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 by ELIXIR Estonia
- 29.05.2025 Bring your own DMP workshop - Registration open
If you would like to be notified about the events, trainings and workshops running by ELIXIR Estonia, consider subscribing to the announcements mailing list
Latest news and announcements
ELIXIR Estonia Contributes to the University of Tartu Data Management and Open Science Network
On May 14th, the University of Tartu’s Data Management and Open Science competence network held its second training session, organised by the University of Tartu Library. ELIXIR Estonia was proud to contribute to this initiative that supports the advancement of data management and open science across the university.
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.
Courses from others
Online: Towards open and standardised imaging data: an introduction to Bio-Formats, OME-TIFF, and OME-Zarr
This webinar is suitable for any researcher, data manager, or imaging specialist working with microscopy data who is interested in improving data accessibility, interoperability, and scalability. No prior experience with file formats or image data standards is required, but an undergraduate level understanding of biological imaging concepts will be useful.
Date: 28 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
Online: Data management in a bioimage informatics data flow
This webinar is suitable for marine biologists and environmental scientists collecting samples from the natural environment, generating, visualising, annotating and analysing large, multimodal datasets such as imaging data, and sharing their data by submitting them to public data repositories.
Date: 4 June 2025
UK: Making Toxicology Educational Resources more FAIR
This workshop is the fourth in a row of five workshops, designed for all toxicology and bioinformatics trainers, teachers, educational material providers, and curriculum developers who are interested in learning how to make to make toxicology educational resources more FAIR - Findable, Accessible, Interoperable, and Reusable. This workshop will help educators and researchers better organise and describe their educational resources to improve their discoverability and interoperability.
Introductory webinar: June 6 2025
Event date: 24-25 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
Sweden: Introduction to Data Management Practices
The course is geared towards life scientists wanting to take the first steps towards a more systematic and reproducible approach to analysing and managing research data.
Deadline for registration: 11 June 2025
Date: 9-11 September 2025
A FAIR and scalable workflow for plankton phenogenomics at single cell level
This webinar is suitable for marine biologists and environmental scientists collecting samples from the natural environment, generating, visualising, annotating and analysing large, multimodal datasets such as imaging data, and sharing their data by submitting them to public data repositories. The webinar will support you to set up an efficient data flow that is aligned with FAIR principles.
Date: 11 June 2025
WEBINAR SERIES: AI in the life sciences: Exploring possibilities, inspiring change
Join us for a series of webinars where we explore how Artificial Intelligence (AI) is shaping the future of life sciences! This series provides an accessible introduction to AI while giving direct access to experts and practical insights into real-world applications. Designed to inspire and help you recognise potential applications of AI in the life sciences, these webinars will spark new ways of thinking so that you can start applying AI in your work. A foundational session covering AI basics, its evolution, and why it matters for life sciences. Watch the recording: https://www.youtube.com/watch?v=sbVzcrD-wko
Dates: 11 June, 2 July, 29 July, 26 August, 2 September
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: Best Practices in Programming
This workshop will focus on learning and internalising the practices of unit testing, refactoring, and version control through hands-on experience. The first morning will begin with an introduction to these concepts and the tools that support them. In the afternoon and on the second day, we will transition to a code clinic, where we will work together in small groups to apply these practices and improve the code brought by participants. Due to the hands-on nature of the course, which involves a lot of code handling, discussions, and sharing experiences, it will not be taught remotely. The focus of this course is not object-oriented programming, software architecture, design patterns or algorithms. The goal of this course is to introduce skills and techniques for effectively developing software.
Deadline for registration: 10 June 2025
Date: 1-2 July 2025
Hybrid: AI x BIO
Our new conference will showcase advances in artificial intelligence and machine learning in biology, and the potential of these emerging approaches for medical science.
Deadline for registration: 16 June 2025
Date: 23-25 June 2025
UK: Metagenomics bioinformatics at MGnify
This course is aimed at life scientists who are working in the field of metagenomics and are currently in the early stages of data analysis. Participants should have some prior experience of using bioinformatics in their research. The practical sessions in the course require a basic understanding of the Unix command line and the R statistics package
Deadline for registration: 22 June 2025
Date: 6-10 october 2025
Online: Open FAIR data: the role of public data archives
This webinar is suitable for wet-lab and data scientists at all career stages who are interested in learning how to make their samples and imaging data open and available to the community. No prior knowledge of FAIR principles, BioSamples or the BioImage Archive is required.
Date: 25th of June
Switzerland: Single-Cell Transcriptomics with R
This course is intended for life scientists and bioinformaticians familiar with “Next Generation Sequencing” who want to acquire the necessary skills to analyse scRNA-seq gene expression data.
Deadline for registration: 25th June 2025
Date: 2-4 July 2025
Online: Make your research FAIRer with Quarto, GitHub and Zenodo
This course is addressed to computational biologists, bioinformaticians, researchers, scientists and trainers working in the life sciences who want to learn how to make their research and training FAIRer with reproducible notebooks and websites.
