This week's highlights
2023 ELIXIR All Hands virtual option registration opens
5-8 June | Dublin, Ireland
Registration deadline: 31 May 2023
Want to join this years ELIXIR All Hands meeting, but cant be in Dublin to participate in person? We have open registration for virtual participation. Please see the website homepage for the details of the hybrid and streamed sessions.
Virtual option registration link
Event website
Building European capacity in single-cell omics
A six-month staff exchange, funded by ELIXIR, has been successful in building capacity for single-cell analysis in ELIXIRs Czech Node.
ELIXIR Tech Team Webinar series:
Compute Platform
16 March 2023 | 15:00 -16:00 CET
Join the ELIXIR Tech Team Webinar series next Thursday. This month's topic will focus on the Compute Platform, its activities and how the Platform will work under the new 2024 Programme.
Register now
ELIXIR Communications Group meeting
20 March 2023 | 14:00-15:00 CET
The next ELIXIR Communications Group meeting will be at 14-15 CET on Monday 20 March. The meeting will focus on "Node impact videos - learning from ELIXIR-UK". All are welcome and no registration is necessary.
Rolling agenda (with Zoom link)
Recommended reads
Transformer-based tool recommendation system in Galaxy
A Galaxy preprint
Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses. Tool recommender system predicts a collection of tools that can be used to extend an analysis. In this work, a tool recommender system is developed by training a Transformer-based neural network on workflows available on Galaxy Europe. Compared to the existing tool recommender system on Galaxy Europe that trains a recurrent neural network, the transformer-based neural network achieves two times faster convergence, has a four times lower model usage (model loading + prediction) time and shows a better generalisation that goes beyond training workflows.
Read more
Lipidomics Moves to Center Stage of Biomedicine
An ELIXIR-UK Implementation Study
Lipids comprise the majority of metabolites in human tissues. They include thousands of molecules, including vitamins, hormones, and signaling molecules. Lipids are essential for vaccine development, pharmaceuticals, and nutrition. Dynamic fluxes in lipids reflect genetic, transcriptomic, and environmental impacts. For this reason, their accurate measurement in cells and tissues, including human cohort samples, is of increasing interest for clinical diagnostics, biomarker discovery, and precision medicine. Beyond biomarkers, they provide information on disease mechanisms, including potential druggable targets for intervention. Understanding of lipids starts to reveal significant mechanistic insights, for example, in cardiovascular, Alzheimers, Parkinsons diseases, and cancer.
Read more
Updates from Nodes
Organoids grown from stem cells boost cancer research
Organoids grown from stem cells enable new ways to model a variety of diseases such as cancer. At the University of Oulu, new techniques to engineer embryonic tissue are used to find cancer genes.
Read more
Register to the Data Stewards Interest Group (DTL DSIG) meeting
23 March 2023 | 14:45 - 13:30 CET
The meeting will discuss practical applications of FAIR data principles in qualitative research, training and tools (a.o. the FAIR Data coursebook) and best practices for qualitative data sharing within different disciplines.
More information and registration
Updates from Platforms
CDR selection process for 2023 is now opened
The ELIXIR Hub has opened the CDR selection process for 2023. The expression of interest (EOI) period expires on 13 March 2023.
Nodes are requested to send a simple list of the names of intended biodata resources applicants. This list is to be sent by your respective Head of Node/Node leadership to core-resources [at] elixir-europe.org. Please contact your relevant Node leaders to ensure your resource is included.
For further dates and updates please check the CDR timeline web page
For any further queries please contact fabio.liberante [at] elixir-europe.org (Fabio Liberante)
RIR selection process for 2023 is now opened
The ELIXIR Hub has opened the RIR selection process for 2023. The expression of interest (EOI) period expires on 13 March 2023.
Prospective RIR applicants must send names of intended applicants to clare.garrard [at] elixir-europe.org (Clare Garrard) with the subject 'ELIXIR RIR expression of interest'.
