IFB French Institute of Bioinformatics

The French Institute of Bioinformatics (CNRS IFB) is a national service infrastructure in bioinformatics. IFB’s principal mission is to provide basic services and resources in bioinformatics for scientists and engineers working in the life sciences. IFB is the French node of the European research infrastructure, ELIXIR.

IFB French Institute of Bioinformatics http://tess.elixir-uk.org/content_providers/ifb-french-institute-of-bioinformatics The French Institute of Bioinformatics (CNRS IFB) is a national service infrastructure in bioinformatics. IFB’s principal mission is to provide basic services and resources in bioinformatics for scientists and engineers working in the life sciences. IFB is the French node of the European research infrastructure, ELIXIR. /system/content_providers/images/000/000/049/original/logo-ifb-couleur.svg?1663599376
Showing 138 materials out of 138. View all results.
Variants: alignment and pre-treatment; GATK

Variant calling practical session

Keywords: Genomics

Welcome and Introduction

 

Introduction message of the EGDW 2017
 

Getting started with Bioschemas

"How to do" guidelines about:

  • What and why schema.org
  • What and why bioschemas.org
  • How-to select the right profile for your resource
  • How-to mark up your own resource with Bioschemas

Keywords: Bioschemas, Standards

FAIR principles applied to bioinformatics

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

Chip-seq: Pattern Analysis tutorial

Goal
The aim is to :

Get familiar with motif analysis of ChIP-seq data.
Learn de novo motif discovery methods.

In practice :

Motif discovery with peak-motifs
Differential analysis
Random controls

Keywords: Chip-seq, NGS, Pattern recognition

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

Keywords: Plant Phenotyping, Data-format, data sharing

Resource type: Training materials

IFB Shiny training

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

WheatIS DataDiscovery webinar

The WheatIS project aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is...

Scientific topics: Data management

Keywords: wheat, information system, data discovery

Resource type: Webinar, Slides, Video

Variant Filtering

Some use cases :

  • Extract a subset of variants (localization, type)

  • Combine variants from several analyses

  • Compare obtained variants from several data types (RNA

...

Keywords: Genomics

Sequencing 6000 chloroplast genomes : the PhyloAlps project

Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding...

Keywords: metagenomics

Prototyping the new PSICQUIC 2.0

Prototyping the new PSICQUIC 2.0

Keywords: biohackaton 2018

RGP finder: prediction of Genomic Islands

Prediction of Region of Genomic Plasticity (RGPs) and CoDing Sequences (CDSs) and visualization

Keywords: CDS, Data visualization, Genomics, RGP

Chip-seq: Functional Annotation tutorial

Global Objective

Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Chip-seq, Functional Annotation, NGS

MG-RAST — experiences from processing a quarter million metagenomic data sets

MG-RAST has been offering metagenomic analyses since 2007. Over 20,000 researchers have submitted data. I will describe the current MG-RAST implementation and demonstrate some of its capabilities. In the course of the presentation I will highlight several metagenomic pitfalls. MG-RAST:...

Keywords: metagenomics

bio.tools & EDAM drop-in hackathon & discussions

bio.tools, EDAM drop-in hackathon and discussions

Keywords: biohackaton 2018

200 billion sequences and counting: analysis, discovery and exploration of datasets with EBI Metagenomics

EBI metagenomics (EMG, https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of...

Keywords: metagenomics

Multiple Comparative Metagenomics using Multiset k-mer Counting

Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can...

Keywords: metagenomics

From Samples to Data : Assuring Downstream Analysis with Upstream Planning

Metagenomic studies have gained increasing popularity in the years since the introduction of next generation sequencing. NGS allows for the production of millions of reads for each sample without the intermediate step of cloning. However, just as in the past, the quality of the data generate by...

Keywords: metagenomics

Exploiting collisions between DNA molecules to characterize the genomic structures of complex communities

Meta3C is an experimental and computational approach that exploits the physical contacts experienced by DNA molecules sharing the same cellular compartments. These collisions provide a quantitativeinformation that allows interpreting and phasing the genomes present within complex mixes of species...