Deadline for registration: 30 June 2025
Date: 8 July 2025
Online: A journey to FAIR bioimage data
This webinar is suitable for marine biologists and environmental scientists collecting samples from the natural environment, generating, visualising, annotating and analysing large, multimodal datasets such as imaging data, and sharing their data by submitting them to public data repositories. The webinar will support you to set up an efficient data flow that is aligned with FAIR principles.
Date: 2 July 2025
HYBRID: ISMB/ECCB 2025
The world’s largest bioinformatics and computational biology conference ISMB/ECCB 2025 is happening in July 20–24 in Liverpool, United Kingdom virtually and in person. More info: https://www.iscb.org/ismbeccb2025/home. There will be a series of in-person and virtual tutorials prior to the start of the conference (registration deadline 10th of July unless sold out)
Virtual:
- Tutorial VT1: Visualising and interpreting your -omics results using ggplot2 and R
- Tutorial VT2: OmicsViz: Interactive Visualization and ML for Omics Data
- Tutorial VT3: Computational approaches for deciphering cell-cell communication from single-cell transcriptomics and spatial transcriptomics data
- Tutorial VT4: An applied genomics approach to crop breeding: A suite of tools for exploring natural and artificial diversity
- Tutorial VT5: Comprehensive Bioinformatics and Statistical Approaches for High-Throughput Sequencing Data Analysis, Including scRNA-seq, in Biomarker Discovery
- Tutorial VT6: Beyond Bioinformatics: Snakemake for Versatile Computational Workflows
- Tutorial VT7: Assessing and Enhancing Digital Accessibility of Biological Data and Visualizations
- Tutorial VT8: Generative AI for Single-Cell Perturbation Modeling: Theoretical and practical considerations
- Tutorial VT9: Biomedical text mining for knowledge extraction
In-person:
- Tutorial IP1: Machine Learning for Omics: Best practices and Real-Life Insights with TidyModels
- Tutorial IP2: Massively parallel reporter assays in functional regulatory genomics and as part of the IGVF data resource
- Tutorial IP3: Genomic Variant Interpretation & prioritisation for clinical research
- Tutorial IP4: Quantum Machine Learning for multi-omics analysis
- Tutorial IP5: Introduction to Causal Analysis using Mendelian Randomisation
- Tutorial IP6: Hello Nextflow: Getting started with workflows for bioinformatics
- Tutorial IP7: AI large cellular models and in-silico perturbation
- Tutorial IP8: Representation Learning and Feature Engineering for Genomic Sequences Analysis
Online: Structural bioinformatics
This course is aimed at scientists generating structural data or scientists utilising structural data in their analysis and/or interpretation. No previous experience in the field of structural bioinformatics is required, however good knowledge of protein structure and function would be of benefit.
Deadline for registration: 27 July 2025
Date: 27-31 October 2025
UK: Genome bioinformatics: from short- to long-read sequencing
The course is aimed at PhD students and post-doctoral researchers who are starting to use high-throughput sequencing technologies and bioinformatics methods in their research. The content is most applicable for those working with eukaryotic genomes, especially in the area of human genomics.Participants will require knowledge of the Unix command line and GitHub in order to adequately complete the practical sessions. Additionally, a short pre-course session on BASH and GitHub will be offered. Please note that participants without basic knowledge of these resources will have difficulty in completing the practical sessions.
Deadline for registration: 3 August 2025
Date: 17-21 November 2025
Belgium: Train the Trainer
This course introduces trainers to learning principles, training techniques, design and deliver training, as well as assessment and feedback. It offers guidance, ideas and tips for : Designing and Developing training activities; Deliver training, participation and engagement; All based on research-driven educational principles. Examples and discussions will also focus on the challenges presented by academic teaching.
Deadline for registration: 24 August 2025
Date: 3-4 September 2025
Online: Workshop in Epigenomics Data Analysis
The aim of this workshop is to introduce best practice bioinformatics methods for processing, analyses and integration of epigenomics data. The online teaching includes lectures, programming tutorials and interactive group sessions. This workshop is run by the National Bioinformatics Infrastructure Sweden (NBIS).
Deadline for registration: 25 August 2025
Date: 22 - 26 September 2025
Belgium: Introduction to Protein Structure Analysis and Prediction
This two-day training covers the basics of protein structure analysis, starting with exploring online databases like AlphaFoldDB, visualizing with ChimeraX, comparing homologues, and using tools like MutateX or PROSS to quantify interactions on day one. The second day focuses on accessing structure predictions via online tools (AlphaFold3, Chai-1) and HPC installations (AlphaFold2, Boltz-1, AlphaPulldown), culminating in an afternoon session where participants apply these tools to their own research questions and learn AlphaPulldown for protein-protein interaction screens.
Deadline for registration: 25 August 2025
Date: 8-9 September 2025
Switzerland: Bioinformatics meets AI: shaping the future of data-driven biology
The [BC]2 Basel Computational Biology Conference is the flagship scientific meeting of the SIB Swiss Institute of Bioinformatics, held every two years. As Switzerland’s leading event in computational biology and one of the largest of its kind in Europe, [BC]² attracts around 500 scientists from academia, industry, and healthcare. Attendees explore cutting-edge advancements in bioinformatics, ranging from evolutionary and environmental dynamics to infectious diseases, cancer research, protein design, single-cell omics, and AI-driven innovations in clinical data science.
