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.

Introduction message of the EGDW 2017

Assessing the FAIRness of Training Materials

JSON schema validation with ontologies

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

"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

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

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

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...

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

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

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...

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...

Introduction to statistics with R

Small RNAseq data analysis for miRNA identification

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...

How to use the administation panel of Galaxy

How to handle Users, Groups, and Quotas in Galaxy

Some use cases :

• Extract a subset of variants (localization, type)

• Combine variants from several analyses

• Compare obtained variants from several data types (RNA

...

OmicsPath: Finding Relevant omics datasets using pathway information

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

Variant calling practical session

BioBlend module, a python library to use Galaxy API

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...

CWL support in Galaxy

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...

Prototyping the new PSICQUIC 2.0

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

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

Global Objective

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

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:...

bio.tools, EDAM drop-in hackathon and discussions

How to install a local instance of Galaxy

Pathway effect prediction for protein targets

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

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

Variant calling practical session

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...

Import workflows into TeSS Concept Maps

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...

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...

Enrichment and propagation of metagenomic experimental metadata

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...

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)

Find Rapidly OTU with Galaxy Solution

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

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...

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...

Development of BioJS components

RNA-seq: Differential gene expression analysis practical session

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).

Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships

Transfer of Research Assets between FAIRDOM SEEKs

How to add biological meaning to peaks

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...

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...

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

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment

Putting structured data into individual entry pages in biological database

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

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

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...

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

ProtVista (protein annotation viewer) extension using Bioschemas data

Galaxy training material improvement and extension

What is Docker?
Building an image
BioShadock Orchestration

How to configure your local instance of Galaxy

Introduction to RADSeq through STACKS on Galaxy

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...

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...

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

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

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

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...

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

Add meta-information on variant to facilitate interpretation

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

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

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...

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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

No description available

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

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

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...

Quality, normalisation and peak calling

Opening an x2go session to the IFBcloud

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
   

   1. Visualizing results

      2.1 Install and run the X2Go client on your host computer
      2.2...

Using blockchain in biomedical provenance, the identifiers use case

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

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

Objectives:

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

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....

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

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

Find Rapidly OTU with Galaxy Solution

Questions

How can visualization plugins benefit science?

Objectives

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

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...

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

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....

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

Practical session on transciptome de novo assembly

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

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 )

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)....

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...

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

Design, describe, explore and model

R and RStudio overview.

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

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

Installation and configuration of NGiNX for Galaxy

Detection of Copy Number Variations

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

Visualisation of next-gen sequencing data with Integrative Genomics Viewer

Adding bioschemas markup to data repository

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

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...

Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)

How to choose a database for Galaxy and configure it

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)

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...

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...

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).

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...

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...

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...

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...

Global Objective

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

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...

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...

Workflow 1: Rules and targets

Workflow 2: Introducing wildcards

Workflow 3: Keywords

Workflow 4: Combining rules

Workflow 5: Configuration file

Workflow 6: Separated files

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...

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...