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2021

  • 1 min read

FAIR principles in life science research practice online seminar

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

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.

 

 

  • 2 min read

ELIXIR Nextflow course 22.-23.11.2021 Tartu

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.

 

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

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

BY-COVID: A new EU project coordinated by ELIXIR

 

logo of the BY-COVID project

A new EU funded project coordinated by ELIXIR has been launched today. BY-COVID is a €12million Horizon Europe project striving to tackle the data challenges that can hinder effective pandemic response. 

This interdisciplinary project involves 53 project partners from across 19 countries within Europe and draws together experts from the life sciences, policy and social science ensuring that the project is driven by a diverse range of science. 

ELIXIR-Estonia is part of the consortium and associate professor Hedi Peterson from University of Tartu is leading the actions from Estonian side.

Find out more in the news release on the BY-COVID website.

  • 2 min read

ELIXIR UNIX Shell Courses - Autumn 2021

ELIXIR Estonia is organising two Unix Shell Courses (Basic and Advanced) in coming weeks (September 28th, October 5th).

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 and we are here to teach you to obtain skills to master the terminal in your future work.

Basics Course 28th of September, 10:15-16:00, University of Tartu, Delta #2005

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.

Objectives:

  • 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.

No prior knowledge expected. 

Requirements: Lecture venue is computer class with linux computers. In case you bring your own Windows laptop, please make sure to have gitBASH (https://gitforwindows.org/) or Putty application (https://www.putty.org/) beforehand.

The lecturer is Dr. Priit Adler.

The course is free but please register responsibly at  https://forms.gle/7oHXsQWs1H5BjvRg7  (closes at 23:59 on 25.09 or when the course gets full).

Unix Shell Advanced Course 5th of October, 10:15-16:00, University of Tartu, Delta #2005 (COURSE FULL) and  New edition on 19th of October, 10.15-16.00, University of Tartu, Delta #2005

This course is aimed to streamline your skills in Linux and the 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 have gitBASH (https://gitforwindows.org/) or Putty application (https://www.putty.org/) beforehand.

The lecturer is Dr. Priit Adler.


The course is free but please register responsibly at  https://forms.gle/DEoHkbkPCBC1FfQ16 (closes at 23:59 on 17.10 or when the course gets full).

The FAIR Principles Lecture (registration closed)

On the 27th of September, 2021 and on 14th of October, 2021, ELIXIR-Estonia will be holding a new 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. The first course, on 27th of September, will be held in Estonian, and the second course, on 14th of October, will be held in English. 

 

The FAIR Principles Lecture 27th of September, 14:15-17:00 (in ESTONIAN) and 14th of October, 12:15-15:00 (in ENGLISH), Delta #1019

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

Dates: 27.09.2021 in Estonian; 14.10.2021 in English

Time: 14:15 - 17:00 / 12:15 - 15:00

Place: Delta, Narva mnt 18, room 1019

Register: registration closed

Registration closes at 23:59 on 25.09.2021/12.10.2021 (for the Estonian/English lecture, respectively) or when it gets full.

Materials (ENG): https://doi.org/10.5281/zenodo.5572352

Materials (EST): https://doi.org/10.5281/zenodo.5533534

FAIR Flyer: https://doi.org/10.5281/zenodo.5769084

 

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

 

Data management courses held in the future (may be up to change): 

  • OpenRefine (October 2021)
  • Excel - how to make your data reusable (November 2021)
  • Data licensing (2022)
  • How to organise your files BYOD workshop (2022)
  • How to write a good metadata and README file (2022)
  • Personal data in data management (2022)
  • 1 min read

ELIXIR Hungary published a Multiple Testing Correction web-tool

MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction

Scientists from nearly all disciplines face the problem of simultaneously evaluating many hypotheses.To facilitate multiple-testing corrections, ELIXIR Hungary developed a fully automated solution not requiring programming skills or the use of a command line. The registration free online tool is available at www.multipletesting.com and compiles the five most frequently used adjustment tools. 
 

 

  • 1 min read

Galaxy community’s SARS-CoV-2 Data Analysis and Monitoring with Galaxy - workshop materials available

The Galaxy community held a SARS-CoV-2 Data Analysis and Monitoring with Galaxy workhop in mid August. The video tutorials and slides are available for self-learners at https://galaxyproject.eu/event/2021-06-21-sars-cov-2-data-analysis-monitoring-training/

The topics that were covered ranged from basic Galaxy introduction to more specific topics such as:

  • Galaxy for SARS-CoV-2 genome surveillance projects
  • Variant calling, reporting, consensus building (with Galaxy GUI)
  • The usegalaxy.eu SARS-CoV-2 bot in action
  • Upload data to ENA
  • Using and Customising ObservableHQ

 

  • 1 min read

ELIXIR’s latest report: “Open data: A driving force for innovation in the life sciences”

Open access life science resources such as data and software, are fundamental for breakthrough discoveries, scientific excellence and entrepreneurial endeavours. Seventy-six percent of companies surveyed in our newest report “Open data: a driving force for innovation in the life sciences” state that their product or service would not exist without data on open repositories. 

While the importance of these freely available resources is widely accepted, there are sparse efforts to quantify the benefit, despite the need to demonstrate value to funders and policymakers. This report is an up-to-date quantification on the benefit of open data to industry and innovation, with an extensive survey, testimonials, and analysis of the hotspots of European innovation. 

Find the full report at https://bit.ly/SMEreport_news