Early registration: 10 March - 30 June 2025. Standard registration: 1 July - 1 September 2025
Tutorials and workshops : Monday 8 September 2025. Main conference: 8-10 September 2025
Belgium: Analysis of single cell RNASeq data
In this course, we will go through the whole pipeline to analyze short-read scRNASeq data. We will teach you how to:
- Do proper quality control and filtering on the gene level and the cell level
- Remove as much noise as possible
- Cluster your cells and create UMAP plots
- Get potential markers for these subsets of cells
- Identify genes that are differentially expressed genes between conditions
The content of the course is tailored to the participants’ needs. On the second day, participants can bring their data to analyze.
Deadline for registration: 9 September 2025
Date: 23 and 26 September 2025
Germany: European Galaxy Days (EGD)
The first two days will give an overview of the current state of the Galaxy framework and community with several talks, demonstrations, and Birds of a Feather sessions. As part of a CoFest, the third day offer the opportunity to continue the discussions, to code and hack as well as enjoy the Galaxy community.
Date: 1st October 2025
Belgium: XVII Vibrational Spectroscopy and Chemometrics Training Course
Theoretical and practical course dedicated to scientists and industry professionals seeking to discover or improve their skills in spectroscopy and chemometrics.
Date: 29 September - 3 October 2025
Belgium: FAIR training material made by Design
By the end of the course, participants will be able to: Create a FAIR and open training material from the start, Apply FIAR principles to all elements of training material, Use AI tools in the content creation of FAIR training material. Course material: https://elixir-europe-training.github.io/ELIXIR-TrP-FAIR-Material-By-Design/
Deadline for registration: 10 October 2025
Date: 21-23 October 2025
Material: Discover the Pathogen Data Network (PDN)
On 29 April, PDN hosted its first public webinar for a wide audience of pathogen data practitioners. It offered a global perspective on the project’s aims and latest advances, including a demo of the central Pathogen Portal, and the perspective from one of the community-led Node in Sweden, to an audience of hundred of participants from around the globe. The recording is now available, including a lively Q&A session, reflecting the engagement of the audience and timeliness of the initiative.
Material: Spatial Omics Data Analysis
This course delves into the cutting-edge field of Spatial Omics, focusing on Spatially-Resolved Transcriptomics (SRT) technology which provides unprecedented insights into the spatial organization of gene expression within tissues.Participants will explore both imaging-based and sequencing-based SRT technologies, learning to navigate the entire workflow of SRT data analysis. The course covers essential topics such as pre-processing techniques for data cleaning, normalization, and quality control, methods for identifying and characterizing spatial domains within tissues, strategies for integrating SRT data with single-cell RNA sequencing data, and statistical approaches to analyze spatial patterns and relationships. Additionally, participants will investigate interactions between cells within their spatial context. By the end of this course, participants will be equipped with the knowledge and skills to construct a complete workflow for SRT data analysis, from raw data to meaningful biological insights.
Material: Mastering data management: Go FAIR, Go Open, Go Smart — EMO BON and TREC showcases
Making data FAIR (findable, accessible, interoperable and reusable) and open benefits both for the data provider and future users. In this webinar, we will discuss how making data FAIR and open has allowed us to develop smart and efficient data management workflows in the context of the EMBRC EMO BON (European Marine Omics Biodiversity Observation Network) project. By focusing on the interoperability and reusability of our (meta)data, codes, and analysis results, we can use the web itself to make our data findable and accessible. We will then present examples of metadata curation from EMBL’s Planetary biology flagship expedition TREC (Traversing European Coastlines), an expedition to study coastal ecosystems and their response to the environment, from molecules to communities. We will see how one can go FAIR, Open and Smart by registering sample metadata at EMBL-EBI’s BioSamples service using checklists, controlled vocabularies and ontologies.
Material: Principles of research data management
This webinar introduces fundamental principles behind academic data management. We will describe the research data lifecycle, explore how data moves through typical research workflows, common challenges in handling it, and strategies for organising, documenting, and sharing data responsibly. Regardless of your research area, these foundational principles are becoming increasingly important, whether you’re working with small spreadsheets or high-throughput instruments, and understanding them can help you build a more robust and transparent data flow for your projects.
Material ELIXIR SPLASH
The ELIXIR Training SPLASH has been designed to guide the trainer in their efforts to plan, design, develop, deliver and evaluate training activties. It is based on the various steps of the training life cycle, although not all the steps will be relevant to everyone.
Material of webinar series: UniProt
All the links: https://www.ebi.ac.uk/training/events/uniprot/. Includes webinars:
- A guide to UniProt for students
- Programmatic access to UniProt using Python
- Uncovering protein function with UniProt
- Automated annotation in UniProt
- Sequence analysis tools in UniProt: BLAST and Align
- UniProt for proteomics scientists
- Exploring Human Disease and Protein Variant Data in UniProtKB and Contextualising Variation with ProtVar
- Navigating UniProt: a brief overview and recent updates
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.