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Summer school in bioinformatics

 

European Bioinformatics Institute United Kingdom in association with Elixir Estonia are organising summer school in bioinformatics. This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research.

Participants will initially be introduced to bioinformatics theory and practice, including best practices for undertaking bioinformatics analysis, data management, and reproducibility. To enable specific exploration of resources in their particular field of interest, participants will then be divided into focused groups to work on a project.

Participants will be required to review some pre-recorded material prior to the start of the course.

Information about the summer school

Date: 12 - 16 June 2023

Application deadline: 05 March 2023

Cost: £825.00 inclusive of four nights accommodation and catering, including dinner

Participant limit: Open application with selection 30 places

More info: https://www.ebi.ac.uk/training/events/summer-school-bioinformatics-0/

Group projects:

  • Genome variation across human populations 
  • Interpreting functional information from large scale protein structure data
  • Modelling cell signalling pathways
  • Networks and pathways
  • Reusing FAIR Bioimage data: an AI application

Who is this course for?

Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their knowledge and skills further. No previous knowledge of programming is required for this course; group projects may give you the opportunity to learn basic programming, but participants will be supported in this by their mentors. Depending on your chosen project, an introductory programming tutorial may be given as homework prior to attending the course.

Learning outcomes

  • After this course you should be able to:
  • Discuss applications of bioinformatics in biological research
  • Browse, search, and retrieve biological data from public repositories
  • Use appropriate bioinformatics tools to explore biological data
  • Describe ways that biological data can be stored, organised and integrated
  • 2 min read

Past Training

2023

 

2022

2021

2020

2019

2018

  • 1 min read

Galaxy Smörgåsbord 2023

Galaxy Smörgåsbord is coming again! The next edition of the GTN Smörgåsbord training event will take place on May 22-26, 2023! 


It will once again be free, online, self-paced, and choose-your-own-adventure style. It will feature all the content of previous editions, plus lots more!


The preliminary program can be found on the course website.  (Several modules are still in development, so check back regularly for the updated program!) 

Registration is now open!

 

 

Data Visualisation I - Figures - 18.04.2023

Due to high demand, on the 4th of April 2023, ELIXIR-Estonia will hold a repeat data management online course: Data Visualization I - Figures. The course will be held in English. 

All researchers will be handling some data at some point in their careers. However, the data, in its regular shape (tables), is quite hard to grasp for most people. Especially if there is a lot of it, this is where data visualization comes to help. The idea is to bring forth the essential aspects of the data - to tell a story. However, just putting data into a graph or figure might do more harm than good. Not only could it give wrong conclusions, but it also might be misleading. This is one of the main reasons why the exact way how you visualize the data is fundamental. 

This lecture is part of a series of lectures and workshops called “Data visualisation.” The first lecture will discuss why data visualisation is important and what we should consider when designing it. This means what chart type to pick, how much information to include, what (and how) to highlight, and so on. This lecture will be followed up by a workshop in May. 

 

Information about the lecture

Date: 18.04.2023

Language: English

Time: 10:00-12:00

Place: Zoom, the link will be sent a couple of days before the lecture

Registration is closed

 

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

 

Learning outcomes for the participants: 

  • Understands how to tell a story through data visualization
  • Knows what chart type to pick for different kinds of data
  • Knows what to pay attention to while designing a figure

Basic LINUX/Unix workshop - 3.03.2023

On the 3rd of March 2023, ELIXIR-Estonia will be organising a face-to-face data management course in English: Basic LINUX/Unix workshop.

This course is aimed to provide basic survival skills in Linux and the 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.​

No prior knowledge is expected. 

 

Information about the lecture

Date: 3.03.2023

Time: 11:00 - 16:00  (lunch break 13:00-14:00)

City: Tallinn 

Place: Akadeemia tee 23 ROOM 109

Requirements: Bring your own laptop and please follow the setup tutorial: https://elixirestonia.github.io/2021-09-28-shell-novice/setup.html 

 

Registration is closed.

 

In order to not miss out a course next time, subscribe to our newsletter at https://lists.ut.ee/wws/subscribe/elixir.news?previous_action=edit_list_request 

 

Learning outcomes:

  • 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.
  • Tips and tricks for effective command line hacks that would save a lot of time.

Bring your own DMP workshop

According to the Estonian Research Council funding agreement, all the projects that have started from 2022 have to submit a data management plan (DMP) within the first 6 months. Since this will be a new thing for a lot of researchers,  ELIXIR Estonia will be doing a data management writing course for this purpose. This workshop is part of a bigger data management course package aimed at DMP writers.

 “Bring your own DMP workshop” workshop (in English) will be a follow-up to “Open Science and DMP in Estonia” lecture. The face-to-face writing sessions will be held both in Tartu and in Tallinn. In case you need any help with the writing of the DMP part, the 7th of March 2023 (14:00-17:00) session will be held in Tartu and the 16th of March (13:00-16:00) session will be held at Tallinn. 

During the workshop, we will be talking about the theory of different aspects of the DMP and giving more practical advice.  There will be 3-4 30min writing sessions, where you can write most of your DMP. Also, if you have any questions, the organizer will help you as best as they can. 

