This week's highlights
Meet the new members of staff at the ELIXIR Hub
Over the past few months we have welcomed a number of new members of staff. All these individuals join ELIXIR in newly created roles, reflecting the expanding portfolio of projects and activities that ELIXIR engages with. If you haven't met them yet (virtually or otherwise), here's your chance to find out a little more about them!
Read more
A further two new staff members have joined the Human Genomics and Translational Data (HGTD) team in the past weeks: Anamika Chatterjee as Scientific Officer, and Giselle Kerry as Programme Manager. We will introduce them in more detail in an upcoming news feature.
Deadline approaching for ELIXIR All Hands Workshop abstract submission
Submission deadline 8 December, next Wednesday!
7 - 10 June 2022 | Amsterdam, Netherlands
The deadline for abstract submissions for workshops to take place at the All Hands meeting is rapidly approaching, please don't miss your opportunity to submit! Workshops will take place on 7 and 9 June 2022.
Full details and link to submission
Recommended reads
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses
An ELIXIR Spain paper
Bollito is an automated, flexible and parallelizable computational pipeline for the comprehensive analysis of single-cell RNA-seq data. Starting from FASTQ files or pre-processed expression matrices, bollito performs both basic and advanced tasks in single-cell analysis integrating >30 state-of-the-art tools. bollito is built using the Snakemake workflow management system, which easily connects each execution step and facilitates the reproducibility of results. bollitos modular design makes it easy to incorporate other packages into the pipeline enabling its expansion with new functionalities.
Read more...
Large scale meta-analysis of preclinical toxicity data for target characterisation and hypotheses generation
An eTRANSAFE paper
Recent technological advances in the field of big data have increased our capabilities to query large databases and combine information from different domains and disciplines. This article proposes the application of meta-analyses at large scale in corporate databases as a tool to exploit data from both preclinical studies and in vitro pharmacological activity assays to identify associations between targets and tissues that can be used as seeds for the development of causal hypotheses to characterise of targets.
Read more...
Updates from Focus Groups
The ELIXIR FAIR training focus group invite you to an event
13 January 2022 | 10:00 CET
The ELIXIR FAIR Training Focus Group is developing (FAIR!) training materials for a lesson on how to develop (FAIR) training materials. During the recent BioHackathon, project 25 made significant progress and the work will continue in the coming period. If you are interested to hear more about this work and / or you want to contribute as an author please join the Slack channel #fg_fairtraining in the ELIXIR workspace and the mailing list
Find out more about BioHackathon project 25
Updates from Nodes
Fill in and share the Research Software Engineer survey
Do you develop software for academic research as part of your work? Please fill in the survey to help the Software Sustainability Institute evaluate: a persons route into the role, the type of work they conduct, their working practices, job satisfaction and demographics. The survey takes ~20 minutes and is available in four languages.
Take the Survey
Share the survey on Twitter
ELIXIR-FI article: In the future, an algorithm may diagnose glaucoma from fundus photos
The Node has released a new article on how learning algorithms to detect glaucoma.
Read the article
Help improve OpenEBench by sharing your feedback
OpenEBench, the Open ELIXIR Benchmarking platform for supporting community-driven efforts, has implemented a new feedback mechanism towards improving the overall platform usability.
As part of the ELIXIR Tools Platform, it serves as the ELIXIR scientific benchmarking and technical monitoring platform for bioinformatics tools, web servers and workflows. Its development is led by the INB/ELIXIR-ES coordination and computational teams at the Barcelona Supercomputing Center (BSC), in collaboration with partners within ELIXIR and beyond.
Fill in the survey
One entry-point to query them all: the SPHN Federated Query System is online
Discover how the Swiss Personalized Health Networks FQS allows querying more than 70 Mio. data elements of over 450'000 patients in a privacy-preserving manner. The systems adoption results from nationwide coordination among clinical partners, piloted by SIBs Personalized Health Informatics Group, as part of the SPHN initiative.
Read more
Updates from other initiatives
Webinar: Open Source Secure Data Infrastructure and Processes (OSSDIP)
3 December 2021 | 10:00-10:30 CET
Andreas Rauber, Head of Information and Software Engineering Group at TU Wien, will present OSSDIP. This pilot Infrastructure allows third parties to securely access and process sensitive data, while data owners retain the access control. If you are interested in testing the OSSDIP infrastructure with your own data, join this session!
For any doubts, contact opencall@eosc-life.eu
Calling all start-ups & SMEs: Expression of Interest for Digital Innovation Hub Business Pilots
Application deadline 3 December 2021
The EOSC Digital Innovation Hub (DIH) is looking to onboard pilots to develop, integrate or validate their services. Onboarded pilots are expected to benefit from using EOSC services and develop/innovate solutions in key, but not limited to, areas such as Industry 4.0, Green Deal, Mobility, Health, Energy, Agriculture, Public Administration, Earth observation or Environmental monitoring.
Find out more
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-DE: 2nd Women in Data Science - Perspectives in industry and academia
2 December 2021 | 15:00 CET
ELIXIR Events and Conferences
ELIXIR's Consultation event on international engagement
30 November 2021 | 14:00-16:00 CET | Virtual
ELIXIR-CONVERGE workshop series: Lessons learned from organising and hosting a hybrid conference
8 December 2021 | 14:00 CET | Virtual
ELIXIR All Hands meeting 2022
7-10 June 2022 | Amsterdam, Netherlands
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
Two positions in image processing for Cryo-Electron Microscopy
National Center of Biotechnology (CNB-CSIC), part of INB/ELIXIR-ES
Postdoc in Machine Learning for Spatial Multi-omics of Glioblastoma
German Cancer Research Institute (DKFZ)
Postdoc multidimensional integration of high throughput sequencing data
Albert-Ludwigs-Universitt Freiburg
Senior expert at data science excellence center in medical imaging
CMIV/AIDA/NBIS/BIGPICTURE
Senior bioinformatician
Oslo University Hospital