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ELIXIR Estonia

Heleri and Diana Participated in the Estonian Research Council Event on Science Communication

ELIXIR Estonia is delighted to share that our Data Managers, Heleri and Diana, recently attended the Estonian Research Council’s event, “Teaduskommunikatsiooni järelkasv: kust tulevad ja kuhu kaovad teaduskommunikaatorid?” (“The Future of Science Communication: Where Do Communicators Come From and Where Do They Go?”).

Citizen Science Seminar Highlights the Need for Collaboration in Estonia

On October 15, citizen science enthusiasts, researchers, and representatives from various institutions gathered in Tartu for a seminar on advancing citizen science in Estonia. The Estonian Research Council hosted the event and attracted participants from universities, museums, government agencies, and beyond. The seminar fostered active discussions and collaboration, emphasising the importance of building and maintaining a strong network to support citizen science initiatives in the country.

Diana, ELIXIR Estonia Training coordinator, attended the ENLIGHT Teaching and Learning Conference “Innovation and Creativity in Higher Education”

The fourth ENLIGHT Teaching and Learning Conference, which was held at the University of Tartu from 7 to 9 October 2024, was themed “Innovation and Creativity in Higher Education.” Our training coordinator, Diana, attended the conference to learn about student-oriented teaching methods.

BY-COVID project wrap-up and success stories

The BeYond-COVID (BY-COVID) project aimed to provide extensive open data on SARS-CoV-2 and other infectious diseases, emphasizing the mobilization of raw viral sequences to monitor the spread of variants. To ensure global collaboration, it enabled federated data analysis, managed metadata, and facilitated long-term cataloguing. Success stories can be read here, on page 16 is project lead by University of Tartu: Infectious Diseases Toolkit.

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

Software carpentry 17.-18.01.2019

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Seminar room Kodavere, University of Tartu Library (W. Struve 1), Tartu. 

When: Jan 17-18, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Reference...

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...

Contact: Please email laura.altin@ut.ee for more information.

See https://elixirestonia.github.io/2019-01-17-tartu-NeIC for more information.

Register here https://goo.gl/forms/84EdtRsalQ6zayHu1