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2023

  • 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

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

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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