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University of Tartu

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.

Boost your Bioinformatics Backchat

Boost your Bioinformatics Backchat

Facilitating communication between individuals from different academic backgrounds in the bioinformatics space





Date: 17 December 2018

Time: 9:30-14:45 

Venue: University of Tartu, Estonia, Paabel (Ülikooli 17) 115/116

Trainer: Kim Gurwitz, University of Cambridge

ELIXIR ESFRI 5y Celebration Week


Audience: Biologists and Computer Scientists (and others) working in the field of Bioinformatics - maximum 14 participants. Registration is available here


This workshop aims to:

- enable workshop participants to develop an understanding of what the other bioinformatics subgroups actually do

- act as a springboard to improve communication between Bioinformatics subgroups (i.e. Biologists and Computer Scientists)

- facilitate the development of a culture of knowledge-sharing between Bioinformatics subgroups



Time (EET)


9:30 - 10:00


10:00 – 10:10


10:10 – 10:30

What do Biologists and Computer Scientists do?  No seriously, what do they really do?

10:30 – 10:45

How did you get into Bioinformatics, anyway?

10:45 – 11:15

tea/coffee break

11:15 – 11:45

What is a cluster? What is DNA?

11:45 – 12:00

Bioinformatics users vs. scientists vs. engineers

12:00 – 12:15

Opening up dialogue

12:15 – 13:15


13:15 – 13:30

Continuing dialogue

13:30 – 14:00

Action plan write up and commitments

14:00 – 14:15

Action plan feedback

14:15 – 14:30

Workshop reflections



*subject to slight changes

Mini workshop about data management 13th December 2018

Most researchers know that data management is an important part of their work and is essential for getting the most out of your data. But what exactly is data management and what can you do to ensure that you’re managing your data well?

In this mini workshop you will learn what to consider when managing life science data and gain hints and tips for submitting your data to a public resource.

Dr. Melissa Burke and Dr. Sarah Morgan from EMBL-EBI training team (see more about them) will share best practicies, trips and tricks about managing your scientific data.

Registration and participation is free of charge. Up to 20 participants can take part. Please register here.

The workshop will take place at Ülikooli 17 (Paabel) on 13th of December at 9:30–12:30.



ELIXIR Info day 14.12.2018 Tartu

ELIXIR Estonia celebrates 5 years of ELIXIR with a series of events.

The major event is ELIXIR Information Day that takes place on 14th of December 2018 at Hotel Lydia Conference Center in Tartu. The day starts with welcoming coffee at 9am and finishes with drinks session around 4pm.

The event is free of charge for all registered participants.

The info day will give researchers from academia and industry, funders, decision makers and wider public an overview what ELIXIR is how it serves the scientific community.

Presenters include: Dr. Mateusz Kuzak (DTL; ELIXIR-Neatherlands), Dr. Ilkka Lappalainen (CSC; ELIXIR-Finland), Dr. Sarah Morgan (EMBL-EBI), Dr. Ulvi Gerst-Talas (TÜ; ELIXIR-Estonia; ETAIS), Dr. Hedi Peterson (TÜ; ELIXIR-Estonia), Prof. Jaak Vilo (TÜ; ELIXIR-Estonia). Learn more about the presenters here.

The purpose of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society.

These resources include databases, software tools, training materials, cloud storage and supercomputers.

The goal of ELIXIR is to coordinate these resources so that they form a single high quality infrastructure. This coordinated infrastructure makes it easier for researchers to find and share dataanalyse their experimentsexchange knowledge, and agree on best practices.

Estonian ELIXIR Node
The Estonian node focuses on developing and maintaining software tools and databaseslinking of bioinformatics and biobanking, and last but not least, training researchers across borders.

ELIXIR Information Day is a day full of opportunities to learn how ELIXIR can be beneficial to researchers' every day task. 

Registration is open - Registration deadline December 9th, 11.59pm

Schedule for the Information Day

09.30 - 10.00 Welcoming coffee
10.00 - 10.30 Prof. Jaak Vilo, ELIXIR Estonia Head of Node - “How ELIXIR helps the life science community”
10.30 - 11.00 Dr. Ilkka Lappalainen, ELIXIR Finland  - “What it takes to handle sensitive human data - Finnish and European experience”
11.00 - 11.30 Coffee and discussions
11.30 - 12.00 Dr. Hedi Peterson, ELIXIR Estonia - “Small but important - Estonian contributions to life science infrastructure”
12.00 - 12.30 Dr. Sarah Morgan, ELIXIR EMBL-EBI - “Improving European life science by providing world class trainings in physical and virtual class rooms”
12.30 - 14.00 Lunch
14.00 - 14.30 Dr. Ulvi Talas, ETAIS and ELIXIR Estonia - “Interaction of infrastructures - making scientific computing easier for life scientists in Estonia”
14.30 - 15.00 Dr. Mateusz Kuzak, ELIXIR-Netherlands "Training life science researchers in foundational coding and data science skills in the Netherlands and ELIXIR.”
15.00 - Closing remarks followed by apéro

The accompanying events include:

Data carpentry workshop

Data Carpentry workshops are mainly meant for researchers with no or very little programming experience who have data they want to analyze. This hands-on workshop teaches basic concepts, skills and tools (including basic programming) for working more effectively with data.

We will cover Data organization in spreadsheets and OpenRefine, Introduction to R, Data analysis and visualization in R. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.


- Dmytro Fishman, Assistant of Data Science, Bioinformatics/Machine Learning, University of Tartu

- Liis Kolberg, PhD student, Bioinformatics/Statistics, Institute of Computer Science, University of Tartu

- Priit Adler, Research Fellow of Bioinformatics, Bioinformatics, Institute of Computer Science, University of Tartu

Registration and participation is free of charge