Keywords: metagenomics

NGS data exploration with the MicroScope Platform

Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools

Keywords: Genomics, NGS, RNA-seq, SNP, Transcriptomics

Gut metagenomics in cardiometabolic diseases

Cardio-metabolic and Nutrition-related diseases (CMDs) represent an enormous burden for health care. They are characterized by very heterogeneous phenotypes progressing with time. It is virtually impossible to predict who will or will not develop cardiovascular comorbidities. There is a clear...

Keywords: metagenomics

A Simple Phylogenetic Tree Construction (part 2)

Understand the method used in identifying an unknown sequence.
Understand the limitations of this method
Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot)

Keywords: Phylogenetics

New perspectives on nitrite-oxidizing bacteria - linking genomes to physiology

It is a generally accepted characteristic of the biogeochemical nitrogen cycle that nitrification is catalyzed by two distinct clades of microorganisms. First, ammonia-oxidizing bacteria and archaea convert ammonia to nitrite, which subsequently is oxidized to nitrate by nitrite-oxidizing...

Keywords: metagenomics

Welcome message

Presentation of the workshop (Chairman: Victoria Dominguez Del Angel)

Keywords: biohackaton

Holistic metagenomics in marine communities

Complex microscopic communities are composed of species belonging to all life realms, from single-cell prokaryotes to multicellular eukaryotes of small size. Each component of a community needs to be studied for a full understanding of the functions performed by the whole assemblage, however...

Keywords: metagenomics

Assessing microbial biogeography by using a metagenomic approach

Soils are highly complex ecosystems and are considered as one of the Earth’s main reservoirs of biological diversity. Bacteria account for a major part of this biodiversity, and it is now clear that such microorganisms have a key role in soil functioning processes. However, environmental factors...

Keywords: metagenomics

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

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

Keywords: Data preserving, Data storage

Resource type: Slides

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

Galaxy III: Visualization

Visualization of Next Generation Sequencing Data using the Integrative Genomics Viewer (IGV)

Keywords: Genomics

REPET: TEdannot Tutorial

TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo

Keywords: Annotation, Genomics

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

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

Resource type: Slides

REPET: TEdenovo tutorial

The TEdenovo pipeline follows a philosophy in three first steps:

Detection of repeated sequences (potential TE)
Clustering of these sequences
Generation of consensus sequences for each cluster, representing the ancestral TE

Keywords: Annotation, Genomics

Genomic copy number Analysis

No description available

Keywords: Copy number, Structural genomics

Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a...

Keywords: metagenomics

Chip-seq Analysis

Quality, normalisation and peak calling

Keywords: Chip-seq, Genomics

x2Go

Opening an x2go session to the IFBcloud

Keywords: Cloud

Galaxy: Initiation II

Galaxy II: common tools, quality control; alignment; data managment

Keywords: Genomics

OmicsPath: Finding Relevant omics datasets using pathway information

 

OmicsPath: Finding Relevant omics datasets using pathway information
 

Keywords: biohackaton 2018

Prokaryotic Phylogeny on the Fly: databases and tools for online taxonomic identification

PPF (Prokaryotic Phylogeny on the Fly) is an automated pipeline allowing to compute molecular phylogenies for prokarotic organisms. It is based on a set of specialized databases devoted to SSU rRNA, the most commonly used marker for bacterial txonomic identification. Those databases are splitted...

Keywords: metagenomics

Rationale and Tools to look for the unknown in (metagenomic) sequence data

The interpretation of metagenomic data (environmental, microbiome, etc, ...) usually involves the recognition of sequence similarity with previously identified (micro-organisms). This is for instance the main approach to taxonomical assignments and a starting point to most diversity analyses....

Keywords: metagenomics

RNA - Seq de novo

Practical session on transciptome de novo assembly

Keywords: RNA-seq

PASTEClassifier Tutorial

The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 )

Keywords: Genomics, Transposons

Soil metagenomics, potential and pitfalls

The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation)....

Keywords: metagenomics

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment

 

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment
 

Keywords: biohackaton 2018

Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases

Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases

Keywords: biohackaton 2018

Visualization of NGS data with IGV

Visualisation of next-gen sequencing data with Integrative Genomics Viewer

Keywords: Data visualization, Genomics, NGS

Revealing and analyzing microbial networks: from topology to functional behaviors

Understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is a complicated...

