Weekly Brief, 15 August 2022

This week's highlights

Welcome to Erika

Today we are joined by Erika Balsyte who starts her role as "External Relations Officer" in the External Relations Team.

ELIXIR webinar on DisProt

16 & 23 August 2022 | 15:00 CEST

Join the webinar hosted by ELIXIR IDP Community to find out more about Database of Intrinsically Disordered Proteins (DisProt).

ELIXIR outreach webinar with India

17 August 2022 | 11:00 - 13:30 CEST

ELIXIR is holding our first joint webinar with Asia Pacific Bioinformatics Interaction & Networking Society (APbians) and ISCB RSG India. The webinar will focus on Data management, human data and infectious diseases: Opportunities for engagement.

Recommended reads

Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR

An ELIXIR implementation study

In this opinion article, the authors discuss the formatting of files from plant genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. VCF is an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant data, but none currently have the reach of VCF. In practice, often only sparse descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, the authors propose recommendations for supplying and encoding metadata, focusing on use cases from plant sciences.

Read more

Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort

An EOSC-Life paper

Worldwide, there are intensive efforts to identify repurposed drugs as potential therapies against SARS-CoV-2 infection and the associated COVID-19 disease. To date, the anti-inflammatory drug dexamethasone and the RNA-polymerase inhibitor remdesivir have been shown to be effective in reducing mortality and patient time to recovery, respectively, in patients. Here, the authors report the results of a phenotypic screening campaign within an EU-funded project (H2020-EXSCALATE4COV) aimed at extending the repertoire of anti-COVID therapeutics through repurposing of available compounds and highlighting compounds with new mechanisms of action against viral infection. This study screened 8702 molecules from different repurposing libraries, to reveal 110 compounds with an anti-cytopathic IC50<20M. The result supports the idea that a systematic approach to repurposing is a valid strategy to accelerate the necessary drug discovery process.

Read more

Updates from Nodes

Blog post about FAIR hackathon

The FAIR hackathon took place on 29 June 2022 attracted over 40 participants from various Nodes (and even beyond ELIXIR). The participants created lesson plans for life sciences research organisations to advance their data stewards and researchers FAIR skills.

Read ELIXIR-NL blog post

Reach out to Mijke Jetten or Stephan Nylinder to contribute

Registration open for Health-RI conference

6 October 2022 | Utrecht, the Netherlands

Registrations for the Health-RI ''Setting Data in Motion'' conference are open! The event will be held at the Jaarbeurs Utrecht in person.

More information and registration

Updates from Platforms

Showcase interoperability usage in your Community

The Interoperability Platform are looking for more ELIXIR Communities to provide a 10-minute showcase presentation of interoperability usage in their Community. There are slots available for 6 September and 4 October at 13:00-14:00 CEST on the monthly Interoperability Platform calls.

Please contact Gavin Farrell if you would like to showcase your Community.

Updates from Focus Groups

ELIXIR Europe landscape analysis of RDA involvement

Deadline: 19 September 2022

Is the Research Data Alliance (RDA) a new acronym to you? Or are you already an RDA pro and heavily engaged in RDA activities? The ELIXIR RDA Activities Focus Group are conducting a landscape analysis survey of ELIXIR members and their extent of engagement in the RDA. It takes approximately 5 minutes to complete and contains useful links and information on the RDA and Focus Group throughout.

Fill out the survey

Upcoming ELIXIR events & webinars

ELIXIR Training Courses & Webinars

The ELIXIR TeSS portal has a variety of interesting events and courses organised by the ELIXIR Nodes. For more, visit TeSS portal

ELIXIR Webinar: Exploring structural and functional annotations of IDPs with DisProt
23 August 2022 | 15:00 CEST

SIB: NGS - Genome variant analysis

26-27 September 2022 | Bern, Switzerland

SIB: I ntroduction to Machine Learning with Python
3-4 October 2022 | Virtual

ELIXIR Events and Conference

ELIXIR Innovation and SME Forum: Data driven innovation in healthcare diagnostics
22 September 2022 | 10:00 to 19:00 CEST | Barcelona, Spain

ELIXIR Bioinformatics Industry Forum: Enabling Ecosystems for Machine Learning in the Life Sciences
11 October 2022 | 10:00 to 16:00 CEST | London, UK

BioHackathon Europe

7-11 November 2022 | Paris, France

Job vacancies

All vacancies are also published on the ELIXIR website (also including those from industry). If you need our help communicating your new open positions, you can submit a job advertisement and it will automatically appear on our newsletters. Go to our vacancy page to submit a job

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