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!
Federica Quaglia
Department of Biomedical Sciences (DBS), University of Padova
- 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
RitrainPlus, EOSC-Life, eRImote: Green events - assessing and reducing the environmental impact of your training
16 September 2022 | Virtual
SIB: NGS - Genome variant analysis
26-27 September 2022 | Bern, Switzerland
SIB: Introduction to Machine Learning with Python
3-4 October 2022 | Virtual
SIB: Protein sequence databases and sequence annotation at UniProtKB
14 October 2022 | Virtual
20 October 2022 | Virtual
Data-Interoperability Platforms Hybrid F2F 2022
28-30 November 2022 | Geneva, Switzerland
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