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workshop

Course at Bern, Switzerland: NGS - Genome Variant Analysis

The detection of genetic variation is of major interest in various disciplines spanning from ecology and evolution research to inherited disease discovery and precision oncology. Next generation sequencing (NGS) methods are very powerful for the detection of genomic variants. Thanks to its throughput and cost-efficiency it enables the detection of a large number of variants in a large number of samples. In this two-day course we will cover the steps from read alignment to variant calling and annotation. We will mainly focus on the detection of germline mutations by following the GATK best practices.

Application deadline: 15 February 2024

More Info and Registration

Course at Breda, The Netherlands: RNA-seq data analysis

The 9th edition of the RNA-seq Data Analysis course will be held on 8-12 April – 2024 in Breda, The Netherlands. This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux and R practicals. Also the potential of long-read based RNA-seq and AI based analysis enrichments will be explored.

More Info and Registration

Course at Bern, Switzerland: Single-Cell Transcriptomics with R

Single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression at the single cell level. For example, scRNAseq can help to identify expression patterns that differ between conditions within a cell-type. To generate and analyze scRNAseq data, several methods are available, all with their strengths and weaknesses depending on the researchers’ needs. This 3-day course will cover the main technologies as well as the main aspects to consider while designing a scRNAseq experiment. In addition, it will cover the theoretical background of analysis methods with hands-on practical data analysis sessions applied to droplet-based methods.

Application deadline: 06 March 2024

More Info and Registration

How to make your messy data usable? / OpenRefine - 30.11.2023

  • Time: 30.11.2023 13:00-17:00
  • Type: Workshop
  • Language: English
  • Duration: 4h
  • Location: Delta building, Narva mnt 18 room 1008, Tartu
  • Audience: People, who need to clean messy data
  • Instructor: Diana Pilvar, MSc

The practical workshop on cleaning your messy data with OpenRefine software.

First, we will cover spreadsheet best practices. Then, we will put that knowledge into practice with OpenRefine. This course will explore the depths of OpenRefine software and see what it can offer. This will include cleaning the data in bigger batches and unifying the data in one sweep (transforms and expressions). Additionally, we will introduce the possibility of downloading additional data from other databases and different extensions OpenRefine software has.

Learning outcomes for the participants: 

  • Describe spreadsheet best practices
  • Compare Excel and OpenRefine
  • Apply transforms (cell editing, column editing, transposing) in OpenRefine
  • Write simple expressions in OpenRefine
  • Match your dataset with that of an external source 

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 on a course next time, subscribe to our newsletter at  https://lists.ut.ee/wws/subscribe/elixir.news?previous_action=edit_list_request
Applications are accepted manually within a few days. 

Version Control with Git - RStudio - 5.12.2023 - registration open

  • Time: 5.12.2023 11:00-16:00 
  • Type: Workshop
  • Language: English
  • Duration: 5h
  • Location: Delta building, Narva mnt 18 room 2005, Tartu
  • Audience: Everyone who needs versioning
  • Instructor: Priit Adler, PhD

Version control serves as the digital equivalent of a lab notebook. It is employed by professionals to monitor their progress and collaborate effectively. Its utility extends beyond software development; it can be used for books, papers, small datasets, or any evolving content that requires sharing.

Git is a globally adopted tool that helps developers manage changes in collaborative projects. Keeping a record of changes, complete with timestamps and explanations, becomes exceptionally valuable when returning to a project in the future, like a year later when recollection may be unclear.
 

Learning outcomes for the participants: 

  • Describe the importance of version control
  • Create a repository in Git
  • Track changes and collaborate in Git
  • Solve conflicts in Git

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: https://forms.gle/QnPtaoWXJevLnhJi8

In order to not miss out on a course next time, subscribe to our newsletter at  https://lists.ut.ee/wws/subscribe/elixir.news?previous_action=edit_list_request
Applications are accepted manually within a few days. 

Version Control with Git - 25.05.2023

On the 25th of May 2023, ELIXIR-Estonia will be organizing a face-to-face data carpentry course in English: Version Control with Git.

Git is used across the world to help developers keep track of changes while working on different parts of the same project. Teams are not the only ones to benefit from version control: lone researchers can benefit immensely. Keeping a record of what was changed, when, and why is extremely useful for all researchers if they ever need to come back to the project later on (e.g., a year later, when memory has faded).

Version control is the lab notebook of the digital world: it’s what professionals use to keep track of what they’ve done and to collaborate with other people. Every large software development project relies on it, and most programmers use it for their small jobs as well. And it isn’t just for software: books, papers, small data sets, and anything that changes over time or needs to be shared can and should be stored in a version control system.

 

Information about the lecture

Date: 25.05.2023

Time: 11:00 - 17:00  (lunch break 12:30-13:30, coffee break 15:00)

City: Tartu

Place: Delta, Narva mnt 18 ROOM 2048

Requirements: Bring your own laptop and install git: https://git-scm.com/downloads

Register:  the registration is closed

 Prerequisites: In this lesson we use Git from the Unix Shell. Some previous experience with the shell is expected, but isn’t mandatory.

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:

  • Know how to do version control and why it’s important
  • Know how to set up and create a repository in Git
  • Know how to track changes and collaborate in Git
  • Know how to solve conflicts in Git

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: 

Spring semester ELIXIR courses

ELIXIR Estonia is continuing with the data management-related lectures and workshops this semester. To get more information about these courses, read below and visit https://elixir.ut.ee/training.  

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.