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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. 

Visualisation with RStudio - 14.11.2023

  • Time:  14.11.2023 9:00-12:00
  • Type: Workshop
  • Language: English
  • Duration: 3h
  • Location: Delta building, Narva mnt 18 room 2005, Tartu
  • Audience: students, researchers
  • Instructor: Priit Adler, PhD

“Visualisation with RStudio” will be a follow-up to “RStudio Basic” workshop and “Data visualisation” webinar. We will do data visualisation using ggplot2 package. ggplot2 is a widely-used data visualization package in R, designed to create visually appealing and highly customizable graphics.

Learning outcomes for the participants: 

  • Create insightful data visualisations and customize aesthetics using RStudio
  • Uncover patterns, relationships, and anomalies within datasets

 

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).

Course is full.

 

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. 

Andmehaldus 101 - 12.10.2023

  • Aeg: 12.10.2023 9:30-12:30
  • Tüüp:  zoom (link saadetakse mõned päevad enne koolitust)
  • Keel: Eesti keel 
  • Kestus: 3h
  • Asukoht: online
  • Sihtgrupp: Kõik, kellel on andmed
  • Lektor: Diana Pilvar, MSc

Andmehaldus on oluline osa teadustööst ja on hädavajalik andmetest maksimumi saamiseks. 

Andmehalduses 101 on sissejuhatav online-kursus, mis varustab teadlasi vajalike oskustega uurimisandmete tõhusaks organiseerimiseks ja haldamiseks.  Osalejad saavad teadmisi parimatest praktikatest andmete dokumenteerimise, varundamise ja  jagamise kohta. Teeme läbi harjutusi ning ülesandeid uute teadmiste kinnistamiseks.

Õpitulemused:

  • Rakendada parimaid tavasid failide nimetamisel ja kaustade struktureerimisel
  • Valida ja rakendada asjakohaseid ontoloogiaid ja metaandmete standardeid
  • Kirjeldada andmete salvestamise ja varundamise strateegiaid
  • Valida õige litsents oma andmetele/avaldatud tulemustele

Palume teil registreeruda vastutustundlikult. Kui te ei saa loengule osaleda, palun teavitage meid võimalikult kiiresti e-posti teel (elixir@ut.ee).

 

Uute kursustega kursis olemiseks liituge meie uudiskirjaga meililistiga:  https://lists.ut.ee/wws/subscribe/elixir.news?previous_action=edit_list_request 

Taotlusi võetakse vastu mõne päeva jooksul käsitsi.

Data visualisation - 9.11.2023

  • Time: 9.11.2023 10:00-12:00
  • Type: Zoom (link will be sent a few days before the webinar)
  • Language: English
  • Duration: 2h
  • Location: Online
  • Audience: students, researchers
  • Speaker: Diana Pilvar, MSc

In the course of their work, researchers encounter data in various forms. Yet, when data is presented in its raw, tabular form, it often appears as a complex puzzle. This can be especially overwhelming when dealing with large datasets. Fortunately, this is where the magic of data visualization comes into play. The main idea is to extract the key insights from the data and craft a narrative around it. However, it's important to note that hasty chart-making can lead to confusion. Poorly designed visuals not only risk misinterpretation but can also be misleading. That's why it's crucial to approach data visualization thoughtfully and precisely.

This webinar 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. The webinar will have a theoretical aspect, and we will assess examples from real life.

This lecture will be followed up by a separate workshop on the 14th of November called “RStudio Visualisation,” where you can put your knowledge into practice. 

 

Learning outcomes for the participants: 

  • Choose appropriate chart types
  • Avoid common mistakes in data visualisation
  • Maximise data-ink ratio

 

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.

  • in R, RStudio
  • 1 min read

RStudio Basic - 24.10.2023

  • Time: 24.10.2023  9:00- 12:00
  • Type: Workshop
  • Language: English
  • Duration: 3h
  • Location: Delta building, Narva mnt 18 room 2005, Tartu
  • Audience: students, researchers
  • Instructor: Priit Adler, PhD

R is a free software environment for statistical computing and graphics. It compiles and runs on various UNIX platforms, Windows and MacOS.

RStudio is an essential tool for anyone involved in R programming. It plays a vital role in data analysis by facilitating data import, access, transformation, exploration, visualization, and modeling tasks.If you're embarking on your journey to learn R, now is the perfect moment to familiarize yourself with RStudio. Discover what RStudio is, how to install it, and begin harnessing its capabilities to enhance your data analysis and programming skills.

