Target audience: Any student, postdoc or RA ... or bioinformaticians
The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify...
Keywords: Containers, Nextflow
Resource type: Training materials
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
workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available...
Scientific topics: Workflows
Keywords: Nextflow, DSL2
Resource type: Presentation, course materials
Course organised by the French Institute of Bioinformatics (IFB) with the help of the Swiss Institute of Bioinformatics (SIB) in french
- 1st edition: 9-10 July 2019, Institut Pasteur (trainer: Frédéric Schütz)
- 2nd edition: 12-13 September 2019, Institut Pasteur (trainers: Christophe Malabat...
Keywords: R-programming, Reproducible Science
The French Institute of Bioinformatics (IFB) has organised in partnership with the Institute of Integrative Biology (I2BC) a training course for bioinformaticians and biostatisticians wishing to implement the "FAIR" principles (Findable, Accessible, Interoperable, Reusable) in their analysis and...
Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing
Resource type: Training materials
DE-Sim is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as NumPy, Scipy,...
Scientific topics: Computational biology, Mathematics, Computer science, Simulation experiment
Operations: Visualisation, Modelling and simulation
Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science
Resource type: examples, Tutorial, Jupyter notebook, API reference
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
This tutorial demonstrate how to use V-pipe - Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.
For the purpose of this toturial, we use the sars-cov2 branch of V-pipe and analyse SARS-CoV-2 runs downloaded from NCBI SRA.
Scientific topics: Workflows, Genetic variation, Virology
Operations: Read pre-processing, Alignment, Variant calling
Keywords: coronavirus, NGS bioinformatics, Variant-calling
Resource type: Computer Software, workflow
This is an online tutorial where you can learn how to write tool wrappers and workflows using the Common Workflow Language (CWL). The materials provided here describe the first stable version of the CWL - Version 1.0. The tutorial is hosted on the [ELIXIR-SI eLearning...
Scientific topics: Workflows
Keywords: commonwl, common workflow language, CWL, Workflows, eLearning, EeLP
Resource type: Installation instructions, Manual
FAIRify your data: FAIRification & Data modelling using linked data
Keywords: linked data, Wikidata, data management
Resource type: Slides
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
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
Module also available as self-study material in data carpentry style
Scientific topics: Data management
Keywords: system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers
Resource type: course materials
Wikidata
fairification
Keywords: FAIR, linked data, ontologies, metadata
Resource type: Slides
Managing increasing numbers of data objects
Sharing data from different sourcesamongst researchers
Data needs to be (globally) identifiable and addressable to ensure reuse of data
Data citation
Linking data from different source
Keywords: Referencing data and code, Findability of data and code, Identifying data and code, data management
Resource type: Slides
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
This guide will introduce you to writing tool wrappers and workflows using the Common Workflow Language (CWL). This guide describes the current stable specification, version 1.0.
Keywords: CWL, commonwl, Workflows
Resource type: Tutorial
These are the materials of the talks and demo that were presented at the ECCB18 Workshop “Implementation of Data Management Plans & Data Stewardship in practice” on Sept 11, 2018 in Athens.
Collecting, curating, storing and exchange or sharing research data is a constant challenge that has...
Scientific topics: Data submission, annotation, and curation, Data management
Keywords: data management, data stewardship, eLearning, EeLP
Resource type: course materials, Training materials, Slides
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
This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API.
Scientific topics: Pharmacology, Drug discovery
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
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
This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...
Keywords: Programming, Python, Python biologists