Weekly Brief, 5 September 2022

This week's highlights

New Head of Operations joins ELIXIR Hub

A warm welcome to Ivana Veri who joined ELIXIR as our new Head of Operations last week.

Ivana comes to us from the Consortium of Social Science Data Archives (CESSDA ERIC) where she held the position of Chief Operations Officer.


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Welcome to the Hub!

Manthos Pitoulias joined the ELIXIR Hub two weeks ago as Senior Scientific Officer. He will assist in coordination of the Tools and Training Platforms.

Zuzana Clarke joins us today as Senior Administrative Officer - Events.

Call for new member of the ELIXIR Industry Advisory Committee

Deadline: 30 September 2022

Applications are particularly encouraged from experts in plant and crop, food and nutrition sciences, as well as scientific publishing and AI/machine learning in the life sciences.

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ELIXIR Position Paper on the benefits of utilising existing infrastructures in implementing the 1+MG initiative

ELIXIR has published a position paper encouraging the use of existing research infrastructures such as ELIXIR for the implementation of the 1+MG initiative whenever possible, ensuring less fragmentation of efforts and cost savings for Member States.

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Webinar: MobiDB, a database of protein disorder

This Wednesday 7 September!

• What is MobiDB and how to use it
• Navigating the MobiDB database
• Using the MobiDB documentation

Recommended reads

APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry

A Proteomics Community paper

We revisit a case study on the automated composition of proteomics workflows. We use the same four workflow scenarios but we explore workflows directly on bio.tools. We use the Automated Pipeline Explorer (APE), a reimplementation and extension of the workflow composition method previously used. Moving into the wild opens up an unprecedented wealth of tools and a huge number of alternative workflows. Automated composition tools can be used to explore this space of possibilities systematically. Inevitably, the mixed quality of semantic annotations in bio.tools leads to unintended or erroneous tool combinations. However, our results also show that additional control mechanisms (tool filters, configuration options, and workflow constraints) can effectively guide the exploration toward smaller sets of more meaningful workflows.

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The RDConnect GenomePhenome Analysis Platform - accelerating research and diagnosis for rare diseases

An ELIXIR EXCELERATE paper

The RDConnect GenomePhenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genomephenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users. The platform also enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. The RDConnect GPAP provides a powerful userfriendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.

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Updates from Platforms

Registration open: UK Conference of Bioinformatics and Computational Biology

In partnership with ELIXIR-UK, the three day UK-CBCB conference will cover the breadth of biological data management, analysis and sharing.

There will be breakout discussion groups to exchange expertise and challenges, working together to provide multidisciplinary solutions to complex problems.

Register

New bioinformatics train-the-trainer resources published

• Introducing the Mastery Rubric for Bioinformatics read more
• Using the Mastery Rubric for Bioinformatics read more

Updates from Communities

Two new co-leads of Marine Metagenomics/emerging Microbiome Community

We welcome Brnice Batut (ELIXIR-DE) and Eric Pelletier (ELIXIR-FR). Both will be a great addition to the leadership team and will introduce themselves in the next Community call (scheduled for September 20, details to follow).

Registration open: Galaxy Community Meeting

October 4/5 2022 | Freiburg, Germany

Join the upcoming ELIXIR Galaxy Community meeting, part of the European Galaxy Days.

Updates from Other Initiatives

Call for funding: EOSC Future Project and RDA
Deadline: 15 September 2022

The EOSC Future Project is developing a single-sign-on environment with professional data services, open research products and infrastructure that will support European researchers in managing the data lifecycle.

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