Weekly Brief, 12 September 2022

This week's highlights

ELIXIR report of the 19th Plenary of the RDA

The ELIXIR RDA-Activities Focus Group are pleased to share a report of the 19th Research Data Alliance Plenary event which took place in June of 2022. This report was compiled by the Focus Group members who attended the event with the intentions of summarising and sharing core information from the event sessions. Content included is of relevance to those working in the life sciences domain and intended to be a valuable read for all ELIXIR members.

Please find the report linked here

ELIXIR Communications Group meeting: impact and communications

19 September 2022 | 14:00-15:00 CEST

All are welcome to the next ELIXIR Communications Group meeting where we will be discussing impact and communications.

Find out more

Recommended reads

ELIXIR Software Management Plan for Life Sciences

A BioHackathon Europe paper

Data Management Plans are now considered a key element of Open Science. They describe the data management life cycle for the data to be collected, processed and/or generated within the lifetime of a particular project or activity. A Software Management Plan (SMP) plays the same role but for software. Beyond its management perspective, the main advantage of an SMP is that it both provides clear context to the software that is being developed and raises awareness. Although there are a few SMPs already available, most of them require significant technical knowledge to be effectively used. ELIXIR has developed a low-barrier SMP, specifically tailored for life science researchers, aligned to the FAIR Research Software principles. Future plans of the ELIXIR SMP include a human- and machine-readable version, that can be automatically queried and connected to relevant tools and metrics within the ELIXIR Tools ecosystem and beyond.

Read more

Lightweight Distributed Provenance Model for Complex Realworld Environments

A BY-COVID & EOSC-Life paper

Provenance is information describing the lineage of an object, such as a dataset or biological material. Complete provenance chains can provide traceability and contribute to reproducibility and FAIRness of research objects. In this paper, the authors define a lightweight provenance model based on W3C PROV that enables generation of distributed provenance chains in complex, multi-organizational environments. The application of the model is demonstrated with a use case spanning several steps of a real-world research pipeline starting with the acquisition of a specimen, its processing and storage, histological examination, and the generation/collection of associated data, ending with training an AI model for the detection of tumor in the images. The proposed model has become an open conceptual foundation of the currently developed ISO 23494 standard on provenance for biotechnology domain.


Read more

Updates from Platforms

Registration open: PerMedCoE webinar

11 October 2022 | 15:00-16:00 CEST

PerMedCoE webinar series will continue in October 2022 with the session "Data protection and security aspects of running simulations on personal data with HPC".

Register now

Updates from Communities

Register for European Galaxy Days

3 -7 October 2022 | Freiburg, Germany

Join the European Galaxy Days 2022 to discuss recent and future Galaxy developments in Freiburg. There are 3 events co-locating on the same week:

ELIXIR Galaxy Implementation Study (IS2021) meeting,

European Galaxy Days (EGD), talks, discussions and updates, including ELIXIR-Galaxy community meeting

EuroScienceGateway (ESG) kick-off, an EU-funded project to build a mature network of national Galaxy servers and Pulsar endpoints in European clouds and HPC centers.

More information and registration

Updates from Other Initiatives

Webinar: Towards broadly applicable standards for in silico approaches in personalized medicine

14 September 2022 | 14:30-16:30 CEST

The webinar co-organised by EU-STANDS4PM and the European Commission will take place on Wednesday, 14 September 2022 from 14:3016:30 (CEST) via Zoom.

It will provide an overview of the process and challenges of developing formal as well as community based standards for predictive computational models in personalized medicine.

For 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 Innovation and SME Forum: Data driven innovation in healthcare diagnostics
22 September 2022 | 10:00 to 19:00 CEST | Barcelona, Spain

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
 

Software developer ELIXIR Norway

University of Bergen

Senior engineer, software development

University of Bergen

Research associate (data scientist)

Leibniz Institute of Plant Biochemistry

Research associate (computational metabolomics)

Leibniz Institute of Plant Biochemistry