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GTN Smörgåsbord: A Global Galaxy Course, February 15-19 2021

 

For Estonian scientists the most important facts are:

  • https://galaxy.hpc.ut.ee/ will ensure that all the tools covered during the course will be available afterwards at the local instance
  • If you register to the Global Galaxy Course, please notify the UT Galaxy team (galaxy@hpc.ut.ee) as well, so you would be informed about future Galaxy events and local developments among the first ones.
  • Also, in case you have not used UT Galaxy instance at https://galaxy.hpc.ut.ee before, then please include your UT username (in case you have it) to the email above (galaxy@hpc.ut.ee) so your local Galaxy account can be created.


Galaxy Training event showcasing a wide variety of GTN (Galaxy Training Network) tutorials. This will be an online event, spanning all time zones. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers will be available via online support to answer all your questions.

The program covers a general introduction to the Galaxy platform, NGS Analysis (DNA-seq and RNA-seq), Proteomics, and also features a Choose your own adventure day on Friday, where we encourage you to explore all the tutorials that the GTN training repository has to offer, and follow those that are of interest to you. The GTN tutorials cover a wide range of scientific topics, from NGS to ecology, climate science, machine learning, visualization, and many more. All the tutorials can be found on the GTN website

When: February 15-19, 2021 (all time zones)
Who: Open for everybody
Cost: Free
Format: Virtual event, all training session are pre-recorded, you can work through these at your own pace, with instructors available online for support
Support: Slack Channel (link will be provided here before the course)
Organized by: The Galaxy Training Network (GTN), CINECA, The Galaxy Project, Australian BioCommons, Erasmus Medical Center, Albert-Ludwigs-Universität Freiburg, Avans Hogeschool, The Gallantries Project, The GalaxyP Team, The ProteoRE Team, INAB-CERTH, EMBL-EBI, Institute of Surgical Pathology - University Medical Center Freiburg.

More info and registration is available at https://shiltemann.github.io/global-galaxy-course/. 

Do not miss the great opportunity!

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We launched ELIXIR TeSS Club

ELIXIR Training eSupport System TeSS had its kick off meeting on October 23rd.

ELIXIR TeSS club brings together all parties interested in further developing TeSS further.
The group gathered for the first time on 23 October and will take place biweekly on Fridays betwen 10–11 CET.

The next meeting will be on 6 November to discuss the prioritisation of tasks for 2021.

ELIXIR Estonia is one of the Nodes helping to develop TeSS further.

 

 

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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.

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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 Advanced Training courses March 17 and 20

Unix Shell Advanced Courses 17th and 20th of March 2020, 10.15-14.00, Delta #2005

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

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.

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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.

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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/