Weekly Brief, 25 April 2022

This week's highlights

SIS-Containers: Opportunity to submit use case proposals

Deadline 11 May

ELIXIR Communities and Focus Groups are encouraged to submit use case proposals benefitting from adopting and deploying containers. Selected use cases will engage with the Strategic Implementation Study on Containers to make their scientific results more reproducible.

Find out more and propose use cases through this short survey.

Read more

Recommended reads

DS Wizard Meets DAISY: Solving data protection requirements in data management planning

A BioHackathon 2021 paper

As a data information system for GDPR compliance, DAISY is focused on a single goal gathering all information required for GDPR accountability of biomedical research projects. On the other hand, DSW is very flexible and can be used beyond data management planning. We worked on the integration between both tools on two fronts. Firstly, we created a new Knowledge Model in DSW together with a document output template to be able to generate a data protection impact assessment (DPIA). Secondly, we introduced a new integration type between projects in DSW and DAISY that allows the querying of DAISY data upon document generation in DSW. Finally, we provide the related materials as an on-demand training course in the ELIXIR eLearning Platform.

Read more

DOME: recommendations for supervised machine learning validation in biology

An ELIXIR Machine Learning Focus Group paper

DOME is a set of community-wide recommendations for reporting supervised machine learningbased analyses applied to biological studies. Through a community-driven consensus, we propose a list of minimal requirements asked as questions to machine leaning (ML) implementers that, if followed, will help to assess the quality and reliability of reported methods more faithfully. We have focused on data, optimization, model and evaluation (DOME) as each component of an ML implementation usually falls within one of these four topics. Our recommendations are made primarily for the case of supervised learning in biological applications in the absence of direct experimental validation, as this is the most common type of ML approach used.

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Updates from Nodes

New series of user meetings on FAIRDOM-SEEK for data management

Starting 9 May | Virtual | 14:00 CET

ELIXIR-DE, ELIXIR-BE, ELIXIR-NO and ELIXIR-UK are running a new series of online user meetings to share stories and updates on using FAIRDOM-SEEK for data management.

Find out more and register

Combining biobank data with health register data

Find out about ELIXIR-FI's work enabling research in personalised treatment and illness risk factors identification and prediction.

Open for registration: BioSB bioinformatics and systems biology courses

RNA-seq data analysis | Systems medicine | Constraint based modelling | Machine learning | Algorithms for genomics

Find out more and register

Updates from Platforms

Join the next ELIXIR AAI engagement call

4 May | 10:00-11:00 CET

The call is open to anybody interested in the GA4GH Cloud APIs and their integration with ELIXIR/Life Science AAI.

Find out more

Updates from Communities

Reminder: next VIB-VUB webinar Quantitative biology at the molecular & cellular levels: leveraging the power of AI

This Thursday 28 April
Ellen Zhong, Massachusetts Institute of Technology

Find out more

Reminder: The future of metabolomics in ELIXIR 2024-2028

23/24 June (half days) | Hybrid - Valencia, Spain

The ELIXIR Metabolomics Community is holding a F2F/hybrid meeting immediately after the International Metabolomics Society Conference.

Up to two people (seasoned PIs and more junior researchers) per ELIXIR Node can be supported (flight, one night accommodation). Selection is based on your motivation for participation in the meeting section on the registration form (deadline Monday 1 May).

Register

Updates from Focus Groups

Appointment of ELIXIR Biodiversity Focus Group co-leads

A warm welcome to the three newly appointed co-leads of the ELIXIR Biodiversity Focus Group:

Toni Gabaldn (ELIXIR-ES)
Robert Waterhouse (ELIXIR-CH)
Josephine Burgin (ELIXIR-EE)

Find out about the Biodiversity Focus Group

Updates from other initiatives

Guy Cochrane appointed Executive Director of Global Biodata Coalition

Guy Cochrane is currently Team Leader and Head of the European Nucleotide Archive at EMBL-EBI. With this new appointment, his time will be shared between his role at the EMBL-EBI and the GBC.

Find out more

Check out the first Goblet newsletter

Find out more about GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training.

Browse newsletter

Call for nominations: PRACE HPC Excellence Award

Closing 20 May

The PRACE HPC Excellence Award recognises an outstanding individual or team for ground-breaking research, through the usage of high-performance computing, that leads to significant advances in any research field.

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

Galaxy introduction for life scientists

27 April 2022 | Lausanne, Switzerland

Metabolomics and integrative omics: from data production to analysis
28-29 April 2022 | Bari, Italy

Gentle hands-on introduction to Python programming

4,11,18 May 2022 | Virtual

Nordic train-the-trainer course

10-13 May 2022 (half days)| Virtual | Deadline to apply: 3 April

10th RepeatExplorer workshop on the application of NGS to repetitive DNA

24-26 May 2022 | esk Budjovice, Czech Republic

3rd hands-on computational enzyme design workshop

30 May - 1 June 2022 | Virtual

Intermediate Python

3 June 2022 | Bern, Switzerland

Functional exploration of genetic variants in cardiac diseases

14-15 June | Lyon, France | Apply by 1 May

Summer school on genetic epidemiology

29 June - 2 July 2022 | Davos, Switzerland

ELIXIR Events and Conferences

Compute Platform meeting

25-26 April 2022| Hotel Berlin, Berlin

FAIRplus Innovation and SME forum 2022
17 May 2022 | Hybrid - Berlin, Germany

ELIXIR All Hands meeting 2022

7-10 June 2022 | Amsterdam, Netherlands
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

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