharing on COVID-19 has happened from day one thanks to publicly funded databases and analysis tools. Research infrastructures - such as ELIXIR - play a vital role in connecting and coordinating these resources and ensuring that COVID-19 research data can be shared and accessed easily.
ELIXIR’s priority is to make sure that there is an infrastructure to support this sharing and to ensure preparedness for any future pandemics. To support this effort, ELIXIR has today published a web page listing the bioinformatics services run by ELIXIR Nodes to assist researchers working on SARS-CoV-2.
Public databases are key to ensuring that SARS-CoV-2 datasets — from short-read sequence data to protein structures — are stored over the long-term and accessed by scientists in academia and industry. For example, EMBL-EBI’s Pathogen Portal provides access to genes, protein structures, electron microscopy images and scientific publications related to the novel coronavirus.
The COVID-19 case study also reveals the strong need for reproducible analytics. It is no longer acceptable to publish results whose analytics procedures are not fully reproducible and transparent. Galaxy, one of ELXIR's Communities, has already been used to re-analyse and assess the reproducibility of the first COVID-19 genome papers.
ELIXIR partners are organising a Virtual BioHackathon on COVID-19 data, which is open to the wider community for participation. Work is also underway to curate a list of relevant tools and software for COVID-19 data analysis in BioTools, ELIXIR’s registry of tools.
Compute resource provision
Many national computing facilities within ELIXIR have been mobilising their cloud capacity to support hackathons on coronavirus data and grant access to research projects on COVID-19.
For example, ELIXIR Italy and de.NBI (ELIXIR Germany) are offering advanced cloud-based compute servers and development frameworks to ELIXIR and partners. This includes Galaxy instances on-demand, access to Docker orchestrators, OpenStack access and advanced graphical GPU processors. These combined efforts make it possible to aggregate and analyse large, dynamic datasets at the scale required.