Weekly Brief, 13 June 2022

This week's highlights

Thank you for joining us in Amsterdam!

Thank you to all that attended, spoke at and engaged with the ELIXIR All Hands 2022. It was great to see everyone having lively discussions in person. We look forward to meeting with you all again next year in Ireland, 5-8 June 2023!

Show and Tell - ELIXIR Strategic Implementation Study on Impact

24 June | 11:00-12:00 CEST | Virtual

This Show and Tell, chaired by Kim De Ruyck (ELIXIR Belgium), will be a team presentation by ELIXIR Greece on their work in relation to scientific impact:

Thanasis Vergoulis, Scientific Associate at ATHENA RC, will speak about Facilitating fair researcher assessment with BIP! Scholar
Christos Ouzounis, Professor of Bioinformatics-AUTH/Director of Research-CERTH, will speak about Impact of bioinformatics tools in the literature and the importance of normalization

Recommended reads

Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

An EJP-RD paper

To grasp the complexity of biological processes, the biological knowledge is often translated into schematic diagrams of, for example, signalling and metabolic pathways. These pathway diagrams describe relevant connections between biological entities and incorporate domain knowledge in a visual format making it easier for humans to interpret. Still, these diagrams can be represented in machine readable formats, as done in the KEGG, Reactome, and WikiPathways databases. However, algorithms struggle when the diversity in drawing approaches increases. This study focuses on how the graphically-modelled biological knowledge in diagrams can be semantified and harmonized, and exemplify how the resulting data is used to programmatically answer biological questions.

An EMBL-EBI paper

The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBIs data resources and core bioinformatics analytical tools. EBI Search provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, the authors describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.

The Biodiversity Focus Group embarked on the journey to become an ELIXIR Community

Next monthly TC: 22 June 2022 | 16:00 CEST

The ELIXIR Head of Nodes recently agreed to support the transition of the Biodiversity Focus Group to become a Community. ELIXIR colleagues are invited to join the group and contribute to its further development by signing up to the Community mailing list on the website.

For further information, get in touch with Katharina Heil

Join this group

Updates from Other Initiatives

BiCIKL Open Call for projects

The BiCIKL project invites submissions of Expression of Interest (EoI) to the First BiCIKL Open Call for projects. The purpose of this call is to solicit, select and implement four to six biodiversity data-related scientific projects that will make use of the added value services developed by the Research Infrastructures that make the BiCIKL project.

For 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

Functional exploration of genetic variants in cardiac diseases

14-15 June 2022 | Lyon, France | Apply by 1 May

ELIXIR Webinar: ELIXIR Operations
16 June 2022 | 15:00 CEST | Virtual

Checking for preprint and article updates
16 June 2022 | 16:00 CEST | Virtual

Elixir Engagement AAI call

22 June 2022 | 10:00-11:00 CEST | Virtual

Research Data Management and Data Management Plan

23-24 June 2022 | Lausanne, Switzerland

Summer school on genetic epidemiology

29 June - 2 July 2022 | Davos, Switzerland

Training course on facilitation and moderation skills

7-8 July 2022 | Hague, Netherlands

ELIXIR Events and Conference

BY-COVID: National-level experiences of pathogen-related data sharing in pandemic times and beyond

23 June 2022 | 13-15:00 CET | Online

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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