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DATA SCIENTISTS FOR LIFE - AROUND COVID-19 - AROUND MACHINE LEARNING
Supporting international research How did SARS-CoV-2 arise? How is it spreading and evolving? What are its weak points? Early on, SIB Groups were able to provide a range of tools and resources to help answer such questions.
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Here are some of the actions undertaken by resources managed at SIB in the context of the emergency:
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“The topic of sustainable research infrastructure, and the funding associated with it, has become more visible than ever. At a meeting of the Global Biodata Coalition (SEE P. 20), it was noted that the availability of key databases, such as those developed at SIB, is instrumental in enabling a fast scientific response to COVID-19.” Ron Appel SIB Executive Director
— The coronavirus entries in the universal protein knowledgebase Uniprot – an international collaboration between the Swiss-Prot group led by Alan Bridge, EMBL-EBI, and PIR – were made available as a pre-release independently and faster than the general UniProt release cycle. — Nextstrain (SEE COVER), co-developed by the group led by Richard Neher and to which other SIB Groups and resources (e.g. V-pipe) contribute, started incorporating SARS-CoV-2 genomes as soon as they were shared publicly. It enables clinical researchers to track in real time how the coronavirus genome evolves. (SEE P. 33)
he first coronavirus genome sequence was published on 10 January 2020. Our scientists reacted swiftly to offer support to clinical researchers, and to make sure that the science could move fast. This reaction involved developing new features in existing software tools or repurposing them (SEE V-PIPE P. 23), issuing new releases in record time through coordinated international efforts, etc. It was made possible by our scientists’ exceptional dedication, and by the fact that most resources were already available, funded, and with teams ready to operate the necessary developments.
Knowledge of the virus genome’s evolution, its proteins, their function and structure is key to understanding how it replicates and spreads, and to identifying potential targets for drugs or vaccines.
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162% increase in ViralZone monthly usage figures* since the SARS-CoV-2 pages were created * as compared to the same period the previous year
— Through a dedicated portal of SWISS-MODEL, developed by the group led by Torsten Schwede, threedimensional models of the viral proteins could be created, which shed further light on their evolution, functional properties and potential weaknesses, in the context of drug development. — PROSITE was used to highlight the potential role of integrins in host-cell entry by the virus, making them interesting targets for COVID-19 treatment. — New SARS-CoV-2 dedicated pages on ViralZone provide further biological insights (see key figure), including a detailed comparison with the SARS virus genome as well as cross-links to complementary resources. — Literature triage services, such as CovidTriage developed by the group led by Patrick Ruch, as part of their SIBiLS resource, makes it possible to prioritize articles according to an ontology specific to COVID-19, thereby guiding scientists through the maze of published works on the virus.