This week's highlights
New opinion piece on pathogen genomics data sharing
Colleagues from EMBL-EBI and ELIXIR have published an opinion piece to inform the discussion around pathogen genomics data sharing. The article, published in Zenodo, outlines a set of principles for pathogen genomic data sharing which would allow researchers and public health authorities to leverage the potential of new genome sequencing technologies.
Find out more
Reminder: All Hands 2022 poster submission
Deadline: This Thursday, 31 March
The poster session will share the broad variety of ELIXIR-related work and foster partnerships across the ELIXIR network. Submissions can include any activities within the ELIXIR Programme and a judging panel will award prizes during the event.
Find out more (Registered participants at All Hands)
Recommended reads
How Far Are We from the Completion of the Human Protein Interactome Reconstruction?
An ELIXIR-GR paper
After more than fifteen years from the first high-throughput experiments for human proteinprotein interaction (PPI) detection, how complete is the genome-scale human PPI network reconstruction, what needs further exploration, and are the biological insights gained from the current network valid and useful? PICKLE, a meta-database of the human experimentally determined direct PPI network developed by our group, now covers ~80% of the UniProtKB/Swiss-Prot reviewed human complete proteome, enabling the evaluation of the interactome expansion by comparing the successive PICKLE releases since 2013. Our observations, combined with a largely overlapping k-core between PICKLE releases and a network density increase, imply that an almost complete picture of a structurally defined network has been reached.
Read more
Single cell RNA sequencing in autoimmune inflammatory rheumatic diseases: applications, challenges & towards precision medicine
An ELIXIR-SI paper
Single cell RNA sequencing (scRNA-seq) is a new large scale and high throughput technique for analysis of the whole transcriptome at the resolution of an individual cell. There is an unmet need to investigate, in depth, the cellular and molecular mechanisms driving the pathogenesis of rheumatic diseases and drug resistance, identify novel therapeutic targets, as well as make a step forward in using stratified and informed therapeutic decisions, which are amenable to single cell approaches. This review summarizes the current use of scRNA-seq in studying different rheumatic diseases, based on recent findings from published in vitro, in vivo, and clinical studies, and discusses the potential implementation of scRNA-seq in the development of precision medicine in rheumatology.
Read more
Updates from Nodes
ELIXIR Belgium newsletter highlights two upcoming meetings
ELIXIR Belgium: FAIR Data for Life Sciences Research
18 May | Brussels, Belgium
Empowering Biodiversity Research Conference 2022
24-25 May 2022 | Tervuren, Belgium
Updates from Platforms
Registration open for Compute Platform face-to-face event
25 April 12:00 CET - 26 April 16:00 CET| Hotel Berlin, Berlin
Registration deadline:Friday 8 April
Come and reconnect and meet new Platform members, reflect on past Platform activities, and look ahead to the 2024+ Programme with topics such as EOSC, AAI Migration and Service Sustainability.
The event will be in face-to-face format and limited to 50 attendees. A dedicated accommodation booking link for the venue is in the registration confirmation email.
Draft agenda and registration link
Updates from Communities
Reminder: Call for 3 co-leads of the Biodiversity Focus Group
Deadline: This Thursday, 31 March
The Biodiversity Focus Group is entering a new phase of work and requires three co-leads.
To be considered, candidates should self-nominate, submitting a short statement including their background and what they bring to the role.
To find out more or submit a self-nomination, contact Katharina Heil
Join the Biodiversity Focus Group mailing list
Join the Biodiversity Focus Group ELIXIR Europe Slack channel
Launch of Galaxy Mentor Network
The new program involves:
- Gmentees (Galaxy Mentees): Galaxy members needing support and guidance
- Gmentors (Galaxy Mentors): experienced Galaxy members driven to give back and make their expertise and experience available
Updates from other initiatives
Call for Proposals for Transnational Access Projects at EASI-Genomics
Deadline: 10 April 2022
EASI-Genomics will support integrative projects covering expertise not available at the applicants home institution sites, including high-throughput and cutting-edge sequencing and complex bioinformatics analysis.
Global Core Biodata Resource selection process open
Deadline: 22 April 2022
The call for Expressions of Interest is for biodata resources (or consortia of resources) from anywhere in the world that would like to be considered for selection as a Global Core Biodata Resource.
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
Applied statistics: data analysis in practice
5-6 April 2022 | Lausanne, Switzerland
First steps with R
5-7 April 2022 (half days) | Virtual | Limited spaces
Galaxy introduction for life scientists
27 April 2022 | Lausanne, Switzerland
Metabolomics and integrative omics: from data production to analysis
28-29 April 2022 | Bari, Italy
Nordic train-the-trainer course
10-13 May 2022 (half days)| Virtual | Deadline to apply: 3 April
10th RepeatExplorer workshop on the application of NGS to repetitive DNA
24-26 May 2022 | esk Budjovice, Czech Republic
3rd hands-on computational enzyme design workshop
30 May - 1 June 2022 | Virtual
Summer school on genetic epidemiology
29 June - 2 July 2022 | Davos, Switzerland
ELIXIR Events and Conferences
Data access, movement and management workshop
31 March 2022 | Virtual | 09.30 - 12.30 CET
Tools Platform meeting
4-6 April 2022 | Hybrid - Brussels, Belgium
Emerging systems biology Community meeting
12-13 April 2022 | Hybrid - Amsterdam, Netherlands | 12:00-14:00 CET
Compute Platform meeting
25-26 April 2022| Hotel Berlin, Berlin
FAIRplus Innovation and SME forum 2022
17 May 2022 | Hybrid - Berlin, Germany
ELIXIR All Hands meeting 2022
7-10 June 2022 | Amsterdam, Netherlands
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
Science / Technical Officer - Life Science Communities & Open Science
Elixir
Bioinformatics Data Analyst (RE1)
Barcelona Supercomputing Center (BSC)
Postdoctoral bioinformatics position at the Interuniversity institute of Bioinformatics in Brussels
Universite Libre de Bruxelles and the Interuniversity institute of Bioinformatics in Brussels
Scientific Coordinator / Knowledge Graph Engineer
SIB Swiss Institute of Bioinformatics