Keywords: metagenomics

Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)

 

Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)
 

Keywords: biohackaton 2018

DNA - seq Bioinformatics Analysis

Detection of Copy Number Variations
 

Keywords: DNA-seq

The IFB cloud for bioinformatics

Practical work to introduce basic and advanced usage of the IFB cloud
Howto launch virtual machines
Managing your data in the cloud ;
Howto to connect to your VMS (SSH, web, remote desktop)
Personalizing your VMs (approver, galaxy, docker)

Keywords: Cloud computing, Virtual machine

Hidden in the permafrost

The last decade witnessed the discovery of four families of giant viruses infecting Acanthamoeba. They have genome encoding from 500 to 2000 genes, a large fraction of which encoding proteins of unknown origin. These unique proteins meant to recognize and manipulate the same building blocks as...

Keywords: metagenomics

Dr Jekyll and Mr Hyde: The dual face of metagenomics in phylogenetic analysis

The aim of this lecture is to present the impact of metagenomics and single-cell genomics on public databases. These new powerful approches allow us to have access to the diversity of life on our planet. However, care has to be taken when using these data for posterior analyses, such as...

Keywords: metagenomics

Deciphering the human intestinal tract microbiome using metagenomic computational methods

In 2010, the MetaHIT consortium published a 3.3M microbiota gene catalog generated by whole genome shotgun metagenomic sequencing, representing a mixture of bacteria, archaea, parasites and viruses coming from 124 human stool metagenomic samples [Qin et al, Nature 2010].
However most of the genes...

Keywords: metagenomics

Plant Phenotyping Data managment Webinar (MIAPPE)

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

Resource type: Video, Slides

Snakemake tutorial: Gene regulation

Workflow 1: Rules and targets
Workflow 2: Introducing wildcards
Workflow 3: Keywords
Workflow 4: Combining rules
Workflow 5: Configuration file
Workflow 6: Separated files

Keywords: Gene regulation, Snakemake

Fast filtering, mapping and assembly of 16S ribosomal RNA

The application of next-generation sequencing technologies to RNA orDNA directly extracted from a community of organisms yields a mixtureof nucleotide fragments. The task to distinguish amongst these and tofurther categorize the families of ribosomal RNAs (or any other givenmarker) is an...

Keywords: metagenomics

Reconstructing genomes from metagenomes: The holy grail of microbiology

Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information...

Keywords: metagenomics

Variants: alignment and pre-treatment; GATK

DNA-seq Bioinformatics Analysis: from raw sequences to processed alignments

Keywords: Genomics

A Simple Phylogenetic Tree Construction (part 1)

Understand the method behind constructing a phylogenetic tree from the search for sequences to the analysis of the tree.
Get to grips with various bio-informatic software (BLAST, CLUSTALw, SeaView and Phylo_win).

Keywords: Phylogenetics

Chip Seq: Annotation and visualization Lesson

How to add biological meaning to peaks

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Import workflows into TeSS Concept Maps

 

Import workflows into TeSS Concept Maps
 

Keywords: biohackaton 2018

Pathway effect prediction for protein targets

 

Pathway effect prediction for protein targets
 

Keywords: biohackaton 2018

Initiation to Galaxy

DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.

Keywords: DNA Analysis, Galaxy, Variant calling

Adding bioschemas markup to data repository

 

Adding bioschemas markup to data repository
 

Keywords: biohackaton

Variant Filtering

Use cases:
Extact a subset of variants
Combine variants from several analysis

Compare obtained variants from several data types

Identify new variants compare to a reference list

Apply specific filters for Chip Design

Keywords: NGS, Variant calling

Defining and importing genomes, Data Managers into Galaxy

Intro to built in datasets
Built in data hierarchy
Some problems
Data Managers

Keywords: Galaxy

Genomic copy number Tutorial

We will analyze the copy number variations of a human tumor (parotid gland carcinoma), limited to the chr17, from a WES (whole-exome sequencing) experiment. All genomic coordinates correspond to the 2009 build of the reference human genome (hg19 / GRC37).

