This week's highlights
A warm welcome to new faces at ELIXIR Hub
- Alice Gregory joined ELIXIR Hub a few weeks ago as an "Administrative Assistant" in the Administration and Operations Team.
- Clare Garrard starts her role as "Scientific Officer - Life Science Communities & Open Science" today. She will support the activities of the Communities and Platforms and promote their connection to ELIXIR members, projects and users.
Two job positions closing this week
Project Manager: Scientific Services and Support
Deadline: 14 July 2022
Apply now
Project Manager: Technical Support
Deadline: 14 July 2022
Apply now
ELIXIR Bioinformatics and Industry Forum registration opens
11 October 2022 | London, UK
EBIF brings together bioinformaticians to discuss visionary ideas in the data-driven life science sector. The theme of EBIF this year focuses on making Machine Learning in the Life Sciences.
More information and registration
Provide comments on the NIH "Federal Big Data Research and Development Strategic Plan"
Deadline: 29 July 2022
The NIH is inviting ELIXIR partners to provide comments on the updated Federal Big Data Research and Development Strategic Plan (USA). The following 3 sections are the ones relevant to ELIXIR:
- Strategy 3: Build and enhance research cyberinfrastructure that enables Big Data innovation in support of agency missions
- Strategy 4: Increase the value of data through policies that promote sharing and management of data
- Strategy 5: Understand Big Data collection, sharing, and use with regard to privacy, security, and ethics
Comment on the strategic plan
Please inform Corinne Martin if you have commented on the strategic plan.
Recommended reads
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles
An ELIXIR Europe paper
Residue interaction networks (RINs) are used to represent residue contacts in protein structures. RINs have been proved effective as an alternative to coordinate data in the analysis of complex systems. The RING server calculates high quality and reliable non-covalent molecular interactions based on geometrical parameters. The new RING 3.0 version extends the previous functionality in several ways. The underlying software library has been re-engineered to improve speed by an order of magnitude. RING now also supports the mmCIF format and provides typed interactions for the entire PDB chemical component dictionary, including nucleic acids. Moreover, RING now employs probabilistic graphs, where multiple conformations are mapped as weighted edges, opening up new ways to analyze structural data. The web interface has been expanded to include a simultaneous view of the RIN alongside a structure viewer, with both synchronized and clickable.
Linking PubDictionaries with UniBioDicts to support Community Curation
A BioHacakthon Europe paper
One of the many challenges that biocurators face, is the continuous evolution of ontologies and controlled vocabularies and their lack of coverage of biological concepts. To help biocurators annotate new information that cannot yet be covered with terms from authoritative resources, the authors produced an update of PubDictionaries: a resource of publicly editable, simple-structured dictionaries, accessible through a dedicated REST API. PubDictionaries was equipped with both an enhanced API and a new software client that connects it to the Unified Biological Dictionaries uniform data exchange format. This client enables efficient search and retrieval of ad hoc created terms, and easy integration with tools that further support the curators specific annotation tasks. A demo that combines the Visual Syntax Method interface for general-purpose knowledge formalization, with this new PubDictionaries-powered UBD client, shows it is now easy to incorporate the user-created PubDictionaries terminologies into biocuration tools.
Updates from Nodes
EOSC Association Taskforce Data stewardship update
EOSC Association Newsletter July 2022, featuring the EOSC Association Taskforce Data stewardship, curricula and career paths, which is chaired by Ilire Hasani-Mavriqi (TU Graz) and Celia van Gelder (DTL/ELIXIR-NL/Health-RI)
More information
Updates from Platforms
Reminder: Training Gap Analysis
Deadline: 20 July 2022
The ELIXIR Training platform would like your input to help identify potential gaps in current training in Life Sciences across Europe, and to continue taking measures to fill the gaps identified with appropriate training.
Save the date: Data and Interoperability Platforms joint annual event
28-30 November 2022 | Hybrid - Geneva, Switzerland & Online
The Data and Interoperability Platforms will be holding their joint annual event on 28-30 November 2022. This event will be run in full hybrid format with the face-to-face element for in-person attendees taking place in Geneva, Switzerland. Further details will be available and registration distributed in the coming weeks.
Updates from Communities
Reminder: Call for two co-leads
Deadline: 26 August 2022
The ELIXIR Metabolomics Community is looking for two new co-leads to join the current Community leadership team. The Community is opening a self-nomination process. Candidates should submit a short statement of their background and what they believe they will bring to the role.
For any questions or nominations, please contact Katharina Heil
Reminder: 3D BioInfo Community F2F/hybrid meeting
2-4 November 2022 | Hybrid - EMBL-EBI, UK & Online
Deadline: 31 July 2022
The ELIXIR 3D BioInfo Community is inviting its Community members to participate in and contribute to the 3D BioInfo Community Annual General Assembly. This will be a hybrid meeting with F2F attendance at EMBL-EBI, Hinxton. Funding is available for a number of people, the selection of funding will be based on submitted abstracts.
Register and submit an abstract by 31 July 2022
Updates from Other Initiatives
ISIDORe emergency call for proposals
Deadline: 5 August 2022
ISIDORe has launched an open call for free of charge transnational access to ISIDORe capacities for supporting and advancing research on Monkeypox Virus.
GA4GH 10th Plenary registration and poster submissions
22-23 September 2022 | Barcelona, Spain
GA4GH 10th Plenary will bring together organizations and stakeholders from the genomics and health community for two days of keynotes, talks, and workshops that will focus on genomic and clinical data sharing. Participants attending in person are invited to submit posters for the meeting.
More information on the event website
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 Train the Trainer
19-22 July 2022 | Hybrid - Heidelberg, Germany & Online
SIB: Advanced Statistics: Statistical Modelling
22 - 25 August 2022 | Lausanne, Switzerland
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: Good practice in high-throughput experiments
19-20 September 2022 | Basel, 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
PhD students at the Molecular Modeling and Bioinformatics research group
Institute for Research in Biomedicine (IRB Barcelona)
Bioinformatician at the Bioinformatics Unit
Spanish National Cancer Research Centre (CNIO)
Bioinformatician (m/f/d)
Senckenberg Gesellschaft fr Naturforschung
Project Manager
Elixir
Project Manager - Elixir Programme & Commissioned Services
Elixir