Weekly Brief, 18 September 2023

This week's highlights

All Hands 2023 meeting report published

Two versions of the All Hands 2023 meeting report have been published:

External version - with external links to posters and presentations which have been uploaded to F1000

Internal version - with internal links to all agendas, posters and presentations

The report is the first public communication of the structure of the new ELIXIR Scientific Programme 2024-28. It may be useful as an external reference point until full Programme details are released at the end of the year.

ELIXIR's Impact Toolkit

The Impact Toolkit collates a range of impact-related materials, including training documents and materials, worked examples, factsheets, lists of indicators, key publications, case studies, and presentation slides. These have been created and brought together using a bottom-up approach that tries to reflect the varied needs of Nodes in ELIXIR member countries.

Find out more

Reminder: Contribute to ELIXIR 10 years anniversary social media campaign

ELIXIR Hub is planning a social media campaign for ELIXIR 10 years anniversary. In October, we would like to have a series of posts dedicated to members from ELIXIR Nodes. Please fill in the following questions by 22 September (Friday), we will select up to 10 responses to post on social media as part of the campaign.

Fill out the form

Webinar: Increasing capacity in impact evaluation in a life science research infrastructure

3 October 2023 | 12:00-13:00 CEST | Online

This ELIXIR impact webinar will present the outcomes of the project "Impact evaluation at Node-level - getting it done", funded by ELIXIR-CONVERGE and ELIXIR. The project aimed to increase capacity in impact evaluation across a set of national ELIXIR Nodes.

More information and registration

Recommended reads

FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards

An ELIXIR-FR paper

The authors propose FAIR-Checker, a web-based tool to assess the FAIRness of metadata presented by digital resources. FAIR-Checker offers a Check module providing a thorough metadata evaluation and recommendations, and an Inspect module which assists users in improving metadata quality and therefore the FAIRness of their resource. FAIR-Checker leverages Semantic Web standards and technologies such as SPARQL queries and SHACL constraints to automatically assess FAIR metrics. The authors evaluate FAIR-Checker in the context of improving the FAIRification of individual resources, through better metadata, as well as analyzing the FAIRness of more than 25 thousand bioinformatics software descriptions.

Read more

Wikidata Subsetting: Approaches, Tools, and Evaluation

A BioHackathon paper

Wikidata is a massive Knowledge Graph including more than 100 million data items and nearly 1.5 billion statements, covering a wide range of topics such as geography, history, scholarly articles, and life science data. In this paper the authors survey the available subsetting approaches, introducing their general strengths and weaknesses, and evaluate four practical tools specific for Wikidata subsetting in terms of execution performance, extraction accuracy, and flexibility in defining the subsets. During the experiments, the authors defined multiple subset use cases and analyzed the extracted subsets, obtaining valuable information about the variety and quality of Wikidata, which would otherwise not be possible through the public Wikidata SPARQL endpoint.

Read more

Updates from Communities

3D-BioInfo Community Webinar: New Era of Structure Abundance - Insights into Protein Function

10 October 2023 | 17:00-18:00 CEST | Online

ELIXIR 3D-BioInfor Community is holding a webinar on New Era of Structure Abundance - Insights into Protein Function. Dr Joana Pereira will talk about Uncovering new families and folds in the natural protein universe and Dr Manjeet Kuamr will talk about Eukaryotic Linear Motif (ELM) resource - updates, annotation challenges, and impact of AlphaFold2 and AlphaFold DB on motif-mediated PPIs

More information and registration

Register for the ELIXIR hCNV Community F2F/hybrid meeting

30 November-1 December 2023 | Hybrid - Hinxton, UK

Registration deadline: 23 October (f2f) | 29 November (virtual)

The meeting will gather the hCNV Community experts points of view by providing updates and discussing the progress of (ongoing) activities, offering feedback and promoting knowledge exchange. The meeting will also include a discussion/session on current Communities' achievements, presentations, workshops, participant engagement and a dedicated session regarding the ELIXIR Scientific Programme 2024-2028.

Register now

Updates from other initiatives

1st Conference on Research Data Infrastructure a success

The 1st Conference on Research Data Infrastructure, organised and run by the German NFDI (a major programme investing in Research Data Infrastructure in Germany), was a huge success.

It is noticeable that ELIXIR Nodes' members were there in force:

• Carole Goble (ELIXIR-UK) was the Conference Programme Chair
• Bjrn Grning (ELIXIR-DE) and Celia van Gelder (ELIXIR-NL) were Track Chairs and chaired sessions
• ELIXIR presentations on Galaxy, RDMkit, WorkflowHub, Training and skills, FAIRDOM-SEEK and so on.

HealthyCloud/EOSC-Life Secure Processing Environments Workshop report

EOSC-Life and HealthyCloud held a fruitful two-day workshop on Secure Processing Environments (SPEs) on June 19-20. The workshop brought together experts from academia, industry, and policy makers to exchange their relevance for the realisation of the European Health Data Space (EHDS) and in connection with recent developments within the European Open Science Cloud (EOSC).

Read the workshop report

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

SIB course: Introduction to Containers and Snakemake for Reproducible Research
12 - 13 October 2023 | Davos, Switzerland

ELIXIR Events and Conferences

Galaxy Community meeting
4-6 October 2023 | Hybrid - Freiburg, Germany

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

3D BioInfo Community meeting
15-17 November 2023 | Hybrid - Prague, Czech Republic

Federated human data (FHD) Community meeting
16-17 November 2023 | Hybrid - 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
 

ELIXIR Project Administrator

ELIXIR

Legal & Ethics Officer

ELIXIR Hub

Bioinformatician for Metabolic Pathway Reconstruction

Leibniz Institute DSMZ

Data Steward

Luxembourg National Data Service

Senior Data Steward

Luxembourg National Data Service