Keywords: Copy number, Structural genomics

RADSeq Data Analysis

Introduction to RADSeq through STACKS on Galaxy

Keywords: NGS

Statistics with RStudio

Introduction to statistics with R

Keywords: R

Prototyping the new PSICQUIC 2-0

 

Prototyping the new PSICQUIC 2.0
 

CWL support in Galaxy

 

CWL support in Galaxy
 

Keywords: biohackaton 2018

Using blockchain in biomedical provenance, the identifiers use case

 

Using blockchain in biomedical provenance, the identifiers use case
 

Keywords: biohackaton 2018

JSON schema validation with ontologies

 

JSON schema validation with ontologies
 

Keywords: biohackaton 2018

ProtVista (protein annotation viewer) extension using Bioschemas data

 

ProtVista (protein annotation viewer) extension using Bioschemas data
 

Keywords: biohackaton 2018

Development of a GA4GH-compliant, language-agnostic workflow execution service

 

Development of a GA4GH-compliant, language-agnostic workflow execution service
 

Keywords: biohackaton 2018

Data clearinghouse, validation and curation of BioSamples - ENA - Breeding API endpoints - MAR databases

 

Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases
 

Docker and Galaxy

Questions
Why Docker? What is it?
How to use Docker?
How to integrate Galaxy in Docker to facilitate its deployment?
Objectives
Docker basics
Galaxy Docker image (usage)
Galaxy Docker (internals)
Galaxy flavours

Keywords: Docker, Galaxy

Users, Groups, and Quotas in Galaxy

How to handle Users, Groups, and Quotas in Galaxy

Keywords: Galaxy

Galaxy Interactive Tour

Questions
What is a Galaxy Interactive Tour?
How to create a Galaxy Interactive Tour?
Objectives
Discover what is a Galaxy Interactive Tour
Be able to create a Galaxy Interactive Tour
Be able to add a Galaxy Interactive Tour in a Galaxy instance

Keywords: Galaxy

Eukaryotic small RNA

 

Small RNAseq data analysis for miRNA identification
 

Keywords: RNA-seq

Development in Galaxy

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project.

Keywords: Galaxy

Connecting Galaxy to a compute cluster

Problems
Running jobs on the Galaxy server negatively impacts Galaxy UI performance
Even adding one other host helps
Can restart Galaxy without interrupting jobs
Solution:
Connecter Galaxy to a computing cluster

Keywords: Cluster, Galaxy

Searching for sequence: Tutorial

Quick Search is dedicated to a quick search for sequences or sequence families in the databases available on the PBIL server. It is an alternative to WWW Query which allows more complex queries. Quick Search allows you to retrieve sequences or sequence families associated to a single word without...

Keywords: genomics, pattern recognition

RNA-Seq: isoform detection and quantification

transcriptome from new condition
tissue-speci c transcriptome
different development stages
transcriptome from non model organism
cancer cell
RNA maturation mutant
 
How to manage RNA-Seq data with genes subjected to di erential
splicing?
Is it possible to discover new isoforms?
Is it possible to...

Keywords: Isoforms, RNA-seq, Transcriptomics

Development of BioJS components

 

Development of BioJS components
 

Keywords: biohackaton 2018

Building a semantic search engine for biology publications using event stream processing

 

Building a semantic search engine for biology publications using event stream processing
 

Keywords: biohackaton 2018

Tool development and integration into Galaxy

Questions:
What is a tool for Galaxy?
How to build a tool/wrapper with the good practices?
How to deal with the tool environment?
 
Objectives:
Discover what is a wrapper and its structure
Use the Planemo utilities to develop a good wrapper
Deal with the dependencies
Write functional tests
Make a...

Keywords: Galaxy

Enrichment and propagation of metagenomic experimental metadata

 

Enrichment and propagation of metagenomic experimental metadata
 

Keywords: biohackaton 2018

Application of RDF-based models and tools for enhancing interoperable

 

Application of RDF-based models and tools for enhancing interoperable use of biomedical resources
 

Keywords: biohackaton 2018

Exploring Microscope Platform

 

How to use the Microscope Platform to annotate and analyze microbial genomes.
 

