News and announcements

Weekly News 14.09.2020

COVID-19 Viral Beacon

A beacon in the ocean of SARS-CoV-2 data

The COVID-1 Viral Beacon is an ELIXIR Spain platform that allows researchers to browse SARS-CoV-2 variability at the genome, amino acid, structural and motif level
Bioinformaticians from the Center for Genomic Regulation (CRG) have built this time-saving tool with an extremely friendly interface. 

More information at https://elixir-europe.org/news/beacon-ocean-sars-cov-2-data 

 

Online X-omics festival "The future is now!"

28 September 2020 | 9:30 - 14:00 (CEST)

If you are a researcher working in -omics (genomics, proteomics, metabolomics) and / or deal with data analysis, integration & stewardship join the online X-omics festival. Read more on the event website.

Unix Shell Advanced Training courses on March 17th and 20th - POSTPONED TO UNFORESEEN FUTURE

WE HAVE POSTPONED THE COURSES TO UNFORESEEN FUTURE.

Advanced computing power is hidden away in clouds/cluster/supercomputers that you do not have click and point access. As a general rule these high performance computer resources use Linux operating systems and are accessible only by a shell terminal.

This course is aimed to streamline your skills in Linux and terminal environment. We will teach you how to make your life easier by creating maintainable and flexible bash scripts for your commonly used workflows or SLURM jobs.

Objectives:

  • Learn how to iterate operations over many input files with bash loops and conditions.
  • Learn how to combine complicated command line based workflows into maintainable bash scripts.
  • Add additional useful utility functions and tools to your toolbox.

Expected prior knowledge:
Experience in using the basic commands covered in the Basics course (e.g. cd, ls, mkdir, mv, cp, head, cat, find, less, pwd).

Requirements:
Lecture venue is computer class with linux computers. In case you bring your own Windows laptop, please make sure to install Putty application (https://www.putty.org/) beforehand.

Materials:
https://elixirestonia.github.io/2020-03-17-tartu/

Registration:
Application is open at https://forms.gle/pzWrKDNcxpStEADk8

Time:
March 17, 2020
10:15–14:00

March 20, 2020
10:15–14:00

 

Venue:
Auditorium 2005 (the Linux classroom)
UT Delta Centre
Narva mnt 18
51009 Tartu
Estonia

Unix Shell Basics training course March 3rd

Advanced computing power is hidden away in clouds/cluster/supercomputers that you do not have click and point access. As a general rule these high performance computer resources use Linux operating systems and are accessible only by a shell terminal.

This course is aimed to provide basic survival skills in Linux and terminal environment. We will teach you how to access files and folders, move around and hopefully shake off the fear of getting stuck somewhere along the way.

Objectives:

  • Obtain basic knowledge on dealing with files using command line (Linux or Mac)
  • Learn how to use search over several text files, combine files, extract certain knowledge.
  • Master tips and tricks for effective command line hacks that would save a lot of time.

Requirements:
Lecture venue is computer class with linux computers. In case you bring your own Windows laptop, please make sure to install Putty application (https://www.putty.org/) beforehand.

Materials:
https://elixirestonia.github.io/2020-03-03-tartu/

Registration:
The course is full!

Time:
March 3, 2020
10:15–14:00

Venue:
Auditorium 2005 (the Linux classroom)
UT Delta Centre
Narva mnt 18
51009 Tartu
Estonia

NB! Two weeks later we will run an Unix Shell Advanced course for people who have already basic knowledge.

Estonia Joined the Nordic e-Infrastructure Collaboration Initiative

On February 11th Estonia joined the Nordic e-Infrastructure Collaboration NeIC by signing the collaboration agreement at the Delta Centre in Tartu. This agreement gives Estonian research infrastructures the possibility to maintain and enhance their competitiveness and do more international cooperation.

The agreement was signed by Arne Flåøyen, Director for NordForsk, an institution  that facilitates and provides funding for cooperation on research across the Nordic region, and Andres Koppel, the chairman of the board of the Estonian Research Council.

More information is available at 

https://www.etag.ee/en/estonia-joined-the-nordic-e-infrastructure-collaboration-initiative/

https://neic.no/news/2020/01/09/estonia-joins-neic/

 

 

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

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