This week's highlights
ELIXIR at the ISMB/ECCB 2023 in Lyon
On 23-27 July 2023, ELIXIR was in Lyon for ISMB/ECCB 2023 with more than a thousand bioinformaticians around the world. As a sponsor of the event, ELIXIR had a dedicated booth and hosted a track programme with NIH ODSS on BioData Ecosystems.
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Recommended reads
eTRANSAFE: data science to empower translational safety assessment
An eTRANSAFE article
Drug safety is not the main domain for competition between pharmaceutical companies, and so it is more feasible to develop collaborative projects in this area. Significant steps forward in this direction were taken by the eTOX and eTRANSAFE projects. The eTOX project, which focused on sharing preclinical toxicological data, was carried out from 2010 to 2017. More recently, the eTRANSAFE project, addressing translational drug safety assessment through integrative knowledge management, has been running from 2017 to 2023. Here, the authors highlight the achievements of the eTRANSAFE initiative and discuss the impact of the tools it has developed.
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Genomic Landscape of Normal and Breast Cancer Tissues in a Hungarian Pilot Cohort
An ELIXIR Hungary paper
A limited number of studies have focused on the mutational landscape of breast cancer in different ethnic populations within Europe and compared the data with other ethnic groups and databases. The authors performed whole-genome sequencing of 63 samples from 29 Hungarian breast cancer patients. This study, as the first breast tumor/normal sequencing study in Hungary, revealed several aspects of the significantly mutated genes and mutational signatures, and some of the copy number variations and somatic fusion events. Multiple signs of HRD were detected, highlighting the value of the comprehensive genomic characterization of breast cancer patient populations.
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Updates from Nodes
Funded ARISE infrastructure Fellowship position
ARISE - Career Accelerator for Research Infrastructure Scientists offers employment at EMBL for three years, a chance to work on method and technology development, career support and exclusive training curricula.
More information
Exploring gene and environmental exposure interactions to understand human health and disease
19 - 23 February 2024 | EMBL-EBI, UK
Application deadline: 5 November 2023
This introductory course explores the complex interplay between genes and the environment in shaping human phenotypes. Participants will gain knowledge of cohort datasets, environmental readouts, and bioinformatics tools to investigate gene-environment interactions.
More information and registration
Register for the [BC]2 conference
11-13 September 2023 | Basel, Switzerland
The [BC]2 Basel Computational Biology Conference, Switzerland's main event in Computational Biology, brings together around 500 participants from pharma/biotech companies and academia. This year the conference will focus on Big data in biology promises and challenges and feature keynote speakers, presentations of the latest scientific results and methods in the field, workshops and tutorials, and poster sessions along with networking activities.
Register by 4 September
Updates from Communities
Register for the Emerging Microbiome/Marine Metagenomics Community meeting
12-13 September 2023 | Hybrid - Barcelona, Spain
Registration deadline: 17 August (in person) | 12 September (online)
The Emerging Microbiome/Marine Metagenomics Community will hold its F2F/hybrid Meeting in September. The meeting is held back to back with the Biodiversity Community and focuses on the final touches of the Community white paper and first ideas of upcoming Community activities. There will be time for updates, presentations, progress reports and discussions. A part of the meeting will be dedicated to the 2024-2028 Scientific Programme and the Community's possible role and activities.
Register now
Register for the Biodiversity Community F2F & Implementation Study meeting
13-15 September 2023 | Hybrid - Barcelona, Spain
Registration deadline: 17 August (in person) | 12 September (online)
The Biodiversity Community will hold its F2F/hybrid meeting in September. The meeting is held back to back with the emerging Microbiome Community and links the Community F2F with an Implementation Study meeting. There will be time for updates, presentations, progress reports and discussions. A part of the meeting will be dedicated to the 2024-2028 Scientific Programme and the Community's possible role and activities.
Register now
Reminder: IDP Community call for two new co-leads
Deadline: 18 August 2023
The ELIXIR IDP Community is looking for two new co-lead to join the Community leadership team (Wim Vranken). Candidates should submit a short statement of their background and what they believe they will bring to the role.
A big thank you goes to both Zsuzsanna Dosztanyi and Damiano Piovesan for their work as a co-leads, we wish you all the best.
For any questions please contact katharina.heil [at] elixir-europe.org (Katharina Heil)
More information
hCNV Community call for a new co-lead
Deadline: 18 August 2023
The ELIXIR hCNV Community is looking for one new co-lead to join the Community leadership team (Michael Baudis nd Christophe Broud). Candidates should submit a short statement of their background and what they believe they will bring to the role.
A big thank you to David Salgado for his work as a co-lead and we wish him all the best.
For any questions please contact katharina.heil [at] elixir-europe.org (Katharina Heil) or giselle.kerry [at] elixir-europe.org (Giselle Kerry)
More information
Updates from other initiatives
Webinar: Computational chemistry workflows with cycles and conditions using Maize
5 September 2023
In this webinar, the speaker will give an introduction to Maize and demonstrate solutions to common problems in computational chemistry and early-stage drug discovery projects, such as de-novo small molecule generation, docking, and their combination in an active learning pipeline.
More information and registration
First HealthData@EU Pilot Stakeholder forum
19 October 2023 | Hybrid - Paris, France
The HealthData@EU pilot project invites experts, professionals and decision-makers in the (digital) health sector across Europe to the first stakeholder forum of the project. This will be the opportunity to present and discuss the progress of the pilot project testing the first implementation of the European health data space for the secondary use of health data.
More information
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
SIB course: First Steps with Python in Life Sciences
27 - 29 September 2023 | Zurich, Switzerland
SIB course: Introduction to Machine Learning with Python
9 - 10 October 2023 | Zurich, Switzerland
SIB course: Introduction to Containers and Snakemake for Reproducible Research
12 - 13 October 2023 | Davos, Switzerland
EMBL-EBI: Introduction to RNA-seq and functional interpretation
12 - 16 February 2024 | Online
ELIXIR Events and Conferences
Emerging Microbiome/Marine Metagenomics Community meeting
12-13 September 2023 | Hybrid - Barcelona, Spain
Biodiversity Community F2F & Implementation Study meeting
13-15 September 2023 | Hybrid - Barcelona, Spain
BioHackathon Europe 2023
30 October - 3 November 2023 | Barcelona, Spain
3D BioInfo Community meeting
15-17 November 2023 | Hybrid - Prague, Czech Republic
Federated human data (FHD) Community meeting
16-17 November 2023 | Hybrid - Barcelona, Spain
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
Research Associate in Biomedical NLP
Imperial College London
IT System Administrator for Science-IT
Technical University of Munich
PhD position in "Machine learning tools and Interoperability resources for the management and analysis of biomedical data in the context of the European infrastructure ESFRI ELIXIR"
Biocomputing group - University of Bologna
Auxiliary RESEARCHER (M/F) in the area of Bioinformatics/Data Science
Centro de Ciencias do Mar (CCMAR)
Semantic Web Architect
UK CEH