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics

Chip-seq: Motif Analysis Tutorial

Introduction
Goal
The aim is to :
Get familiar with motif analysis of ChIP-seq data.
Learn de novo motif discovery methods.
In practice :
Motif discovery with peak-motifs
Differential analysis
Random controls

Keywords: Chip-seq, Motif analysis, NGS, Pattern recognition

Docker tutorial: Gene regulation

Get started with Docker!
Create a Docker account
Install Docker on your local host
Create shared repositories and download source data
Fetch the Docker image and run it with shared folders
Execute the pipeline

JVH / Mac

Keywords: Docker, Gene regulation

Development of a catalog of federated SPARQL queries in the field of Rare Diseases

 

Development of a catalog of federated SPARQL queries in the field of Rare Diseases
 

Keywords: biohackaton 2018

Chip-seq: Peak calling tutorial

The aim is to :
Understand how to process reads to obtain peaks (peak-calling).
Become familiar with differential analysis of peaks
In practice :
Obtain dataset from GEO
Analyze mapped reads
Obtain set(s) of peaks, handle replicates
Differential analysis of peak

Keywords: Chip-seq, NGS, Peak calling

Exercices on Galaxy: metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

Alternative episodes for the 4 Open Source Software

 

Alternative episodes for the 4 Open Source Software (4OSS) lesson focused on different Open Source technologies: Github, Docker, Jupyter Notebook and so on
 

Keywords: biohackaton 2018

Galaxy Administration

How to use the administation panel of Galaxy

Keywords: Galaxy

Analysis of community composition data using phyloseq

Learn about and become familiar with phyloseq R package for the analysis of microbial census data

Keywords: Microbiomes, R

Docker for Beginners

What is Docker?
Building an image
BioShadock & Orchestration

Keywords: Docker

(Proxy) Web Server Choices and Configuration

Installation and configuration of NGiNX for Galaxy

Keywords: Galaxy, NGiNX

Galactic Database

How to choose a database for Galaxy and configure it

Keywords: Galaxy

Assessing the FAIRness of Training Materials

 

Assessing the FAIRness of Training Materials
 

Keywords: biohackaton 2018

Galaxy Docker Training Tutorial

Galaxy docker integration
Enable Galaxy to use BioContainers (Docker)
Galaxy with Docker swarm

Keywords: Docker, Galaxy

Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships

 

Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships
 

Keywords: biohackaton 2018

Exploring microbiomes with the MicroScope Platform

This module is separated in different courses:
MicroScope: General overview, Keyword search and gene cart functionalities

Functional annotation of microbial genomes

Functional annotation of microbial genomes: Prediction of enzymatic functions

Relational annotation of...

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics

Galaxy Configuration Hierarchy

How to configure your local instance of Galaxy

Keywords: Galaxy

Cross Taxa Tutorial

How query databases according to complex taxonomic critera
Cross-Taxa allows to retrieve gene families that are shared by a given set of taxa, or which are specific to a set of taxa. It is also possible to select genes families which are associated to a certain set of taxa but which are not found...

Keywords: genomics

Chip Seq: Annotation and visualization Tutorial

Global Objective
Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Annotation, Chip-seq, Data Visualization, NGS

BioBlend API

BioBlend module, a python library to use Galaxy API

Keywords: API, Galaxy, Python

Transcriptome de novo assembly

Not available

Keywords: Transcriptomics

Variant annotation

Add meta-information on variant to facilitate interpretation

Keywords: Variant analysis

Differential analysis of RNA-Seq data

Design, describe, explore and model

Keywords: Genomics, RNA-seq

RNA-seq: Differential gene expression analysis

Transcriptome analysis provides information about the identity and quantity of all RNA molecules

Keywords: Genomics, RNA-seq

Third generation sequencing : the revolution of long reads

Introduction on sequencing: available technologies, library types, applications ...

Keywords: Genomics

Training on Galaxy : Metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

A Quick and focused overview of R data types and ggplot2 syntax

R and RStudio overview.

Keywords: Graphical analysis, R, Statistics

Docker Tutorial

Docker is free software that automates the deployment of applications in software containers executant in isolation. A Docker container, away from traditional virtual machines, requires no separate operating system and not providing any but relies instead on the core functionality and uses the...

Keywords: Docker

HOVERGEN tutorial

HOVERGEN is a database containing homologous vertebrate protein and nucleotide sequences. It allows to easily select similar gene sequences from a wide range of vertebrates. Hence it becomes particularly useful in comparative genomics, phylogeny and evolutionary studies on a molecular level....

