Galaxy Training

GitHub repository and its website companion containing a collection of training materials for teaching next generation sequencing data analysis uing Galaxy.

Galaxy Training http://tess.elixir-uk.org/content_providers/galaxy-training GitHub repository and its website companion containing a collection of training materials for teaching next generation sequencing data analysis uing Galaxy. /system/content_providers/images/000/000/078/original/GTNLogo1000.png?1501677361
Showing 476 materials out of 476. View all results.
Galaxy Server administration - Galaxy from an administrator point of view

Resources related to configuration and maintenance of Galaxy servers

Introduction to 'Epigenetics'

Slides for Epigenetics

Scientific topics: Epigenomics

Resource type: slides

Introduction to Galaxy - Multisample Analysis

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Resource type: Tutorial

Introduction to 'Transcriptomics'

Slides for Transcriptomics

Scientific topics: Transcriptomics

Resource type: slides

Introduction to 'Proteomics'

Slides for Proteomics

Scientific topics: Proteomics

Resource type: slides

Introduction to 'Genome Annotation'

Slides for Genome Annotation

Resource type: slides

Introduction to 'Variant Analysis'

Slides for Variant Analysis

Scientific topics: Genetic variation

Resource type: slides

Slides for 'Galaxy workflows in Dockstore' tutorial

The objectives are:
- What is Dockstore?
- Why use Dockstore?
- How to find workflows on Dockstore?
- How to launch workflows from Dockstore?
- Getting started with Galaxy workflows on Dockstore
- Register your Galaxy workflow on Dockstore

Keywords: galaxy-interface

Resource type: slides

Slides for 'Functionally Assembled Terrestrial Ecosystem Simulator (FATES)' tutorial

The questions this addresses are:
- What is FATES?
- How can I use FATES?

\nThe objectives are:
- Have an understanding of what FATES is and how it works

Keywords: climate, climate, ecology

Resource type: slides

Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • What are benefits and drawbacks of different quantitation methods?
  • How to choose which quantitation method bests suits my need?

Objectives of the tutorial:

  • Choose your quantitation method.

Resource type: Tutorial

Sequence analysis - Mapping

Analyses of sequences

Questions of the tutorial:

  • What two things are crucial for a correct mapping?
  • What is BAM?

Objectives of the tutorial:

  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data

Resource type: Tutorial

Galaxy Server administration - Docker and Galaxy

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • Why Docker? What is it?
  • How to use Docker?
  • How to integrate Galaxy in Docker to facilitate its deployment?

Objectives of the tutorial:

  • Docker basics
  • Galaxy Docker image (usage)
  • Galaxy...

Resource type: Slides

Statistics - Interval-Wise Testing for omics data

Statistical Analyses for omics data

Questions of the tutorial:

  • How to visualize high-resolution omics data in different groups of genomic regions?
  • How to evaluate differences in high-resolution omics data between groups of genomic regions?
  • How to detect locations and scales at which the...

Resource type: Tutorial

Metagenomics - Analyses of metagenomics data - The global picture

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Questions of the tutorial:

  • How to analyze metagenomics data?
  • What information can be extracted of metagenomics data?
  • What is the difference between amplicon and shotgun data?
  • What are the difference...

Resource type: Tutorial

Slides for 'Introduction to ATAC-Seq data analysis' tutorial

The questions this addresses are:
- What is ATAC-Seq?
- What are the quality parameters to check for each dataset?
- How to analyse ATAC-Seq data?

\nThe objectives are:
- Understand ATAC-Seq
- Quality Parameters for ATAC-Seq
- Understand Peak calling for ATAC-Seq

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: slides

Transcriptomics - Reference-based RNA-Seq data analysis

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • What are the effects of Pasilla (PS) gene depletion on splicing events?
  • How to analyze RNA sequencing data using a reference genome?

Objectives of the tutorial:

  • Analysis of RNA sequencing data using...

Resource type: Tutorial

Development in Galaxy - Tool development and integration into Galaxy

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What is a tool for Galaxy?
  • How to build a tool/wrapper with the good practices?
  • How to deal with the...

Resource type: Tutorial

Proteomics - Peptide and Protein ID using OpenMS tools

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to convert LC-MS/MS raw files?
  • How to identify peptides?
  • How to identify proteins?
  • How to evaluate the results?

Objectives of the tutorial:

  • Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Sequence analysis - RAD-Seq de-novo data analysis

Analyses of sequences

Questions of the tutorial:

  • How to analyze RAD sequencing data without a reference genome for a population genomics study?

Objectives of the tutorial:

  • Analysis of RAD sequencing data without a reference genome
  • SNP calling from RAD sequencing data
  • Calculate...

Resource type: Tutorial

Introduction to Galaxy Analyses - Galaxy 101

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • Which coding exon has the...

Resource type: Tutorial

Assembly - Unicycler Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Transcriptomics - Introduction to Transcriptomics

Training material for all kinds of transcriptomics analysis.

Train the trainers - Good practices to run a workshop

Train the trainers

Questions of the tutorial:

  • What do we need to take care when running a workshop?
  • What are the good practices?

Objectives of the tutorial:

  • Reflect on the things to do before, during and after a workshop

Introduction to Galaxy Analyses - Introduction to Genomics and Galaxy

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • Do genes on opposite strands...

