Target audience: Biologists
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
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
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
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
The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org), 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: Data submission, annotation, and curation, Data quality management, Phenomics, Plant biology
Operations: Standardisation and normalisation
Resource type: Video, Slides
Course given at BioSB 2019 for biologists about SPARQL.
Scientific topics: Biology
Operations: Query and retrieval
Keywords: Sparql queries, Sparql syntax
Resource type: Tutorial
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: Data management, Plant biology, Phenomics
Operations: Formatting, Annotation
Keywords: Plant Phenotyping, Data-format, data sharing
Resource type: Training materials
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
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
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: Ontology and terminology, Toxicology
Resource type: Tutorial
Background
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
Background
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
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
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
Programme
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)
Tuesday...
Scientific topics: RNA-Seq
Keywords: RNA-Seq, Single Cell technologies, scRNA-seq
Resource type: course materials
Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language.
Scientific topics: Chemistry, Cheminformatics
Resource type: Book
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
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
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: Genomics, Genetic variation
Keywords: ELIXIR RIR, BridgeDb
Resource type: Tutorial
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
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
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
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
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: Data mining, Natural language processing, Metagenomics, Microbial ecology
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
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
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
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
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
Although there are many tools designed for structural variation (SV) analysis there has been no bench mark study to guide scientists in choosing the best tool for their particular data set. In this test case, AllBio Test Case 2 – Identification of Large Structural Variants, a researcher is eager...
Keywords: Ngs bioinformatics, Structural variations