Weekly Brief, 10 October 2022

This week's highlights

ELIXIR Human Data Infrastructure Maturity Model pilot open for Nodes


The ELIXIR Hub has been leading the creation of the ELIXIR Human Data Infrastructure Maturation Model. This set of tools is designed to assist Nodes create their human data access and sharing roadmap to guide them along a harmonised pathway. We are looking for Nodes to join a Second Wave pilot. Please contact melissa.konopko [at] elixir-europe.org (Melissa Konopko) if interested.

Link to the model

Recommended reads

Ensembl Genomes 2022:
an expanding genome resource for non-vertebrates

An Ensembl paper


Ensembl Genomes provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project. The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. The article details new efforts in gene annotation, emerging support for pangenome analysis, efforts to accelerate data dissemination through the Ensembl Rapid Release resource and new AlphaFold visualization. Finally, the authors present details of future plans including updates on integration with Ensembl, and how to improve support for the microbial research community.

Read more

Deep learning tools are top performers in long non-coding RNA prediction

An ELIXIR-Finland paper


The increasing amount of transcriptomic data has brought to light vast numbers of potential novel RNA transcripts. Accurately distinguishing novel long non-coding RNAs (lncRNAs) from protein-coding messenger RNAs (mRNAs) has challenged bioinformatic tool developers. This study compared the performance of deep learning tools with other predictive tools that are currently used in lncRNA coding potential prediction. Computational resources were utilized differently between the top-ranking tools, thus the nature of the study may affect the decision of choosing one well-performing tool over another. Nonetheless, the results suggest favouring the novel deep learning tools over other tools currently in broad use.


Read more

Updates from Nodes

European Registry of Materials identifier to make research output more FAIR

In collaboration with various European H2020 projects, Jeaphianne van Rijn (BiGCaT, NUTRIM, Maastricht University) proposed an open, global, unique identifier for nanomaterials, the European Registry of Materials identifier, to make research output more FAIR.

Read more

ELIXIR-CONVERGE FAIR hackathon finalising the first package of lesson

After the kickoff on 29 June 2022 and report back session on 10 September 2022, the FAIR hackathon group of CONVERGE WP2 is working on finalising the first package of lesson plans for life sciences research organisations to advance their data stewards and researchers FAIR skills.
Contact mijke.jetten [at] dtls.nl (Mijke Jetten (ELIXIR-NL)) or stephan.nylinder [at] nbis.se (Stephan Nylinder (ELIXIR-SE)) for more information or feedback.

Read the lesson plan

VIB looks for Center Director/Research Professor for the new Center for Computational and Quantitative Life Science Research


The goal of the Center for Computational and Quantitative Life Science Research is to drive the quantitative study and predictive modeling of the physiology and disease of living organisms. The centre will bring machine learning and deep learning approaches to the study of biological systems at the integrated level of molecules to cells to tissues and organisms.

More information

Updates from Platforms

ELIXIR CDR 2023 open call and selection


ELIXIR intends to run its next open call and selection for Core Data Resources (CDR) in 2023. The Hub is providing informational preparation sessions before starting the process. The first of session took place on 4 October 2022 at the Data Platform monthly call, further sessions will be advertised through the Data Platform and Weekly Brief.

Full presentation recording
Link to the corresponding slides

ELIXIR Training Platform at CoBLET

At the Colloquium on Bioinformatics Learning, Education and Training (CoBLET) on 11-14 October 2022, there will be several contributions from the ELIXIR Training Platform:

Building skills for managing and exploiting data in ELIXIR and beyond - A FAIR training journey Challenges and solutions for teaching single-cell omics data analysis Community of Practice in training on Data Managment & Data Stewardship

More information and registration

Updates from Other Initiatives

3rd EOSC-Life Training Open Call

Deadline: 1 November 2022

This call is for training on topics relevant to EOSC-Life. Find all information about eligible topics and this call on the training open call page and the training webpage.

Integrated Services For Infectious Disease Outbreak Research - ICRI 2022 side event

19 October 2022 | Hybrid (Brno, Czech Republic & online)

The event will provide an insight into the experiences of European research infrastructures and infectious disease networks in responding to the COVID-19 emergency, as well as highlighting ISIDORes actions and showcasing opportunities for accessing its resources, to address the challenge of any emerging or re-emerging infectious disease threat.

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

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
 

Project Manager Human Genomics Data

VIB

Bioinformatician(s) at NBIS

Lund University

Technical Portfolio Manager

ELIXIR Hub

EC Project Manager

ELIXIR Hub

Scientific Programmer (EMDB)

EMBL-EBI