Weekly Brief, 6 February 2023

This week's highlights

Welcome to the new ELIXIR Hub staff

Last week, Fabio Liberante joined ELIXIR Technical Team as a Programme Manager - Data and Interoperability.

Measuring the impact of ELIXIRs training

As a distributed infrastructure, ELIXIRs training provision is spread throughout ELIXIRs 22 Nodes. The training aims to enhance data and software skills in the life sciences, for example, building expertise in data management, tools, workflows and standards.

Read the news

BiohHackathon 2023: date and venue announcement

Biohackathon 2023 will be held on 30 October to 3 November 2023 in Barcelona, Spain. The Call for projects will be open at the end of February, all details will be announced on the website and through the Weekly Brief.

Stay tuned to the event

Final Show & Tell: ELIXIR Italy and Belgium case studies

23 March 2023 | 11.00am CET

This final Show and Tell in our series will be hosted by ELIXIR Italy and Belgium, to present on 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

Recommended reads

Mapping OHDSI OMOP Common Data Model and GA4GH Phenopackets for COVID-19 disease epidemics and analytics

A BioHackathon paper

The COVID-19 crisis demonstrates a critical requirement for rapid and efficient sharing of data to facilitate the global response to this and future pandemics. To harness Machine Learning and Artificial Intelligence approaches to discover meaningful patterns in epidemic outbreaks, we need to ensure that data are FAIR, i.e. data and metadata are accessible and actionable by machines. The project aims to enhance interoperability between health and research data by mapping Phenopackets and OMOP schemas, and representing COVID-19 metadata using the FAIR principles to enable discovery, integration and analysis of genotypic and phenotypic data.

Read more

Community-driven Governance of FAIRness Assessment:
An Open Issue, an Open Discussion

An EOSC paper

This white paper identifies three high-level stakeholder categories -FAIR decision and policymakers, FAIR custodians, and FAIR practitioners - and provides examples outlining specific stakeholders' needs. It also examines possible models for governance based on the existing peer efforts, standardisation bodies, and other ways to acknowledge specifications and potential benefits. This white paper can serve as a starting point to foster an open discussion around FAIRness governance and the mechanism(s) that could be used to implement it, to be trusted, broadly representative, appropriately scoped, and sustainable. We invite engagement in this conversation in an open Google Group

Read more

Updates from Nodes

New Deputy Head of Node for ELIXIR-NL

Prof. Dr. Ir. Chris Evelo, Professor of Bioinformatics for Integrative Systems Biology and Head of the Department of Bioinformatics at BIGCaT - Maastricht University, has been appointed as Deputy Head of Node for ELIXIR-NL as of 1 January 2023.

Chris combines his new role with that of ExCo of the ELIXIR Interoperability Platform, which will give him extra opportunities to connect people and technologies within ELIXIR and beyond.

He is replacing Prof. Dr. Morris Swertz who decided to step down after three years in office. We thank Morris for all he has done as deputy HoN and look forward to further collaboration with him as one of the key PIs in ELIXIR-NL and driver of the FAIR data principles on the national and international level.

Data-driven life science and the RDA: Leveraging global data communities in regional initiatives and cross-border infrastructures

24 March 2023 | 9:00 - 13:00 CET | Hybrid - Gothenburg, Sweden

This workshop will showcase how to leverage the Research Data Alliance (RDA) to support life science research today and what role the RDA and international data infrastructures can play in the transition to an increasingly data-driven research practice.

More information and registration

Updates from Platforms

ELIXIR TeSS new user interface

ELIXIRs TeSS has a new user interface (UI), thanks to efforts from Xnia Prez Sitj (ELIXIR-UK) and Ivan Kuzmin (ELIXIR-EE). Please check it out and provide your feedback in #tess-club on Slack.

Check the new user interface

Updates from Communities

GPU-enabled JupyterLab enables interactive AI use-cases in Galaxy

Galaxy news article on democratising GPU infrastructures by providing accelerated JuypterLab instances via Galaxy and combining them with HPC workflows.

Read more

ELIXIR Microbial Biotechnology Community: Call for new co-lead

Deadline: 27 February 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

Provide your feedback on emerging Data Management Community White Paper

Deadline: 30 March 2023

The emerging ELIXIR Data Management Community are presenting their white paper draft for consultation and feedback.

Please add your comments directly to the PDF document or send to ELIXIR's Scientific Officer - Life Science Communities, clare.garrard [at] elixir-europe.org (Clare Garrard)

Read the white paper draft

Updates from Other Initiatives

BY-COVID Workshop: Unlocking the Power of Metadata

14 February 2023 | 14:00-16:00 CET | Online

Join the BY-COVID workshop for a short, hands-on workshop to discover the importance and benefits of metadata.

More information and registration

The Principles of Open Scholarly Infrastructure

In January, The POSI group (Posse) had a call - The Principles of Open Scholarly Infrastructure. The list of organisations that have committed to the principles can be found online and outreach to increase coverage is ongoing. Europe PMC assessed itself against the principles back in Feb 2022.

List of organisations and initiatives committed to the POSI principles

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 Series: Constraint-based modelling
13-17 February 2023 | Wageningen, the Netherlands

ELIXIR-IT: 24th Bologna Winter School: Bioinformatics and deep learning for biodata analysis
14-27 February 2023 | Online
Deadline for application: February 8, 2023

SIB course: NGS - Genome Variant Analysis
20-21 February 2023 | Bern, Switzerland

PerMedCoE webinar: Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models
22 February 2023 |15:00 -16:00 CET | Online

SIB course: First Steps with Python in Life Sciences
1-3 March 2023 | Lausanne, Switzerland

PerMedCoE/BioExcel: Introduction to HPC for Life Scientists
7-8 March 2023 | Barcelona, Spain

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

ELIXIR-DE Spring School
13-17 March | Gatersleben, Germany
Deadline for application: 15 February

SIB course: Reproducible research with R: from data management to communication of results
23-24 March 2023 | Lausanne, Switzerland

ELIXIR Events and Conferences

Training Platform 2023 F2F meeting
7-9 March 2023 | Hybrid - Rome, Italy

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 - 30 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
 

Web Developer at the SILVA database

DSMZ

Junior Researcher Biotechnology in EU project

DSMZ

Web Developer in an EU project

DSMZ

Backend developer Maven / Spring Boot at the SILVA database

DSMZ

DevOps Engineer

PNED G.I.E.