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22 materials found

Scientific topics: Gene expression and microarray  or Bioinformatics 

Tutorial on developing Building Blocks

This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them.

Scientific topics: Personalised medicine, Workflows, Bioinformatics

Keywords: HPC, building blocks

Resource type: Tutorial

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: Data management, Biology, Bioinformatics

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: Data management, Biology, Bioinformatics

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: Bioinformatics, Biology, Data management

Operations: Data handling

Keywords: Data preserving, Data storage

Resource type: Slides

This training is meant specifically for the “Galaxy @Sciensano” that is available at and serves two purposes. First, it serves as an introduction in how to handle and employ the Galaxy instance hosted by Sciensano. Secondly, is also serves as a tutorial into both the...

Scientific topics: Microbiology, Sequencing, Genomics, Public health and epidemiology, Bioinformatics

Resource type: Video, Tutorial

Datanator tutorial

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA...

Scientific topics: Omics, Bioinformatics, Systems biology, Cell biology, Molecular biology

Operations: Filtering, Query and retrieval

Keywords: genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis

Resource type: Tutorial documentation provides essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences.

Some notable documentation links:
- About
- [Installing on your...

Scientific topics: Ontology and terminology, Computational biology, Data submission, annotation, and curation, Bioinformatics

Operations: Data retrieval

Keywords: Tools, Curation, Software, Sofware curation, Tool curation

Resource type: Documentation, API reference

High Performance Computing (HPC) in Life Sciences

High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

Scientific topics: Biology, Bioinformatics, Computer science

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

Learning structural bioinformatics and evolution with a snake puzzle

We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master’s course at the...

Scientific topics: Protein structure analysis, Molecular biology, Evolutionary biology, Bioinformatics

Resource type: course materials

Bioinformática con Ñ

El libro está dividido en seis grandes bloques, que a su vez han sido organizados en dos Volúmenes. El primer volumen trata sobre cuestiones generales, de utilidad independientemente del área de bioinformática en que se pueda estar interesado, como bases de datos o fundamentos de programación....

Scientific topics: Systems biology, Bioinformatics

Keywords: introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management

Resource type: Book

EMBL-EBI Train Online

If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. Train online is here to help you do this quickly and efficiently.

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems

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

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

Train the trainer

Five PowerPoint presentations and an Excel worksheet for a Train the Trainer course developed by Chris Taylor while at the Earlham Institute working for the National Institutes of Science's Bioinformatics and Biomathematics Training hub. The five slide decks cover pedagogical theory, trainer...

Scientific topics: Bioinformatics, Computational biology

Keywords: training, pedagogy

Galaxy for NGS analysis: A web-based platform for data intensive biological research


Galaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The...

Scientific topics: Workflows, High-throughput sequencing, Nucleic acid sequence analysis, Bioinformatics

Keywords: John Innes Centre, JIC

A recipe for setting up a free Virtual Machine environment for bioinformatics training and production

This material is a guideline for any bioinformatics group that would like to manage and distribute a cloud environment of virtual machines (VMs) for their users using only free components, if reasonable powerful compute and storage hardware is available. It is also a record of the creation of our...

Scientific topics: Bioinformatics

Keywords: Cloud computing, Virtual machine

High-throughput sequencing training materials repository

This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis.
Materials have been annotated following the standards and guidelines proposed at the “Best practices...

Scientific topics: Data architecture, analysis and design, Bioinformatics

Keywords: High throughput sequencing analysis, Rna seq chip seq anayses, Variant calling

RNA-seq data analysis: from raw reads to differentially expressed genes

This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of...

Scientific topics: Sequencing, RNA, Data architecture, analysis and design, Bioinformatics

Keywords: Bioinformatics, Differential expression, Ngs, Rna seq

TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers

Hands on course held at TGAC ( on Monday 19 to Friday 23 May 2014
What is this workshop about?
The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on:
Automated and standardized data...

Scientific topics: Sequence analysis, Plant biology, Database management, Bioinformatics

Keywords: Ngs, Ngs bioinformatics, Plants bioinformatics

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Benjamin Good

Online Gaming in Bioinformatics: The ‘Fun’ Model to Online Bioinformatics Education
Benjamin Good, Senior Staff Scientist, Department of Molecular and Experimental Medicine, The Scripps Research Institute.
Dr. Good’s research focuses on games with a purpose in crowdsourcing biological knowledge....

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Gaming, Online learning

Writing functions in Python programming

This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file. 

Scientific topics: Bioinformatics

Keywords: Programming, Python, Python biologists

ArrayExpress: Quick tour

This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress.

This course was updated in December 2015.

An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI...

Scientific topics: Gene expression, Gene expression and microarray, Functional genomics

Keywords: Gene Expression