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
- 29.05.2025 Bring your own DMP workshop - Registration open
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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.
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: 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: 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: 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
Belgium: Scywalker for processing long-read single cell RNASeq data
The scywalker tool was designed to analyze long-read single-cell data to generate gene and transcript count matrices that can be further analyzed to compare gene and isoform expression between samples and cell types. This workshop will provide you with: a detailed description of each step in the scywalker pipeline, a complete overview and description of all the results that are generated (for each output file, we will explain what info it contains an how it can be used for follow-up analysis).
Registration deadline: 26 May 2025
Date: 05 June 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
UK: Methods for infectious disease modelling using genomics
This course is aimed at early-stage researchers and others who are working in the fields of infectious diseases or pathogen evolution and will use mathematical modelling, and for professionals who carry out this type of research in policy making, charities or public health settings. Basic knowledge of R, command line, and biostatistics will be essential.
Deadline for registration: 26th of May
Date: 14-19 September 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
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
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
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: 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
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: 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
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 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.
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.