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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.


Spring semester 2024 free ELIXIR courses in Estonia

Invitation only:

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Online course: Enrichment Analysis

Experiments designed to quantify gene expression often yield hundreds of genes that show statistically significant differences between groups of interest. Once differentially expressed genes are identified, enrichment analysis (EA) methods can be used to explore the biological functions associated with these genes. EA methods allow us to identify groups of genes (e.g. particular pathways) that are over-represented, thereby offering insights into biological mechanisms. One of the EA methods frequently used for high-throughput gene expression data analysis is Gene Set Enrichment Analysis (GSEA). This course will cover GSEA and alternative enrichment methods. Because the implementation of GSEA is directly linked to databases that annotate the function of genes in a cell, the course will also give an overview of functional annotation databases such as Gene Ontology.

Application deadline: 26 February 2024

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Course at Bern, Switzerland: Single-Cell Transcriptomics with R

Single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression at the single cell level. For example, scRNAseq can help to identify expression patterns that differ between conditions within a cell-type. To generate and analyze scRNAseq data, several methods are available, all with their strengths and weaknesses depending on the researchers’ needs. This 3-day course will cover the main technologies as well as the main aspects to consider while designing a scRNAseq experiment. In addition, it will cover the theoretical background of analysis methods with hands-on practical data analysis sessions applied to droplet-based methods.

Application deadline: 06 March 2024

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Online course - NGS - Quality Control, Alignment, Visualisation

In this module, we will introduce the most used sequencing technologies and explain their concepts. Using different datasets, we will practice quality control, alignment of reads to a reference genome and visualize the output. This course is intended for life scientists who are already dealing with NGS data and would like to be able to start analysing them.

Application deadline: 01 April 2024

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Course at Breda, The Netherlands: RNA-seq data analysis

The 9th edition of the RNA-seq Data Analysis course will be held on 8-12 April – 2024 in Breda, The Netherlands. This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux and R practicals. Also the potential of long-read based RNA-seq and AI based analysis enrichments will be explored.

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Course at Milano, Italy: Metabolomics Approaches for ‘One Health’

This workshop focuses on experimental design and sample preparation matrix enabling junior and senior scientists to apply metabolomics approaches to a research-based context. Attendees will be guided through mass spectrometry-based experiment designs, learning about cutting-edge equipment and different technical procedures for metabolomics.

Application deadline: 30th April 2024

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