News and announcements

Weekly news 17.02.2020

ELIXIR Guest Webinar: Text mining of disease-gene networks 

19 February 2020 | Online | 14:00 GMT/15:00 CET

Most of what we know about human diseases and genes/proteins involved in them is buried in the biomedical literature. Text mining is thus a key tool for creating databases with structured data on disease-gene associations and the underlying gene networks.

In this webinar, Lars Juhl Jensen from the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen, Denmark, will describe a highly efficiently text-mining pipeline, which allows his team to systematically mine such information from very large corpora of full-text articles as well as abstracts. The presentation will also cover how this information is made available through interoperable, web-based databases, including the DISEASES database and the STRING database (an ELIXIR Core Data Resource). Finally, Lars will show how the Cytoscape stringApp brings together these databases, allowing users to easily retrieve, analyze, and visualize gene networks for diseases or other topics of interest.

Lars Juhl Jensen is a professor at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen in Denmark. His research group develops state-of-the-art tools for generation and analysis of molecular interaction networks from proteomics data and text mining. The tools are freely available to the scientific community.

More: jensenlab.org


paper on TeSS was recently accepted and published by Oxford University Press to review the training platform's features, workflows and future prospects.

 

ELIXIR events

3-Day Course Single-cell Transcriptomics
1-3 April 2020 | University of Lausanne, Switzerland 

Software Carpentry Course 
30-31 March 2020 | Cologne, Germany

Innovation and SME Forum: Data-Driven Innovation in the Agritech Sector
24 -25 March 2020 | Lyon, France

ELIXIR Bioinformatics Industry Forum 
28 April 2020 | London, UK

Bioinformatics Research and Education Workshop (BREW)

The Institute of Computer Science at the University of Tartu is organising this year's Bioinformatics Research and Education Workshop

The workshop will take place at Delta centre during May 21-22, 2020

BREW is a workshop for PhD students in bioinformatics, which aims to give an introduction to scientific conferences, including submission, peer review and presentation of scientific papers. All participants must submit a paper and take part in reviewing papers from other participants in order to attend the workshop. After the review deadline, students have a chance to make alterations to their paper and deliver a final version. All participants will present their paper at the conference-style meeting.

BREW is open for students and supervisors from the PhD programs in Bioinformatics and Computational Biology in participating universities. For particular details, please contact the organizers via email.

The workshop is free of charge, and will include lunch, snacks and a social evening. Accomodation is paid for by the local organizing committee. More details are available on the corresponding page.

Registration by March 1, 2020

More info at https://brew2020.cs.ut.ee/index.php

EMBO practical course in population genomics in Italy

ELIXIR-IIB is pleased to announce the fourth edition of the EMBO practical course in population genomics, this year there will be added emphasis on programming and machine learning applied to population genomics.

https://elixir-iib-training.github.io/website/2020/04/01/population-genomics-procida.html

Registration deadline is 28 January 2020

This EMBO Practical Course will cover coalescent theory, the effect of demography in space and time, genetic clustering, the detection and quantification of admixture and selection. Lectures on these topics will be complemented by hands-on computer practicals introducing a wide range of software packages, both in R and Python.

This course is aimed at evolutionary biologists who already have basic bioinformatics skills. The main criterion for selection will be how much a candidate can benefit from the course. This implies that PhD students and Postdoc researchers will likely be favoured; however, applications from candidates at all levels will be considered.

Fellowships to cover travel expenses and for childcare are available.

ELIXIR Weekly News 13.01.2020

ELIXIR Spain will be hosting ECCB 2020 in Sitges, near Barcelona 5 - 9 September 2020. Please note the deadline for the call for workshops/SIG applications and tutorial applications is 30 January

publication on “Data Stewardship Wizard” has been released in the Data Science Journal. The Data Stewardship Wizard is a tool for data management focusing on getting the most value out of data management planning.

The Galaxy Machine Learning workbench is now available in Galaxy and provides you with the a Swiss Army knife of scikit-learnKeras (a deep learning library based on TensorFlow) and various other tools to manipulate, convert and plot your data.

 

 

Weekly news 16.12.2019

The last Gallantries Project face-to-face meeting took place at INAB | CERTH, Thessaloniki, Greece 9-10 December. During this meeting the R and RStudio lessons within Galaxy were refactored, along with a pop-up course on making volcano plots in R. Helena Rache put out a blog-post on this, and materials were shared by the Galaxy twitter channel.

ELIXIR-CZ have created a very engaging animated video all about ELIXIR and the Czech Node. Features FAIR data and ELIXIR AAI. Well worth a watch! 

ELIXIR Finland has published a new article about ELIXIR Compute Platform for life and health sciences. Read to find out about how the Compute Platform has helped research across multiple ELIXIR Communities. 

The Dutch Techcentre for Life Sciences (DTL) have released their 2019 highlights newsletter. Read on to find out about their activities with ELIXIR and beyond. 

FAIRplus Innovation and SME Forum: Implementing FAIR data principles in industrial life science research
29 January 2020 | Hinxton, Cambridge, UK

Innovation and SME Forum: Data Driven Innovation in the Agritech Sector
24 -25 March 2020 | Lyon, France

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