Weekly Brief, 28 November 2022

This week's highlights

Code reproducibility training initiative

What? Creating training materials in sustainable and reproducible code, part of ELIXIR-CONVERGE WP2

Who? Those interested in developing training in version control, literate programming, software testing, documentation, design and CI/CD.

Find out more and register your interest by 15 December

Assessing performance and impact of local RIs using global frameworks

F1000 blog by Ana Portugal Melo

Existing frameworks for public-funded European research infrastructure activities have helped inform performance and impact assessment of BioData.pt.

Read more

ELIXIR Communications Group meeting

Monday 5 December | 14-15:00 CET

Building Node capacity in communications
A one-hour workshop to discuss comms priorities for inclusion in upcoming INFRADEV grant proposals. All welcome, no registration necessary.

Agenda and Zoom link

Recommended reads

3D-Beacons: a federated network of protein structure data resources

A BioHackathon Europe paper

The gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modelling approaches. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank.

Read more

Flow karyotyping of wheat-Aegilops additions facilitate dissecting genomes into individual chromosomes

An ELIXIR-CZ paper

Breeding of wheat adapted to new climatic conditions and resistant to diseases and pests is hindered by a limited gene pool due to domestication and thousands of years of human selection. Annual goatgrasses (Aegilops spp.) with M and U genomes are potential sources of the missing genes and alleles. The present study extends the potential of chromosome genomics to allotetraploid Ae. biuncialis and Ae. geniculata by dissecting their M and U genomes into individual chromosomes. Chromosome-specific genomic resources will facilitate gene cloning and the development of molecular tools to support alien introgression breeding of wheat.

Read more

Updates from Communities

Contribute to the Biodiversity Implementation Study

After finalising their whitepaper, the Biodiversity (emerging) Community is working on their Implementation Study.

If you are interested in joining the team, get involved or lead a Work Package, please contact one of the Community co-leads or katharina.heil [at] elixir-euorpe.org (Katharina Heil) ASAP.

Further information: meeting minutes and Implementation Study draft.

Reminder: ELIXIR Single Cell Omics Community Meeting

5 & 6 December 2022 | Hybrid - Stockholm, Sweden

Registration deadline: 4 December (virtual only, F2F now closed)

This hybrid meeting is the first F2F for members of the ELIXIR Single Cell Omics Community. It will include general Community updates, short presentations and activities/actions from the Community Implementation Study, starting in January 2023.

Find out more and register now

Updates from Platforms

Tutorial submission deadlines approaching!

Upcoming Compute presentations

ELIXIR Sweden Compute Activities (Joel Hedlund)

2 December |14-15:00 CET Part of the Compute Platform bimonthly open call
Agenda and Zoom

Upcoming Data presentation

ARCHIVER Project (Joao Fernandes)

6 December |15:30-16:30 CET

Updates from Other Initiatives

Scalable indexing system to link COVID-19 data across research disciplines

The BY-COVID project has implemented a scalable indexing system to link data and metadata on SARS-CoV-2 and COVID-19, along with and other infectious diseases and pathogens, across multiple areas of research.

Read more

FAIRtracks project launches website!

FAIRtracks, an ELIXIR Recommended Interoperability Resource, is a service ecosystem to make genome browser track files more FAIR.

FAIRtracks.net aims to be a central resource for everything related to genomic tracks, providing overviews of different genome browsers, data portals, metadata models, and more to come! Various aspects of FAIR metadata for tracks are explored: identifiers, ontologies, validation, augmentation and transformation of metadata.

Visit FAIRtracks.net

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

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

ELIXIR Single Cell Omics Community F2F/hybrid Meeting
5&6 December 2022 | Hybrid - Stockholm, Sweden

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
 

Senior engineer for Python/Java systems developer

University of Oslo

Bioinformatician at the Bioinformatics Unit

Spanish National Cancer Research Centre (CNIO), part of INB/ELIXIR-ES

Ethical, Legal and Social Implications (ELSI) Services Officer

ELIXIR Hub

Bioinformatics training officer

University of Freiburg

Technical Coordinator

SIB Swiss Institute of Bioinformatics