Weekly Brief, 3 October 2022

This week's highlights

ELIXIR EOSC Strategy 2022


ELIXIR has recently released a document detailing ELIXIR Europe's strategy for engagement with the European Open Science Cloud (EOSC) and how ELIXIR will engage with and contribute to the EOSC.

Read the document

Biodiversity Genomics Europe launched last Wednesday


Biodiversity Genomics Europe (BGE) was launched last Wednesday. The pan-European project will bring together BIOSCAN Europe and European Reference Genome Atlas (ERGA) in an unprecedented effort to reverse the biodiversity crisis through large-scale application of genomics research.

Check the project website

Reminder: EBIF registration closing soon

11 October 2022 | London, UK


This year, EBIF is focusing on enabling ecosystems for Machine Learning in the Life Sciences. The programme includes a mixture of presentations and round table discussions.

More information and registration

Two job vacancies at ELIXIR Project Management Office


Technical Portfolio Manager- Scientific Services and Support


EC Project Manager-Technical Support

Recommended reads

Rhea, the reaction knowledgebase in 2022

 

An ELIXIR-CH paper

Rhea is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI (Chemical Entities of Biological Interest). In this paper, the authors describe a number of key developments in Rhea since our last report in the database issue of Nucleic Acids Research in 2019. These include improved reaction coverage in Rhea, the adoption of Rhea as the reference vocabulary for enzyme annotation in the UniProt knowledgebase, UniProtKB, the development of a new Rhea website, and the designation of Rhea as an ELIXIR Core Data Resource.

Read more

A mosaic PIK3CA variant in a young adult with diffuse gastric cancer: case report

An EJP-RD paper


Hereditary diffuse gastric cancer (HDGC) is associated with germline deleterious variants in CDH1 and CTNNA1. The majority of HDGC-suspected patients are still genetically unresolved, raising the need for identification of novel HDGC predisposing genes. Re-analysis of whole-exome sequencing data from unresolved gastric cancer cases identified a mosaic missense variant in PIK3CA in a female with diffuse gastric cancer (DGC) without familial history for cancer. This report highlights mosaicism as a potential, and understudied, mechanism in the etiology of DGC.

Read more

Updates from Nodes

Top score for the SwissBioData ecosystem (SBDe) proposal in scientific evaluation


Led by SIB and 16 other Swiss institutions, the aim of SBDe is to boost Switzerlands capacity to convert research data into knowledge and innovation. SBDe builds on decades of collaborative projects and in-depth expertise around Open Science and FAIR principles.

Find out more about SBDe

OMA browser for ortholog and paralog needs

The OMA (Orthologous MAtrix) project is a method and database for the inference of orthologs among complete genomes. It is part of the SIB Resource SwissOrthology, and is developed and maintained by the group of Christophe Dessimoz.

Check OMA website

Updates from Platforms

Registration open for the ELIXIR Data and Interoperability Platforms joint Platform event

28-30 November 2022 | Geneva, Switzerland


Registration is possible for both online and in-person participation through the Eventscase website here. The final event programme will be determined and distributed in the coming weeks.

More information

Updates from Communities

Register for the ELIXIR 3DBioInfo Community F2F/hybrid meeting

2 - 4 November 2022 | Wellcome Genome Campus, Hinxton, United Kingdom

Join the 3DBioInfo AGM 2022 at the Wellcome Genome Campus (or online) in November to discuss recent and future 3DBioInfo developments.

More information and registration

Updates from Other Initiatives

Registration open: ELIXIR/ERIC Forum side event at ICRI

19 October 2022 | 19:00-20:30 CEST | Hyrbid


The ERIC Forum, in collaboration with ELIXIR, will be organising a side event in the frame of ICRI 2022. The event will bring together policymakers, Research Infrastructures and the general public to raise awareness about Research Infrastructures role and contribution to the attainment of the Sustainable Development Goals (SDGs).

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


SIB: First steps with R in Life Sciences
10-11 October 2022 | Zurich, Switzerland

SIB: Protein sequence databases and sequence annotation at UniProtKB
14 October 2022 | Virtual

 

20 October 2022 | Virtual

LS2 Prestige Webinar on Biodiversity informatics
25 October 2022 | 14:00-15:00 CET

 

SIB: Docker and Singularity for reproducible research: getting started with container
26 October 2022 | Virtual

 

SIB: Single-cell transcriptomics

14-16 November 2022 | Bern, Switzerland

 

SIB: NGS - Quality control, Alignment, Visualisation
21-23 November 2022 | Online

 

Data-Interoperability Platforms Hybrid F2F 2022
28-30 November 2022 | Geneva, Switzerland

 

 

ELIXIR Events and Conferences


ELIXIR Bioinformatics Industry Forum: Enabling Ecosystems for Machine Learning in the Life Sciences
11 October 2022 | 10:00 to 16:00 CEST | London, UK

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
 

Bioinformatician(s) at NBIS

Lund University

Technical Portfolio Manager

ELIXIR Hub

EC Project Manager

ELIXIR Hub

Scientific Programmer (EMDB)

EMBL-EBI

Frontend developer

NBIS