In case of questions, you can contact ELIXIR Estonia (elixir@ut.ee). 

 

Information about the lecture in Tartu

Date: 7.03.2023

Language: English

Time: 14:00-17:00

Place: Delta, Narva mnt 18 ROOM 1006

Register: the registration is closed

 

Information about the lecture in Tallinn

Date: 16.03.2023

Language: English

Time: 13:00-16:00

Place: Rävala pst 10, 6th floor conference room

Register: the registration is closed

 

We ask you to register responsibly. If you can't attend the lecture, please let us know as soon as possible via email (elixir@ut.ee). 

 

In order to not miss out a course next time, subscribe to our newsletter at https://lists.ut.ee/wws/subscribe/elixir.news?previous_action=edit_list_request 

 

Learning outcomes: 

  • Knows how to write a DMP
  • Knows where to get more information about data management

 

Useful materials: 

Data Visualisation I - Figures - 4.04.2023

On the 4th of April 2023, ELIXIR-Estonia will hold a data management online course: Data Visualization I - Figures. The course will be held in English. 

All researchers will be handling some data at some point in their careers. However, the data, in its regular shape (tables), is quite hard to grasp for most people. Especially if there is a lot of it, this is where data visualization comes to help. The idea is to bring forth the essential aspects of the data - to tell a story. However, just putting data into a graph or figure might do more harm than good. Not only could it give wrong conclusions, but it also might be misleading. This is one of the main reasons why the exact way how you visualize the data is fundamental. 

This lecture is part of a series of lectures and workshops called “Data visualisation.” The first lecture will discuss why data visualisation is important and what we should consider when designing it. This means what chart type to pick, how much information to include, what (and how) to highlight, and so on. This lecture will be followed up by a workshop in May. 

 

Information about the lecture

Date: 4.04.2023

Language: English

Time: 10:00-12:00

Place: Zoom, the link will be sent a couple of days before the lecture

Register: registration is closed

 

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

 

Learning outcomes for the participants: 

  • Understands how to tell a story through data visualization
  • Knows what chart type to pick for different kinds of data
  • Knows what to pay attention to while designing a figure

Data Visualisation I - Figures workshop - 2.05.2023

“Data Visualisation I - Figures workshop” will be a follow-up to “Data Visualisation I - Figures” lecture. During the face-to-face workshop held in English we will do data visualisation using ggplot2 and Tableau. We will compare the user experience and the aesthetics of the results of both visualisation options. We will also put to use our knowledge of good practices in data visualisation we learned in the lecture.

 

Information about the lecture

Date: 2.05.2023

Language: English

Time: 14:00-17:00

City: Tartu 

Place: Delta, Narva mnt 18 ROOM 1005

 

Registration closed.

 

Bring your own laptop!

 

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

 

In order to not miss out a course next time, subscribe to our newsletter at https://lists.ut.ee/wws/subscribe/elixir.news?previous_action=edit_list_request 

 

Learning outcomes for the participants: 

  • Knows what chart type to pick for different kinds of data
  • Knows what to pay attention to while designing a figure
  • Knows how to compare user experience with ggplot2 and Tableau
  • Knows how to make informative and visually appealing figures in ggplot2
  • Knows how to make informative and visually appealing figures in Tableau

FAIR in a Nutshell - 16.02.2023

On the 16th of February 2023, ELIXIR-Estonia will be holding an online data management course in English: FAIR in a Nutshell. This lecture will be a short overview of the FAIR principles and is part of a bigger data management course package aimed at DMP writers and grant applicants.

In recent years, more attention has been put on what researchers do with the data they produce. Especially in Europe (think GDPR), but also everywhere else. The main idea is that when researchers use taxpayers' money, the taxpayers themselves should also have access to the results free of charge. This means that the research should be published in open-access journals, and data should be made publicly available.

Good data management helps to make the whole process of making data reusable easier. In general, you should think about how to manage your data at the beginning and during the project and know what you plan to do with it at the end of the project. However, what is “good data management” exactly is up for debate. The FAIR Principles concentrate on making your data findable, accessible, interoperable and reusable, so this is a good start. And let’s be honest, some of these things you probably are already doing.

In this course, we will be going over all the FAIR Principles and how they are applied in real life. This way, you will already know what to consider while writing a grant, filling out your data management plan or doing your research.

 

Information about the lecture

Date: 16.02.2023

Language: English

Time: 10:00 - 12:00

Place: Zoom, link will be sent a couple of days before the lecture

 

We ask you to register responsibly. If you can't attend the lecture, please let us know as soon as possible via email (elixir@ut.ee).

 

Register: closed

 

In order to not miss out a course next time, subscribe to our newsletter at  https://lists.ut.ee/wws/subscribe/elixir.news?previous_action=edit_list_request

 

Learning outcomes:

  • Understands the importance of a good data management
  • Knows what are the FAIR principles and what they mean
  • Knows how to implement FAIR principles throughout the research project
  • Knows where to get more information about the FAIR Principles