Keywords: genomics, proteomics

Chip-seq: Introduction to the Workshop

Data visualization, quality control, normalization & peak calling
Peak annotation
From peaks to motifs

Keywords: Chip-Seq

IFB Cloud tutorial: Gene regulation

  1. Using the Gene-regulation appliance
    1.1 Requirements
    1.2 Virtual disk creation
    1.3 Creation of an instance
    1.4 Connection to the device
    1.5 Download source data
    1.6 Execute workflow

  2. Visualizing results
    2.1 Install and run the X2Go client on your host computer
    2.2 Visualize...

Keywords: Cloud Computing, Gene Regulation

ToolShed upload and tool-iuc PR

Questions
What is a Tool Shed?
How to install tools and workflows from a Tool Shed into a Galaxy instance?
What are the Tool Shed repository types?
How to publish with Planemo?
Objectives
Discover what is a Tool Shed
Be able to install tools and workflows from a Tool Shed into a Galaxy...

Keywords: Galaxy

bio-tools - EDAM drop-in hackathon - discussions

bio.tools, EDAM drop-in hackathon and discussions

Galaxy Installation

How to install a local instance of Galaxy

Keywords: Galaxy

Galaxy Visualisation - Slides

Questions

How can visualization plugins benefit science?

Objectives

Implement a first Galaxy visualization
Understand the client side vs. server side principle

Keywords: Galaxy

Putting structured data into individual entry pages in biological database

 

Putting structured data into individual entry pages in biological database
 

Keywords: biohackaton 2018

Galaxy training material improvement and extension

 

Galaxy training material improvement and extension
 

Keywords: biohackaton 2018

Transfer of Research Assets between FAIRDOM SEEKs

 

Transfer of Research Assets between FAIRDOM SEEKs
 

Keywords: biohackaton 2018

Support tools for rapid adoption of compact identifiers in the publishing process

 

Support tools for rapid adoption of compact identifiers in the publishing process
 

Keywords: biohackaton 2018

From Biotea to Bioschemas: definition of profiles required to represent scholarly publications

 

From Biotea to Bioschemas: definition of profiles required to represent scholarly publications
 

Keywords: biohackaton 2018

DNA-seq analysis: From raw reads to processed alignments

Objectives:
Mapping the DNA-seq data to the reference genome
Process the alignments for the variant calling

Keywords: Alignment, DNA-seq, Genomics, Variant calling

Chip-seq: Discovering motifs in peaks with RSAT

Read mapping: from raw reads to aligned reads.
Peak calling: from aligned reads to regions/peaks of high read density.
ChIP-seq annotation
Identification of genes related to the peaks.
Profiles of ChIP-seq reads around reference points (TSS, histone marks,).
Functional enrichment of the genes...

Keywords: Chip Seq, Motif Analysis, NGS

Differential gene expression analysis : Practical part

RNA-seq: Differential gene expression analysis practical session

Keywords: Genomics, RNA-seq

Galaxy Visualisation - Tutorial

Visualizations may be very helpful in understanding data better. There is a whole range of visualizations, from rather simple scatter and barplots up to projections of high dimensional data or even entire genomes. Many of these visualizations often require a lot of tweaking and changes in...

Keywords: Youri Hoogstrate

RNA-Seq: Differential Expression Analysis

 

Be careful about experimental design : avoid putting all the
replicates in the same lane, using the same barcode for the
replicates, putting different number of samples in lanes etc...
Non- uniformity of the per base read distribution (Illumina Random
Hexamer Priming bias visible on the 13...

Keywords: Differential Expression, RNA-seq, transcriptomics

Improve Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits

 

Improve Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits
 

Keywords: biohackaton 2018

Galaxy Handlers

Galaxy is a web application that uses handlers to perform actions.
There are two main types of actions that are carried out by handlers:
Respond to user requests; These actions are carried out by web handlers
Manage the execution of tools; These actions are performed by job handlers.
By default,...

Keywords: Galaxy

Showing 2 upcoming events. Found 418 past events. View all results.
  • Ecole Thématique de Bioinformatique Intégrative - session 2023 / Integrative Bioinforformatics training school - 2023 session

    16 - 20 January 2023

    Fréjus, France

    ELIXIR node event
  • NGS data analysis on the command line - Session 5

    2 - 6 March 2023

    Strasbourg, France

    ELIXIR node event