Weekly Brief, 13 March 2023

This week's highlights

ELIXIR Tech Team Webinar series:
Compute Platform

16 March 2023 | 15:00 -16:00 CET

Join the ELIXIR Tech Team Webinar series on Thursday. This month's topic will focus on the Compute Platform, its activities and how the Platform will work under the new 2024 Programme.

Register now

Final Show & Tell: ELIXIR Italy and Belgium case studies

23 March 2023 | 11:00 - 12:00 CET

This final Show and Tell in our series will be hosted by ELIXIR Italy and Belgium, to present their impact case studies:

• Assessing the Scientific Impact of ELIXIR-IT: An Analysis of Acknowledgements and Citations from Publications, presented by Francesca de Leo, Chiara Bruno together with Ivan Micetic and Federico Zambelli as co-presenters (ELIXIR Italy)

• Mapping outcome and impact indicators and improving their collection throughout the Belgian ELIXIR Node presented by Kim de Ruyck (ELIXIR Belgium)

This event is part of the ELIXIR Strategic Implementation Study on Impact, in collaboration with ELIXIR-CONVERGE WP4. All participants are welcome to join, especially those involved in ELIXIR and interested in impact evaluation.

Register now

RDMkit Contentathon

22-24 May 2023 | Ghent, Belgium

The Contentathon is a great opportunity to add best practices and guidelines on how to manage life sciences data, software and other research outputs in RDMkit.
More information and agenda

Register by 7 May 2023

For any queries, please reach out to rdm-editors [at] elixir-europe.org

Recommended reads

DrugRepo: a novel approach to repurposing drugs based on chemical and genomic features

An EOSC-Life paper

The drug development process consumes 912 years and approximately one billion US dollars in costs. Due to the high finances and time costs required by the traditional drug discovery paradigm, repurposing old drugs to treat cancer and rare diseases is becoming popular. Computational approaches are mainly data-driven and involve a systematic analysis of different data types leading to the formulation of repurposing hypotheses. This study presents a novel scoring algorithm based on chemical and genomic data to repurpose drugs for 669 diseases from 22 groups, including various cancers, musculoskeletal, infections, cardiovascular, and skin diseases. The analysis is supported by a web tool available at: http://drugrepo.org/.

Read more

K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes

An ELIXIR Implementation Study

The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. This study benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained online.

Read more

Updates from Platforms

Recommended Interoperability Resources - Full Submissions Open

Deadline: 24 April 2023

The ELIXIR RIR call is now open for full applications. We invite FAIR-enabling resource stakeholders to submit their case documents to rir-submissions [at] elixir-europe.org.

Please remember that an EOI must be submitted by today to be eligible for this call.

Further information

Join the ELIXIR network of RDM trainers at their upcoming in-person event

21-22 June 2023 | Berlin, Germany

This RDM Trainer Community Meeting is organised by de.NBI/ELIXIR-DE in the framework of ELIXIR-CONVERGE and the Sub-Working Group Training/Further Education of the DINI/nestor WG Research Data. Everyone working in RDM training and education are invited to the meeting to help the formation of a strong, connected fellowship.

More information and registration

Updates from Communities

ELIXIR Microbial Biotechnology Community: Call for new co-lead

Deadline extended: 20 March 2023

The ELIXIR Microbial Biotechnology Community is looking for one new co-lead to join the Community leadership team (Vitor Martins dos Santos and Anil Wipat). Candidates should submit a short statement of their background and what they believe they will bring to the role.

Thank you to Vincent Fromion for his co-leadership and activity.

For any questions or nominations, please contact clare.garrard [at] elixir-europe.org (Clare Garrard)

More information

ELIXIR Toxicology Community: Call for one new co-lead

Deadline extended: 20 March 2023

The ELIXIR Toxicology Community is looking for one new co-lead to join the current Community leadership team (Rob Stierum, Egon Willighagen and Marvin Martens). Candidates should submit a short statement of their background and what they believe they will bring to the role.

Thank you to Chris Evelo and for his co-leadership and for helping to establish the Community.

For any questions or nominations, please contact clare.garrard [at] elixir-europe.org (Clare Garrard)

More information

Updates from Other Initiatives

Discover drug targets with Europe PMC Machine Learning Dataset and OpenTargets

21 March 2023 | 15:00-16:00 CET | Online

This webinar will introduce the Europe PMC human-annotated full-text corpus for Gene/Proteins, Diseases and Organisms and highlights how it has been used to train machine learning models for systematic identification and prioritisation of potential therapeutic drugs by the Open Targets Platform.

Register now

Read Europe PMC's blog post for more information

PerMedCoE Summer School application extended

Deadline: 16 March 203
25-30 June 2023 | Barcelona, Spain

Join the PerMedCoE Summer School 'From pathway modelling tools to cell-level simulations' to learn about modelling of metabolic networks, signalling pathways and gene regulatory networks, as well as multiscale modelling.

More information

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

BioSB course: Knowledge graphs in the life sciences
13-17 March 2023 | Wageningen, the Netherlands

PerMedCoE webinar: Development of a virtual Rheumatoid Arthritis synovial fibroblast for large-scale dynamic analysis and efficient drug-target identification
23 March 2023 | 15:00-16:00 CET | Online

ELIXIR Events and Conferences

Tools Platform 2023 F2F meeting

27-29 March 2023 | Leiden, Netherlands

ELIXIR Systems Biology Community F2F/hybrid & Implementation Study kick-off Meeting
12 - 14 April 2023 | Hybrid - Braga, Portugal

ELIXIR Innovation and SME Forum: AI in Health Research
13 April 2023 | Utrecht, the Netherlands

ELIXIR All Hands 2023
5-8 June 2023 | Dublin, Ireland

BioHackathon Europe 2023
30 October - 3 November 2023 | Barcelona, Spain

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
 

Research associate (computational metabolomics)

Leibniz Institute of Plant Biochemistry

two Junior Lecturers VU/UvA master Bioinformatics and Systems Biology JD open till April 1st (the link may be down in the first few days of March)

Vrije Universiteit Amsterdam and University of Amsterdam

Administrative Officer - Events

Elixir

Technologist: Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari

CNR

Researcher: Istituto di Tecnologie Biomediche

CNR