ELIXIR Estonia
The purpose of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society. These resources include databases, software tools, training materials, cloud storage and supercomputers.
The goal of ELIXIR is to coordinate these resources so that they form a single high quality infrastructure. This coordinated infrastructure makes it easier for researchers to find and share data, analyse their experiments, exchange knowledge, and agree on best practices.
Estonia joined ELIXIR as a full member in December 2013. The Estonian node focuses on developing and maintaining software tools and databases, linking of bioinformatics and biobanking, and last but not least, training researchers across borders.
Estonian ELIXIR Node is led by University of Tartu. Other partners are Tallinn University of Technology, National Institute for Physics and Biophysics, Tallinn University, and Estonian University of Life Sciences.
Free Spring courses 2025
- 23.-29.04.2025 Statistics for Life Sciences in R Course - Invitation only
- 8.05.2025 Bring your own DMP workshop - Registration open
- 29.05.2025 Bring your own DMP workshop - Registration open
Latest news and announcements
If you would like to be notified about the events, trainings and workshops running by ELIXIR Estonia, consider subscribing to the announcements mailing list
Not professorware - g:Profiler turns 18 and helps thousands of researchers yearly!
g:Profiler, a popular gene list analysis tool, celebrates 18 years since its first publication in Nucleic Acids Research. What began as a student project has become a globally cited resource, with its 2019 update article now surpassing 5,000 citations — a testament to its lasting impact in life sciences.
Belgium: Machine learning and AI Summer School
Our summer school will delve into four pioneering topics: Protein Language Models, Spatial Omics Data Analysis, Data Integration and LLMs, Deep Learning for Protein Structures Prediction
Submission closing date: Tuesday, 29 April, 2025
Date: August 24th, 2025- August 29th, 2025
Switzerland: Introduction to Metagenomics Data Analysis of Microbial Communities
This course will cover the metagenomics data analysis workflow from data generation to downstream analysis. Participants will explore the tools to manage, share, analyze and interpret metagenomics data. The content will include issues of data quality control and how to process the data until publication.Both targeted marker-gene (e.g., 16S) and whole-genome shotgun (WGS) approaches will be covered. Discussions will also explore considerations when selecting the sequencing options (long or short reads), exploring targeted data to OTUs or ASVs, assembling and binning metagenomics data, the analyses that can be carried out, and what downstream analyses options and tools are available.
Application deadline: 30 April 2025
Date: 07 - 09 May 2025
Finland: CSC Summer School in High-Performance Computing 2025
The CSC Summer School brings together students and researchers in different disciplines of scientific computing from all over the world. The school consist of lectures and hands-on training on parallel programming, code performance, and other necessary skills for the development of scientific software for supercomputers. Fee: Late registration price starting from 11.4.2025 onwards is 2299€
Date: 24.6.2025 - 3.7.2025
Deadline for late registrations is 01.05.2025.
Netherlands, Estonia, Germany: AIProHealth: Data Science and AI in Health Summer School
Explore the cutting edge of Artificial Intelligence in healthcare. Create solutions that drive the next generation of healthcare innovation in this practical, hands-on programme.
Application deadline: 4th May Netherlands, 25th May Estonia and Germany
Switzerland: Using Large Language Models for Biodata Exploration: From Theory to Practice
This one-day course will give a gentle introduction into LLMs, going from theoretical concepts towards practical, hands-on experience interacting with LLMs for exploring biodata through a series of exercises provided in Jupyter Notebooks. These will include programmatically interacting with an LLM to construct a simple Retrieval Augmented Generation (RAG) application for answering biological questions using existing SIB resources.
Application deadline: 05 May 2025
Date: 19th of May 2025
Online: Galaxy Training Academy 2025
The Galaxy Training Academy is a self-paced online training event for beginners and advanced learners who want to improve their Galaxy data analysis skills. Over the course of one week, we offer a diverse selection of learning track. Program includes introduction to Galaxy, FAIR training, separate course tracks for proteomics, assembly, transcriptomics, single cell, microbiome, machine learning and Python.
Registration deadline: 8th May 2025
Date: 12-16 May 2025
Webinar: Gene Expression made Useful Easily: Tools and Database of Bgee
This course is addressed to life scientists who need to retrieve curated gene expression, obtain expression-based knowledge on genes of interest, or compare expression between genes and between species.
Application deadline: 09 May 2025
Date: 16th May 2025
Switzerland: Missing Data and Imputation Methods
In this course, we will introduce the concept of missing data, explain the difference between data missing at random (MAR) and data missing not at random (MNAR), and cover several widely-used methods for dealing with missing data. We will use R to apply some of these methods to real data sets, with a focus on data originating from omics technologies. Price: Academic: 100 CHF; For-profit: 500 CHF
Application deadline: 09 May 2025
Date: 22 May 2025
Greece: ELIXIR-GOBLET Train-the-Trainer (TtT) 2025
This course introduces trainers in the life sciences to learning principles, training techniques, lesson, session, course, and material design as well as assessment and feedback. It offers guidance, ideas and tips for designing training/teaching, development and delivery on training activities, all based on research-driven educational principles. Examples and discussions will also focus on the challenges presented by academic teaching.This course has been developed for and by trainers in bioinformatics but is suitable for all trainers and educators in higher education.
