Weekly Brief, 6 November 2023

This week's highlights

Romania joins ELIXIR as Observer

Romania has joined ELIXIR as an Observer, following approval by the ELIXIR Board on 30 October 2023. Observer status enables the Romanian bioinformatics community to engage more deeply with other ELIXIR Nodes and facilitates transition towards full ELIXIR Membership, which is expected to occur in the coming years.

Read more

Successful BioHackathon Europe 2023!

Last week, we held the BioHackathon Europe 2023 in Barcelona, Spain. The event attracted more than 180 on-site and 160 virtual participants from across the world to work on 35 life science projects. The event was a large-scale hybrid event and we're pleased to say that it was a big success! Stay tuned to find out more about the event in our upcoming news release.

Recommended reads

Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool

An ELIXIR supported paper

Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles tailored for research software have been proposed by the FAIR for Research Software (FAIR4RS) Working Group. However, the FAIR4RS principles are aspirational and do not provide practical instructions to the researchers. To fill this gap, the authors propose the first actionable step-by-step guidelines for biomedical researchers to make their research software compliant with the FAIR4RS principles. This workflow is incorporated in FAIRshare, a free and open-source software application aimed at simplifying the curation and sharing of FAIR biomedical data and software through user-friendly interfaces and automation.


Read more

Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis

An ELIXIR-CZ paper

While the workflow for primary analysis of single-cell RNA-seq data is well established, the secondary analysis of the feature-barcode matrix is usually done by custom scripts. There is no fully automated pipeline in the R statistical environment, which would follow the current best programming practices and requirements for reproducibility. The researchers developed scdrake, a fully automated workflow for secondary analysis of scRNA-seq data, which is fully implemented in the R language and built within the drake framework. The pipeline is reproducible and scalable, has an efficient execution, provides easy extendability and access to intermediate results and outputs rich HTML reports.

Read more

Updates from Nodes

Purifying mining wastewater with plant-associated microbes

Using Arctic microbes and plants to purify industrial wastewater can help reduce environmental contamination caused by the mining industry. The suitable plant-associated microbes for bioremediation are mainly determined by sequencing methods, but also by isolating microbes from the moss.

Read more

Empowering pandemic preparedness with LUMI and the European COVID-19 data portal

Big viral data is a technical challenge for the present EuroHPC supercomputers. SARS-CoV-2 data analysis pipelines, utilized for updating the European COVID-19 data portal, are effectively deployed and tested on LUMI.

Read the article

4th Annual Industrial Forum Meeting 2023

23 November 2023 | 13:00-17:00 CET | Online

The programme of the 4th Annual Meeting de.NBI Industrial Forum comprises presentations showcasing current research and use cases in regard to big data handling in the Life Sciences. The meeting is an opportunity to meet and discuss current academic and industrial talking points.

More information and registration

Benelux Metabolomics Days 2023

16-17 November 2023 | Utrecht, the Netherlands

Empowered by Health-RI (ELIXIR-NL), the Benelux Metabolomics Days aims to bring together the Metabolomics community in the Netherlands, Belgium and Luxembourg. The meeting welcomes researchers interested in Metabolomics and Exposome research.

Find out more

SIB Training Courses in 2024

The programme of SIB courses for 2024 is now online. Save the dates for the wide variety of courses and receive notification via the mailing list when courses are open for registrations.

Discover the new SIB training course

Updates from other initiatives

Open Call for Transnational Service Provision

Submission Deadline: 4 January 2024

Under the canSERV Open Call, researchers are welcome to apply to a portfolio of services offered by canSERV to address the research needs of the entire oncology developmental pipeline.

Find out more

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

3D BioInfo Community meeting
15-17 November 2023 | Hybrid - Prague, Czech Republic

Federated human data (FHD) Community meeting
16-17 November 2023 | Hybrid - Barcelona, Spain

ELIXIR Bioinformatics Industry Forum: Trusted research environments for sharing data in life sciences
21 November 2023 | London, UK

ELIXIR hCNV Community F2F/hybrid meeting
30 November-1 December 2023 | Hybrid - Hinxton, UK

RDM Community & Implementation Study Kick-off Meeting
4-6 December 2023 | Hybrid - Bergen, Norway

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
 

6 assistant professor positions (career track) computer science, bioinformatics and AI

Vrije Universiteit