Weekly Brief, 8 August 2022

This week's highlights

New job vacancy at the Hub

Senior Scientific Officer - Cancer data

Deadline: 1 September 2022

ELIXIR outreach webinar with India

17 August 2022 | 11:00 - 13:30 CEST

ELIXIR is holding our first joint webinar with Asia Pacific Bioinformatics Interaction & Networking Society (APbians) and ISCB RSG India. The webinar will focus on Data management, human data and infectious diseases: Opportunities for engagement.

ELIXIR webinar on DisProt

16 & 23 August 2022 | 15:00 CEST

Join the webinar hosted by ELIXIR IDP Community to find out more about Database of Intrinsically Disordered Proteins (DisProt).

2022 Outstanding Contributions to ISCB Award: Reinhard Schneider

The 2022 Outstanding Contributions to ISCB Award recipient is Reinhard Schneider, Full Professor in Bioinformatics, Head of Bioinformatics Core Facility, and Head of the ELIXIR Luxembourg Node at the University of Luxembourg.

Read the news

Recommended reads

eTRANSAFE: Building a sustainable framework to share reproducible drug safety knowledge with the public domain

An eTRANSAFE paper

Integrative drug safety research in translational health informatics has rapidly evolved and included data that are drawn in from many resources, combining diverse data that are either reused from (curated) repositories, or newly generated at source. Each resource is mandated by different sets of metadata rules that are imposed on the incoming data. Combination of the data cannot be readily achieved without interference of data stewardship and the top-down policy guidelines that supervise and inform the process for data combination to aid meaningful interpretation and analysis of such data. The eTRANSAFE Consortium's effort to drive integrative drug safety research at a large scale hereby present the lessons learnt and the proposal of solution at the guidelines in practice at this Innovative Medicines Initiative (IMI) project. The research reproducibility guidelines presented in this study lay the foundation for a comprehensive data sharing and knowledge management plans accounting for research data management in the drug safety space.

Read more

The GA4GH Phenopacket schema defines a computable representation of clinical data

An ELIXIR & EJP RD article

Phenotypic features are of high clinical importance, yet exchanging them in conjunction with genomic variation information is often overlooked or even neglected. In the clinical domain, substantial work has been dedicated to the development of computational phenotypes1. Traditionally, these approaches have largely relied on rule-based methods and large sources of clinical data to identify cohorts of patients with or without a specific disease. However, they were not developed to enable deep phenotyping of abnormalities, to facilitate computational analysis of interpatient phenotypic similarity or to support computational decision support. To address this, the Global Alliance for Genomics and Health (GA4GH) has developed the Phenopacket schema, which supports the exchange of computable longitudinal case-level phenotypic information for diagnosis of, and research on, all types of disease. A Phenopacket characterizes an individual person or biosample, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses and treatments.

Perspective on data sharing and management

In 2021, Carole Goble and Susanna-Assunta Sansone of ELIXIR-UK represented ELIXIR at an NIH hosted workshop on Changing the Culture on Data Management and Sharing, in preparation for the new NIH Data Sharing Policy (to be launched in 2023).

Recently, they shared perspectives from Europe on data sharing and management and about the possibilities for global cooperation in an interview.

Read the interview

New article published on ELIXIR Finlands website

ELIXIR Finland published an article Studying the human microbiome is a key towards holistic understanding of our health. The article gives an insight of the research on developing the machine learning models for screening microbial signatures from large-scale data collections.

New Core Data Resouces timeline

A new Core Data Resources (CDR) timeline is now live on ELIXIR website. The ELIXIR Hub will maintain a visible timeline on the ELIXIR website to keep members up to date with the Data Platform's CDR and EDD activities.

Please find the initial timeline here (exact dates will be updated on the timeline once established).

Showcase interoperability usage in your Community

The Interoperability Platform are looking for more ELIXIR Communities to provide a 10-minute showcase presentation of interoperability usage in their Community. There are slots available for 6 September and 4 October at 13:00-14:00 CEST on the monthly Interoperability Platform calls.

Please contact Gavin Farrell if you would like to showcase your Community.

Updates from Communities

Submit your abstract for 3D BioInfo Community Annual General Meeting

Deadline: 12 August 2022

The ELIXIR 3D BioInfo Community is inviting its Community members to participate in and contribute to the 3D BioInfo Community Annual General Meeting. This will be a hybrid meeting with F2F attendance at EMBL-EBI, Hinxton. Funding, including travel, accommodation and (food) expenses is available for a number of people. Selection will be based on submitted abstracts.

Submit an abstract by 12 August 2022

Registration for the European Galaxy Days is open

3 -7 October 2022 | Freiburg, Germany

Join the Europoean Galaxy Day 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 Focus Groups

ELIXIR Europe landscape analysis of RDA involvement

Deadline: 19 September 2022

Is the Research Data Alliance (RDA) a new acronym to you? Or are you already an RDA pro and heavily engaged in RDA activities? The ELIXIR RDA Activities Focus Group are conducting a landscape analysis survey of ELIXIR members and their extent of engagement in the RDA. It takes approximately 5 minutes to complete and contains useful links and information on the RDA and Focus Group throughout.

Fill out the survey

Updates from Other Initiatives

Register to join a virtual knowledge exchange workshop

16 September 2022

Green events - assessing and reducing the environmental impact of your training is a knowledge exchange workshop where experts share insights and facilitate a series of group discussions on the environmental impact of events and training. The workshop is organised by ELIXIR EMBL-EBI Node through the RItrainPlus project in collaboration with EOSC-Life and eRImote.

More information and registration

New job vacancy: Translational medicine data community manager

Application deadline: 26 August 2022

EATRIS is seeking to recruit a Translational Medicine Data Community Manager to join the EATRIS Coordination and Support office based at the University Medical Centre in Amsterdam.

More information

Open calls from EuroHPC

There are several open calls from The European High Performance Computing Joint Undertaking (EuroHPC JU).

More information

Provide comments on the NIH "Federal Big Data Research and Development Strategic Plan"

Deadline extended: 17 August 2022

The NIH is inviting ELIXIR partners to provide comments on the updated Federal Big Data Research and Development Strategic Plan (USA).

Comment on the strategic plan

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 Webinar: An introduction to DisProt
16 August 2022 | 15:00 CEST

SIB: Advanced Statistics: Statistical Modelling
22 - 25 August 2022 | Lausanne, Switzerland

ELIXIR Webinar: Exploring structural and functional annotations of IDPs with DisProt
23 August 2022 | 15:00 CEST

SIB: Advanced Programming with R
29-31 August 2022 | Lausanne, Switzerland

SIB: Introduction to RNA-Seq: From quality control to pathway analysis
1-2 September 2022 | Basel, Switzerland

SIB: Comparative Genomics
12-14 September 2022 | Lausanne, Switzerland

SIB: NGS - Genome variant analysis

15-16 September 2022 | Bern, Switzerland

SIB: Good practice in high-throughput experiments
19-20 September 2022 | Basel, Switzerland

SIB course: First Steps with Python in Life Sciences

28-30 September 2022 | Lausanne, Switzerland

ELIXIR Events and Conference

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

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