Application deadline: 10 May 2025
Switzerland: Docker and Singularity for Reproducible Research: Getting Started with Containers
This course is addressed to bioinformaticians and life scientists that are doing bioinformatic analyses and want to get introduced to containers. Materials: https://sib-swiss.github.io/containers-introduction-training/latest/ Price: Academic: 100 CHF; For-profit: 500 CHF
Application deadline: 13 May 2025
Date: 27 May 2025
Online: Tools Platform and Single Cell Omics “bring your workflow” to WorkflowHub
Gain insights from experts on the importance of FAIR principles in computational workflows and how they can enhance reproducibility, collaboration, and findability. Watch a live demonstration of workflow registration in WorkflowHub. Using computational workflows for handling and processing Single Cell data as examples, you will see how workflows can be easily registered, discovered, and shared within the scientific community. Participate in an interactive session where you can bring your own workflows and learn how to register and manage them in WorkflowHub.
Date: Tue 13 May 2025 10:30 - 12:00 BST
Online: Spatial transcriptomics (Visium) data analysis with Chipster
This hands-on course in Zoom introduces the analysis of spatially resolved transcriptomics (Visium) data. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, cell type identification and detection of spatially variable genes. You will also learn how to do integrated analysis of multiple samples. The free and user-friendly Chipster software is used in the exercises, and the course is thus suitable for everybody.
Date: 15.5.2025
Italy: Profiling of microbial communities using targeted and shotgun metagenomics
This training course focuses on the study of the microbiota using Next Generation Sequencing (NGS) techniques. The course will introduce DNA metabarcoding and shotgun metagenomics and illustrate the major computational tools for the analysis of metagenomic data. In addition, the course will provide an introduction to Machine Learning methods applied to the analysis of metagenomic data. The course will include both a theoretical introduction to the topics and practical sessions with real data. Fee: 250 Euros for academic attendees and 350 Euros for industry professionals
Deadline for applications: 20th May 2025
Course date: 30 June - 4 July 2025
Finland: VeloxChem on LUMI workshop
This workshop introduces participants to quantum chemistry simulations using VeloxChem on the LUMI supercomputer, with a focus on utilizing the GPU resources on LUMI-G for high-performance electronic structure calculations. Price: 150,60 (VAT 25,5% Incl.)
Date: 26.5.2025 - 27.5.2025
Switzerland: Reproducible and Scalable Research with Snakemake and Software Containers
This course is addressed to all bioinformaticians developing computational pipelines with an interest to increase the reproducibility of their work.
Application deadline: 14 May 2025
Date: 28th of May 2025
Online: UniProt: Focus on Plant Proteins
Are you working on plants and struggling to find information about plant proteins? Are you curious about the biosynthesis of natural compounds like caffeine, capsaicin, and others? Are you interested in the interactions between plant and pathogens? If so, this webinar is for you. UniProt is the world’s leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information. Starting with a biological question (i.e., how to get the list of enzymes involved in the synthesis of CBD or THC), you will explore the different ways of answering it, using UniProt. Hints on how to extend queries to other biological contexts will also be provided.
Application deadline: 02 June 2025
Date: 04 June 2025
Switzerland: Biology-informed Multiomics Data Integration and Visualization
This course is aimed at PhD students, postdoctoral and other researchers in the life sciences who are seeking to understand and visualize multi-omics data, aiming to integrate and interpret high-throughput biological data using R. Fee: Academic: 200 CHF; For-profit: 1000 CHF
Application deadline: 09 June 2025
Date: 16 - 17 June 2025
Switzerland: Causal Inference
This course is addressed to researchers new to causal reasoning who wish to familiarize themselves with the causal language and grasp the foundational concepts for delving into the causal inference literature. Fee: Academic: 200 CHF; For-profit: 1000 CHF
Application deadline: 10 June 2025
Date: 24 - 25 June 2025
Material: OpenRefine for Social Science Data
OpenRefine (formerly Google Refine) is a powerful free and open source tool for working with messy data: cleaning it and transforming it from one format into another.
Materials: Large Language Models and their applications in Bioinformatics
Includes materials:
- Basics of Large Language Models - transformers to LLMs
- Developing a dataset for LLM projects
- LLM generated summaries for protein classification at InterPro
- BioChatter and the future of LLM driven bioscience
- Domain-specific knowledge extraction from scientific texts using LLMs
CodeRefinery workshop materials
Courses including: Shell crash course, version control with Git, collaborative distributed version control, reproducible research, social coding and open software, how to document your research software, Jupyter notebooks, automated testing, modular code develeopment
Main site: https://coderefinery.github.io/2025-03-25-workshop/
Youtube channel: https://www.youtube.com/playlist?list=PLpLblYHCzJACpOmIzO8TywjtfYD7_d93H
Introduction to Machine Learning with Python
Materials: https://github.com/sib-swiss/intro-machine-learning-training
First Steps with SQL for Data Science
Materials: https://gitlab.sib.swiss/clinbio/learning/sql-for-data-science
E-Learning: Metadata in Bioinformatics
Have you heard the word metadata but have no idea what it refers to, what type of content is found in metadata, how it is being used and why to use it? This asynchronous e-learning course (1h) can be completed online, at the desired pace and in the absence of an instructor.
E-learning: Elements of Supercomputing
This free online course is open for everyone interested in supercomputers and high performance computing. Level: Basic, no prerequisites or study rights to higher education institution needed.