Weekly Brief, 23 October 2023

This week's highlights

New staff joins ELIXIR Hub

Mercedes Rothschild Steiner joined ELIXIR Project Management team for 9 months as Project Administrator, to support Laura Carletti and the team with the GDI project.

EBIF: Trusted research environments for sharing data in life sciences

21 November 2023 | London, UK

This years EBIF will focus on "Trusted research environments for sensitive data in the life sciences". The programme features a variety of presentations from industry and academia, offering the participants a chance to learn more about ELIXIR, relevant initiatives and research breakthroughs and outcomes.

Register now

Recommended reads

VarSCAT: A computational tool for sequence context annotations of genomic variants

An ELIXIR Finland paper

The sequence contexts of genomic variants play important roles in understanding biological significances of variants and potential sequencing related variant calling issues. Here, the authors describe the Variant Sequence Context Annotation Tool for annotating the sequence contexts of genomic variants, including breakpoint ambiguities, flanking bases of variants, wildtype/mutated DNA sequences, variant nomenclatures, distances between adjacent variants, tandem repeat regions, and custom annotation with user customizable options.

Read more

Proteomic Analysis on Sequential Samples of Cystic Fluid Obtained from Human Brain Tumours

An ELIXIR Implementation Study

Cystic formation in human primary brain tumors is a relatively rare event whose incidence varies widely according to the histotype of the tumor. Composition of the cystic fluid has mostly been characterized in samples collected at the time of tumor resection and no indications of the evolution of cystic content are available. This research characterized the evolution of the proteome of cystic fluid using a bottom-up proteomic approach on sequential samples obtained from secretory meningioma, cystic schwannoma and cystic high-grade glioma.

Read more

Updates from Nodes

ggCaller: The next step in scaling up bacterial genome annotation

Most genomes are only as useful as their annotation a process that identifies the genes present in a genome and what roles they fulfil. For researchers studying bacteria, genome annotation provides the context required to understand how bacteria adapt to become resistant to treatment, be more virulent, or spread faster. The new ggCaller tool helps researchers annotate thousands of bacterial genomes using genome graphs, and connects these into a pangenome.

Read more

Discover SIB's roadmap for the next five years as Data scientists for life

On SIB's 25th anniversary, the institute is publishing an inspiring and sustainable roadmap for the 5 years to come. Endorsed by the whole SIB community, the aim of this document is to present the institute today, to put its vision and activities into perspective, and to detail its development priorities.

Find out more

Updates from Communities

Register for virtual participation in the 3D BioInfo Community meeting

15 - 17 November 2023 | Hybrid - Prague, Czech Republic
Registration deadline (virtual): 10 November 2023

The 3D BioInfo Community will hold its F2F/hybrid Meeting in November. The meeting is a part of a larger event, coordinate jointly by the ELIXIR 3D BioInfo Community together with the 3D-SIG Structural Bioinformatics Community of the International Society for Computational Biology (ISCB). There will be time for updates, presentations, progress reports, posters and discussions.Virtual registration is now open, free of charge for ELIXIR members (please select the respective option during the registration process).

More information and registration

Updates from Focus Groups

Report on the 20th RDA Plenary for life scientists

A report has been prepared by ELIXIRs RDA Activities Focus Group to showcase the activities of the Research Data Alliance (RDA) from the most recent 20th Plenary event which took place March 2023. The report aims to share information on sessions for ELIXIR members operating in the life sciences domain.

Read the report

 

ELIXIR Health Data Focus Group Call for new co-lead

Deadline: 6 November 2023

ELIXIR looking for a new co-lead to join Tim Beck and Venkata Satagopam in leading the scientific oversight of the ELIXIR Health Data Focus Group. If you have any questions, please contact ELIXIR Human Data Science Officer - Arshiya Merchant

More information

Updates from other initiatives

Bioschemas community monthly call

23 October 2023 | 17:00 - 18:00 CEST (16:00 - 17:00 BST)

The monthly Bioschemas community call is taking place this afternoon. The meeting consists of the presentation on SIB implementation of training profile, its implementation and SIBs plans to increase adoption within SIB and beyond.

Join the call

The Pathogens Portal User Forum event

14 November 2023 | EMBL-EBI, UK

This will be a 1-day event with a dedicated hands-on slot to explore the Portal, Cohort Browser and tools offered, as well as a Q&A session. This is a fantastic opportunity to shape the development of the Portal, which aims to be a community driven project in order to provide maximum utility to users.

More information and registration

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

Webinar: Making container services integratable, sustainable and widely used
26 October 2023 | 15:00-16:00 CEST | Online

SIB course: Data Visualisation with R
2-3 November 2023 | Zurich, Switzerland

ELIXIR Events and Conferences

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

ELIXIR Bioinformatics Industry Forum: Trusted research environments for sharing data in life sciences
21 November 2023 | London, UK

ELIXIR hCNV Community F2F/hybrid meeting
30 November-1 December 2023 | Hybrid - Hinxton, UK

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
 

Bioinformatic technician

Biocomputing group - University of Bologna

Sensitive Data Management Coordinator

CSC IT Center for Science

Research associate in Health Data Science and Human Genetics

University of Geneva

Senior research associate in Health Data Science and Human Genetics

University of Geneva

Bioinformatician / Research Software Engineer (m/f/d) "Databases for molecular pathogen data"

Leibniz Institute DSMZ