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39 materials found

Target audience: Biologists 

Cloud-SPAN Prenomics

Prenomics prepares learners for the Cloud-SPAN Genomics course. It teaches the basics of command-line programming, including: (1) file directory structure, (2) use of command-line utilities to connect to and use cloud computing and storage resources and (3) basic shell commands for file...

Scientific topics: Bioinformatics, Software engineering, Genomics

Operations: Query and retrieval, Data handling

Keywords: Cloud computing, Shell, Command line, Amazon Web Services, genomics, HPC, Data analysis, bioinformatics

Resource type: course materials, online course, Training materials

FAIR data - Module 4 (share and publish data)

Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données

Scientific topics: Bioinformatics, Biology, Data management

Keywords: data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse

Resource type: Slides

FAIR data - Module 3 (Metadata)

Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données

Scientific topics: Bioinformatics, Biology, Data management

Operations: Data handling

Keywords: metadata, data annotation, life science standards, data sharing

Resource type: Slides

FAIR data - Module 2 (data life cycle)

La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données

Scientific topics: Data management, Biology, Bioinformatics

Operations: Data handling

Keywords: Data preserving, Data storage

Resource type: Slides

FAIR data - Module 1 (research data)

Research data and their centrality in the research process.
This material is mostly in French.

Keywords: metadata, Data Life Cycle, Reproducibility, Data management plan

Resource type: Slides

Plant Phenotyping Data managment Webinar (MIAPPE)

The Minimal Information About Plant Phenotyping Experiment, MIAPPE (, has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking...

Scientific topics: Plant biology, Phenomics, Data quality management, Data submission, annotation, and curation

Operations: Standardisation and normalisation

Resource type: Video, Slides

SPARQLing Biology: a beginners course

Course given at BioSB 2019 for biologists about SPARQL.

Scientific topics: Biology

Operations: Query and retrieval

Keywords: Sparql queries, Sparql syntax

Resource type: Tutorial

Plant Phenotyping Data managment (MIAPPE)

This training material has been used in a two-day training workshop on data management organized by Elixir and the Wheat Initiative.

It provides an overview of current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity...

Scientific topics: Phenomics, Plant biology, Data management

Operations: Annotation, Formatting

Keywords: Plant Phenotyping, Data-format, data sharing

Resource type: Training materials

A Tidy Transcriptomics introduction to RNA-Seq analyses

This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.

Scientific topics: RNA-Seq

Keywords: Differential Expression, Gene Expression, RNA-seq, Transcriptomics

Resource type: Tutorial

Initiation to R programming and descriptive statistics

This course material was designed with the on-site teaching program for PhD students at Institut Pasteur in mind.
It teaches the basics of R programming and descriptive statistics, and is hopefully detailed enough to be usable for self-study, with some rough guidelines given...

Keywords: R-programming, Descriptive statistics, Statistics, Bioinformatics

OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Toxicology, Ontology and terminology

Resource type: Tutorial

BLAST and multiple sequence alignment (MSA) programs

The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

Keywords: Blast, E learning, Multiple sequence alignment

Resource type: e-learning

Phylogenetics of animal viral pathogens

The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

Keywords: Animal pathogens, E learning, Phylogenetics

Resource type: e-learning

Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Mascot training course

The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises.

Scientific topics: Proteomics

Keywords: Protein identification, Protein Mass Spectrometry

Resource type: Slides, Video, Training materials

Single cell RNA-seq data analysis with R


Monday 27.5.2019

Introduction to single cell RNA-seq (Jules Gilet)
Quality control and data preprocessing (Åsa Björklund)
Normalisation (Heli Pessa)
Removal of confounding factors (Bishwa Ghimire)
Data integration (CCA, MNN, dataset alignment) (Ahmed Mahfouz)


Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Groovy Cheminformatics with the Chemistry Development Kit

Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language.

Scientific topics: Cheminformatics, Chemistry

Resource type: Book

Single cell RNA-seq data analysis with R

This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene

Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. It explains how to download the IMS Docker and identifier mapping databases (link sets), load the link sets, and test the web interface.

Scientific topics: Genetic variation, Genomics

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial

#metawinterschool contribution by BiGCaT

Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.

Scientific topics: Metabolomics

Keywords: Metabolomics, Identifiers, ELIXIR RIR, BridgeDb

Resource type: Tutorial

BridgeDbR Tutorial

BridgeDb is a combination of an application programming interface (API), library, and set of data files for mapping identifiers for identical objects [1]. Identifier mapping databases are available for gene products and metabolites. This Bioconductor Vignette explains how to use BridgeDb in the R...

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial, Vignette

Biocuration: An Introduction

Claire O'Donovan, leader of the Protein Function Content team at EMBL-EBI, gives an introduction into biocuration and talks about what it is like to work as a biocurator and the skill sets you need.
This webinar was recorded on 2 March 2016 and is best viewed using Google Chrome and in...

Keywords: Biocuration

Introductory image processing on biological images using python.

This is an image processing practical for students with an interest in analysing biologically derived images. It is written in the language python and utilises jupyter notebook for annotation and visualisation of the code. The practical is beginner level, although some knowledge of python is...

Resource type: Jupyter notebook, PDF

Text-mining exercises

Hands-on exercises using a variety of text-mining tools and databases based on text mining, to interpret the results from microbiome studies.

The exercises will teach you how to:

  • automatically highlight named entities in a web page
  • use named entity recognition for synonym-aware...

Scientific topics: Microbial ecology, Metagenomics, Natural language processing, Data mining

STRING exercises

Hands-on exercises using the STRING, STITCH, and DISEASES databases through their respective web interfaces. The exercises will teach you how to:

  • retrieve a STRING network for a protein of interest *...

Scientific topics: Bioinformatics, Molecular interactions, pathways and networks, Protein interactions

Cytoscape stringApp exercises

Hands-on exercises using the stringApp for Cytoscape to retrieve molecular networks from the STRING and STITCH databases.

The exercises will teach you how to:

  • retrieve...

Scientific topics: Bioinformatics, Molecular interactions, pathways and networks, Protein interactions, Proteomics, Data visualisation

Unix and Perl primers for biologists

UNIX is the most commonly used operating system in bioinformatics. Increasingly, the raw output of biological research exists as in silico data, usually in the form of large text files. Unix is particularly suited to work with such files and has several powerful (and flexible) commands that...

Keywords: IBERS, Institute of Biological, Environmental and Rural Sciences

Introduction to Biopython

This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs.

Keywords: Bioinformatics, Biopython, Programming, Python, Python biologists

Bioinformatics approaches to Identify causative sequence variants in farm animals

ALLBIO and DEANN Training course: 12-16 May 2014, SLU, Uppsala, Sweden
The training is mainly intended for researchers that want or already use techniques like genome-wide SNP genotyping, candidate gene sequencing, transcriptome sequencing and other bioinformatics tools in their work to...

Keywords: Allbio, Farm animals, Qtl, Rnaseq, Transcription factors