This workshop will be followed up by “Visualisation with RStudio”  

Learning outcomes for the participants:

  • Navigate RStudio features, write and execute R scripts, and manage projects efficiently within the IDE.
  • Import, clean, and manipulate data

 

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. 

  • in hpc, UT
  • 1 min read

A new course in the University of Tartu - High-performance Computing

A new course for current and future high-performance computer users!

A new course in the University of Tartu curriculum will start in autumn - High-performance Computing (3 ECTS).

The goal is to provide an understanding of high-performance computing and its working principles. The course will introduce HPC best practices and use cases for efficient calculations with large complex data.

We accept participants from all levels of study (bachelor's, master's, doctoral studies). The lecturers are HPC Center's experienced specialists.

Details and registration in ÕIS2.

Rare Diseases Massive Open Online Courses

New sessions of the two MOOCs (Massive Open Online Courses) respectively on Rare Disease Diagnosis and Translational Research for Rare Diseases, developed in the context of the European Joint Programme for Rare Diseases (EJPRD), were recently launched.

EJP RD MOOCs are free and open to anyone, although there are designed for individuals with a prior interest in rare diseases research, especially postgraduate students and medical students. Patient advocacy representatives and advocates as well as health professionals who want to deepen their knowledge in rare diseases research could also find the MOOCs of interest. Both the MOOCs are continuously open for enrollment and the access to the content is free for the first 5 weeks. 

MOOC: Diagnosing Rare Diseases: from the Clinic to Research and Back

Codeveloped by the Foundation for Rare Diseases, the European Reference Networks Genturis and Ithaca, and EURORDIS, this MOOC addresses the diagnostic research progress, types of genetic tests for rare diseases, and the impact of having or lacking a diagnosis on patients' lives.

The topics covered include:

  • The diagnostic process and the types of genetic tests available for rare diseases
  • The differences in rare genetic diseases patient pathways
  • Technological advances for diagnostic research
  • The role of collaborative studies and data sharing in rare diseases diagnosis
  • The impact of having a diagnosis or lacking a diagnosis on patients’ lives
  • The role and place of physiopathology approaches as well as social sciences research in the context of rare diseases diagnosis.

Expert mentors will be readily available on the platform to address any questions that participants may have from May 1st to June 24th.


For more information, please visit: 

https://www.futurelearn.com/courses/rare-genetic-disease 

 

MOOC: From Lab to Clinic: Translational Research For Rare Diseases

This MOOC has been codeveloped by Foundation for Rare Diseases, the European Reference Network EuroNMD,  EURORDIS, the European Infrastructure for Translational Medicine EATRIS, and the Leiden University Medical Center.

It is intended to give an overview of the medicine developmental process for RD, by discussing how the results of the research done in the laboratory are used to develop new treatments and how they are finally brought to the market.

The topics covered include:

  • The landscape of translational research
  • The different phases and main stakeholders of translational research
  • The specific issues encountered when developing a treatment for a rare disease and how they are overcome
  • The different therapeutic approaches for the treatment of rare diseases
  • The role and place of patients living with a rare diseases in this translational process

Expert mentors will be readily available on the platform to address any questions that participants may have from April 17th to June 10th.

For more information, please visit: 

https://www.futurelearn.com/courses/introduction-to-translational-research-for-rare-diseases

Open Science and Data Management - Mandatory and/or Beneficial?

You are invited to participate in the seminar "Open Science and Data Management - Mandatory and/or Beneficial?" on May 5th at 11 am at Tallinn University of Technology and online via livestream. The event will cover the topic of open science and research data management, which is important for all researchers who want to ensure the reliability and transparency of their research results.

Experts from the University of Leiden, Göttingen, Sheffield, and Helsinki will speak about the principles of open science, opportunities for research data management, and best practices. Representatives from the Estonian Research Council, universities, and the DataCite Estonia Consortium will introduce Estonian perspectives and experiences.

The event program and registration link can be found on the DataCite website. The seminar is free and open to all interested parties. The event will be in English.

You can find the registration link for in-person participation HERE (in-person registration ends on the 26th of April). 

You can find the registration link for Zoom participation HERE (this can be shared with those who only want to participate online).

 

Take advantage of the opportunity to learn more about open science and practical recommendations for better research projects and work management.

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