News and announcements

The FAIR Principles lecture - (registration closed)

Submitted by Heleri on

On the 31st of January, 2022, ELIXIR-Estonia will be holding an online data management course: The FAIR Principles. This lecture will be a short overview about the principles and is part of a bigger data management course package.

In recent years, more attention is put on what researchers do with the data (and other resources) they produce. Especially in Europe, 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 may help you with that, at least to make the process easier on the whole. If you think “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, the process at the end will be easier. However, what is “good data management”, is up to debate. The FAIR Principles concentrates 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 are probably 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: 31.01.2022 

Language: English

Time: 10:15 - 13:45

Place: Zoom, link will be sent 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: the registration is closed

Registration closes at 23:59 on 24.01.2022 or when the course gets full. A confirmation email wil be sent on the 25th of January, 2022. 

NB! Since this course is popular, we have added another session of the lecture, on 2nd of February, 2022. 

Register: the 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_...

 

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

Tags: 

FAIR principles in life science research practice online seminar

Submitted by elixir on

An online seminar on FAIR principles in life science research practice by ELIXIR Sweden and ELIXIR Neatherlands takes place on December 9th, 2021. The event is held in zoom, with pre-registration required.

This online workshop will showcase how to put the FAIR principles into practice and is specifically designed to cater to life science researchers at all career stages. It is organised by SciLifeLab Data Centre and NBIS and include international speakers, presenters from the SciLifeLab community and optional hands-on exercises guided by experts from NBIS and SciLifeLab Data Centre. 

More info at https://www.scilifelab.se/event/fair-principles-in-life-science-research-practice/

ETAIS & ELIXIR seminar UT HPC Usage 101 18.11.2021

Submitted by elixir on

During this UT HPC Usage 101 lecture course we will provide the participants basic knowledge required to use to submit, monitor, and control jobs on the compute nodes of UT HPC. We will talk about the principles of computing in a cluster and the difference between computing directly from the command line of a private server. We will introduce the good practices and standards of behavior that good cluster usage practice requires. Also the convenient graphical tools for monitoring the resource of your work will be covered. Finally, we might touch on the basic Slurm commands.

We expect the users to have basic LINUX command line experience, but very little or no cluster compute experience yet.

Learning outcome:
Knowing how to submit, monitor and control jobs at UT HPC.

The seminar will take place in Zoom on 18th of November 2021 at 14.00 and will last approximately 90 minutes. The seminar will not be recorded.

Registration is open at https://forms.gle/pVe86HVqjWB6GpLg8 and will close on 16th of November or when the course gets full. 

The seminar is held in English by Ulvi Gerst Talas and Ott Eric Oopkaup from UT HPC/ETAIS.

 

 

Tags: 

How to make your messy data usable? (registration closed)

Submitted by Heleri on

On the 25th of November 2021, ELIXIR-Estonia will be holding a new data management online course: How to make your messy data usable. The course will be held in English. This course will be in two parts: an 1 hour online lecture on what makes a data table usable for other people held on 25th of November at 13:00 in Zoom. The practical workshop on cleaning your messy data with OpenRefine software will be a video lecture that you can follow in your own time. Additionally, we will hold 3 Q&A sessions in Zoom, where you can talk about any problems you encountered with the OpenRefine software.

 

More attention is put on what researchers do with the data (and other resources) they produce in recent years, especially in Europe, also in everywhere else. Since most of your data needs to be uploaded to a repository, it is essential that the data is tidy and other people understand and can easily read your data.  

In this course, we will be going over how to name your files and variables, version control, compile a data dictionary, and what to do with empty cells. In the second part, OpenRefine software is introduced. With this, you can easily clean up the messy data. For the more practical aspect of using the OpenRefine software, I will share a video that will teach the basics. You can watch it anytime and do the lessons yourself. On three days (29.11, 30.11 and 1.12) there will be a 1h slot (11:00-12:00) on Zoom, when you can come and ask any question you have regarding tables and OpenRefine software. 

 

Information about the lecture

Lecture: 25th of November, 2021 at 13:00 (lecture, 1h)

Q&A session: 29.11, 30.11 and 1.12 at 11:00 (Q&A, feedback, 1h)

Place: ZOOM (link will be sent to your email)

Register: registration closed

Registration closes at 23:59 on 24.11.2021 or when the course gets full.

Materials: https://doi.org/10.5281/zenodo.5720271 

 

Learning outcomes: 

  • Compile a data table that abides by the FAIR Principles
  • Recognize what a clean table for others to use looks like
  • Explain how to use OpenRefine to clean the messy data

Tags: 

ELIXIR Nextflow course 22.-23.11.2021 Tartu

Submitted by elixir on

Overview

Nextflow is a powerful polyglot workflow language that provides a robust, scalable and reproducible way to run computational pipelines. In very practical and interactive sessions, participants will learn about Nextflow technology starting from basic through more advanced concepts, with the expectation they will acquire the proficiency to develop and deploy their own workflows.

This 2-day course will train participants to build Nextflow pipelines and run them. It is designed to provide participants with short and frequent hands-on sessions, while keeping theoretical sessions to a minimum.

A GitHub repository will be provided with all the necessary material and software installation guidelines.

Audience

This hands-on course is designed for absolute beginners who want to start using Nextflow to achieve reproducibility of data analysis. 

Learning outcomes

At the end of the course, participants are expected to be able to:

  • Develop a Nextflow pipeline from scratch.
  • Describe and explain Nextflow's basic concepts.
  • Implement short blocks of code into a Nextflow pipeline.
  • Execute/Run a Nextflow pipeline.
  • Test and modify a Nextflow pipeline.
  • Locate and fetch Nextflow pipelines from dedicated repositories.
  • Run a pipeline in diverse computational environments (local, HPC, cloud).
  • Share a pipeline.

Prerequisites

Knowledge / competencies

Applicants should be comfortable working with the CLI (command-line interface) in a Linux-based environment. If you do not feel comfortable with UNIX commands, you can refresh your knowledge with the UNIX Shell course materials here.

Participants will need to connect during the course to a remote server via the "ssh" protocol. You can learn how does ssh work in here.

Participants should be able to use a command-line/screen-oriented text editor (such as nano or vi/vim, which are already available in the server) or to be able to use an editor able to connect remotely. Instructor will be using VS Code with SSH extension, it is recommended to use the same text editor for ease of comparison. 

Knowledge of containers is not mandatory; however, recommended. 

Participants are preferred to bring their own laptop but also local Linux computers can be used (please let us know about it during the registration). They will work in their local machine to learn the basics and develop their very first pipeline. They will also work in a dedicated UT HPC environment in order to learn running pipelines in different computation environments. 

Schedule

22.11.2021 Day 1: Introduction to Nextflow. Learning the building blocks

23.11.2021 Day 2: Understand, develop and run a basic Nextflow pipeline

The course runs from 10.15-18.00.

Registration

Please register responsively. Due to COVID-19 situation we accept only fully vaccinated persons who must bring and show the vaccination certificate AND take a rapid antigen test before the course starts during Day 1 (9.30 on Monday 22.11.2021). We accept up to 12 people for the course based on the data submitted to the registration form.

This course description is adapted from SIB Nextflow course page.

 

Pages