Weekly Brief, 8 May 2023

This week's highlights

New starter at the Hub

Physilia Chua joined ELIXIR Hub as a Senior Scientific Officer - Biodiversity. She will be working on ELIXIRs biodiversity-related projects and supporting the planning for the Biodiversity, Food Security and Pathogens theme in the new ELIXIR Scientific Programme.

New ELIXIR website homepage

A new design for the ELIXIR website homepage is now live.

Check the new design

Recommended reads

Genomic & proteomic biomarker landscape in clinical trials

An ELIXIR-CONVERGE paper

The use of molecular biomarkers to support disease diagnosis, monitor its progression, and guide drug treatment has gained traction in the last decades. While only a dozen biomarkers have been approved for their exploitation in the clinic by the FDA, many more are evaluated in the context of translational research and clinical trials. This study presents a text-mining strategy to identify proteomic and genomic biomarkers used in clinical trials and classify them according to the methodologies by which they are measured. These data are made available at the Clinical Biomarker App, a new portal that enables the exploration of biomarkers. Overall, the Clinical Biomarker App is a valuable and timely resource about clinical biomarkers, to accelerate biomarker discovery, development, and application.

Read more

Scripting Analyses of Genomes in Ensembl Plants

An ELIXIR Implementation Study

Ensembl Plants offers genome-scale information for plants, with four releases per year. As of April 2020, it features 79 species and includes genome sequences, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the Ensembl genome browser, here the authors review specifically how plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.

Read more

Updates from Nodes

Science Seminar: From Single Cell Genomics to Quantitative Tissue Models

11 May 2023 | 14:00-15:00 CEST | Online

During the seminar, the speaker will present their work on combining persistent labeling with time-series single-cell RNA-Seq to build the first real-time, quantitative model of in vivo tissue dynamics for any mammalian organ.

More information and registration

Extreme dwarf and giant species more likely to go extinct

An international study shows that extreme dwarf or giant species are more likely to go extinct. The findings are supported by software developed by SIB.

Find out more

Explore the range of bioinformatics training materials on GitHub pages with Glittr

GitHub is often used to host bioinformatics training materials, making them FAIR and easier to reuse. A new website from the Training group, Glittr.org, allows users to search and select training materials on GitHub or GitLab that match their interests.

Check these courses to learn new skills

Updates from other initiatives

Challenge-Call on Advancing Personalised Oncology

Deadline: 25 May 2023

The canSERV Consortium announces its first Challenge-Call on Advancing Personalised Oncology. The aim of this call is to accelerate knowledge gain in personalised oncology with specific emphasis on multi-level data-based treatment guidance linked to Molecular Tumour Boards.

More information

FAIR-IMPACT upcoming events in May

The FAIR-IMPACT project is supporting the implementation of FAIR-enabling practices, tools and services across scientific communities. This May, the project is organising three online events:

• Webinar: FAIR-IMPACTs Virtual Clinic for potential applicants to the first Open Call
  16 May 2023 | 15:00 -16:00 CEST | Online
• Webinar: Developing Guidelines for Metadata Collection and Curation for Research Software
  23 May 2023 | 10:30 - 11:30 CEST | Online
• Workshop: PID best practices for complex data citation, semantic artefacts and related services
  25 May 2023 | 12:00 - 14:00 CEST | Online

Subscribe to the GDI project external newsletter

The European Genomic Data Infrastructure (GDI) project is enabling access to genomic and related phenotypic and clinical data across Europe by establishing a federated, sustainable and secure infrastructure to access the data. The project has recently released its first newsletter issue.

Subscribe to the GDI project newsletter

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

ELIXIR Events and Conferences

ELIXIR All Hands 2023
5-8 June 2023 | Dublin, Ireland

IDP Community F2F/hybrid Meeting
3-4 July 2023 | Hybrid - Bratislava, Slovakia

BioHackathon Europe 2023
30 October - 3 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
 

Postdoctoral Research Fellow (Database & Web Developer)

University of Edinburgh

SILVA - Scientist Microbial Ecology & Taxonomy

DSMZ

SILVA - Backend developer Maven / Spring Boot

Leibniz Institute DSMZ

BRENDA - Data Expert Biochemistry/Enzymology

Leibniz Institute DSMZ

Web developers and designers

CRG