For further dates and information please check the RIR timeline web page
For any direct queries please contact fabio.liberante [at] elixir-europe.org (Fabio Liberante)
Join the ELIXIR network of RDM trainers at their upcoming in-person event
21-22 June 2023 | Berlin, Germany
This RDM Trainer Community Meeting is organised by de.NBI/ELIXIR-DE in the framework of ELIXIR-CONVERGE and the Sub-Working Group Training/Further Education of the DINI/nestor WG Research Data. Everyone working in RDM training and education are invited to the meeting to help the formation of a strong, connected fellowship.
More information and registration
Updates from Communities
Provide your feedback on the emerging Data Management Community White Paper
Deadline: 30 March 2023
The emerging ELIXIR Data Management Community are presenting their white paper draft for consultation and feedback.
Please add your comments directly to the PDF document or send to clare.garrard [at] elixir-europe.org (ELIXIR's Scientific Officer - Life Science Communities, Clare Garrard)
ELIXIR Microbial Biotechnology Community: Call for new co-lead
Deadline extended: 20 March 2023
The ELIXIR Microbial Biotechnology Community is looking for one new co-lead to join the Community leadership team (Vitor Martins dos Santos and Anil Wipat). Candidates should submit a short statement of their background and what they believe they will bring to the role.
Thank you to Vincent Fromion for his co-leadership and activity.
For any questions or nominations, please contact clare.garrard [at] elixir-europe.org (Clare Garrard)
ELIXIR Toxicology Community: Call for one new co-lead
Deadline extended: 20 March 2023
The ELIXIR Toxicology Community is looking for one new co-lead to join the current Community leadership team (Rob Stierum, Egon Willighagen and Marvin Martens). Candidates should submit a short statement of their background and what they believe they will bring to the role.
Thank you to Chris Evelo and for his co-leadership and for helping to establish the Community.
For any questions or nominations, please contact clare.garrard [at] elixir-europe.org (Clare Garrard)
Updates from Focus Groups
Machine Learning Focus Group: Synthetic Data Survey
To fully understand the needs and factors surrounding synthetic data, the Focus Group is gathering thoughts and insights from people across different backgrounds and perspectives. Please take this short survey on synthetic genomics to help contribute to the research and provide valuable insights that can help shape the future of the field of Synthetic Data.
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
PreMedCoE webinar: Supercomputer-based modelling and simulation for advanced biomedical applications
9 March 2023 | 15:00 - 16:00 CET | Virtual
BioSB Series: Knowledge graphs in the life sciences
13-17 March 2023 | Wageningen, the Netherlands
SIB course: Reproducible research with R: from data management to communication of results
23-24 March 2023 | Lausanne, Switzerland
SIB course: Enrichment Analysis
31 March 2023 | Virtual
Workshop on Data Visualization in R
17-19 April 2023 | Lund, Sweden
Tools for Reproducible Research online workshop
24-28 April 2023 | Virtual
Galaxy: Smrgsbord 2023
22-26 May 2023 | Online
ELIXIR Events and Conferences
Tools Platform 2023 F2F meeting
27-29 March 2023 | Leiden, Netherlands
ELIXIR Systems Biology Community F2F/hybrid & Implementation Study kick-off Meeting
12 - 14 April 2023 | Hybrid - Braga, Portugal
ELIXIR Innovation and SME Forum: AI in Health Research
13 April 2023 | Utrecht, the Netherlands
ELIXIR All Hands 2023
5-8 June 2023 | Dublin, Ireland
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
Research Engineer ETL for Health Data
Barcelona Supercomputing Center (BSC), part of INB/ELIXIR-ES
two Junior Lecturers VU/UvA master Bioinformatics and Systems Biology JD open till April 1st (the link may be down in the first few days of March)
Vrije Universiteit Amsterdam and University of Amsterdam
Administrative Officer - Events
Elixir
Technologist: Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari (IBIOM)
CNR
Researcher: Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari (IBIOM)
CNR