Resource type: Tutorial

Transcriptomics - Visualization of RNA-Seq results with CummeRbund

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How are RNA-Seq results stored?
  • Why are visualization techniques needed?
  • How to select our desired subjects for differential gene expression analysis?

Objectives of the tutorial:

  • Manage RNA-Seq...

Resource type: Tutorial

Introduction to Galaxy - Using dataset collection

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • How to manipulate large numbers...

Resource type: Tutorial

Galaxy Introduction - Visualization

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Galaxy Server administration - Move from dev instance to production instance

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Questions of the tutorial:

-

Objectives of the tutorial:

-

-

Introduction to Galaxy - Understanding Galaxy history system

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • How do Galaxy histories...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Good practices to run a workshop

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Slides

Galaxy Server administration - Advanced customisation of a Galaxy instance

Resources related to configuration and maintenance of Galaxy servers

Resource type: Slides

Development in Galaxy - BioBlend module, a Python library to use Galaxy API

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What is the use of BioBlend?
  • How to use Galaxy through command line?

Objectives of the tutorial:

  • Get...

Resource type: Slides

Variant Analysis - Microbial Variant Calling

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How do we detect differences between a set of reads from a microorganism and a reference genome

Objectives of the tutorial:

  • Find variants between a reference genome and a set of...

Resource type: Tutorial

Tutorials using public Galaxy at usegalaxy.org - NGS data logistics

This tutorials cover a variety of analyses that can be performed at usegalaxy.org

Questions of the tutorial:

  • How to manipulate and process NGS data

Objectives of the tutorial:

  • Learn about Fastq, SAM, and BAM.

Tutorials using public Galaxy at usegalaxy.org - Calling very rare variants

This tutorials cover a variety of analyses that can be performed at usegalaxy.org

Questions of the tutorial:

  • What is frequency of variants is so low that it is obscured by sequencing error rate?

Objectives of the tutorial:

  • Learn about duplex sequencing and analysis of duplex reads

Train the trainers - Creating a new tutorial - Defining metadata

Train the trainers

Questions of the tutorial:

  • What does Metadata in GTN means?
  • Which kind of metadata can I annotate?
  • For what is metadata used?

Objectives of the tutorial:

  • Adding metadata for a tutorial
  • Defining learning objectives

Development in Galaxy - Galaxy Interactive Tours

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What is a Galaxy Interactive Tour?
  • How to create a Galaxy Interactive Tour?

Objectives of the...

Resource type: Slides

Contributing to the Galaxy Training Material - Set up a Galaxy for Training

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Galaxy Server administration - User, Group and Quota managment

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • How does Galaxy manage users and groups?
  • How can I assign Quotas to specific users/groups?

Objectives of the tutorial:

  • Learn the Galaxy user/group management and assign Quotas.
  • Understand...

Resource type: Slides

User Interface and Features - Workflows: Extracting Workflows from Histories

A collection of microtutorials explaining various features of the Galaxy user interface

Questions of the tutorial:

  • What is a workflow?
  • How can I create a workflow based on my analysis history?

Objectives of the tutorial:

  • Learn how to extract a workflow from a Galaxy history
  • Learn how...

Resource type: Tutorial

Data Manipulation - Data: Getting data into Galaxy

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Slides

Data Manipulation - Collections: Multisample Analysis

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Tutorial

Introduction to Galaxy - Using dataset collection

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • How to manipulate large numbers...

Introduction to Galaxy - Rule Based Uploader

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • How to use the rule based...

Resource type: Tutorial

Tutorials using public Galaxy at usegalaxy.org - Calling variants in diploid systems

This tutorials cover a variety of analyses that can be performed at usegalaxy.org

Questions of the tutorial:

  • How to find variable sites in diploid genomes?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in human genome.

Metagenomics - Introduction to metagenomics

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Introduction to Galaxy Analyses - Introduction to Galaxy

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

ChIP-Seq data analysis - Introduction to ChIP-Seq data analysis

ChIP-sequencing is a method used to analyze protein interactions with DNA.

Tutorials using public Galaxy at usegalaxy.org - Calling variants in non-diploid systems

This tutorials cover a variety of analyses that can be performed at usegalaxy.org

Questions of the tutorial:

  • How does frequency of mitochondrial polymorphisms change from mother to child?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in bacteria,...

Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How is raw CLIP-Seq data processed and analysed?
  • How do I find binding motifs and targets for a protein (e.g., RBFOX2)?

Objectives of the tutorial:

  • Remove Adapters, Barcodes and Unique Molecular...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Contributing with GitHub via command-line

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Development in Galaxy - Galaxy Interactive Environments

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What are Galaxy Interactive Environments (GIEs)?
  • How to enable GIEs in Galaxy?
  • How to develop your own...

Resource type: Slides

Train the trainers - Creating a new tutorial - Building a Docker flavor for a tutorial

Train the trainers

Questions of the tutorial:

  • How can we define the technical infrastructure for a tutorial?
  • How to define the tools needed for a tutorial?
  • How to add the needed data directly in an instance?
  • How to add the workflows related to a tutorial?
  • How can we check the...

ChIP-Seq data analysis - Identification of the binding sites of the Estrogen receptor

ChIP-sequencing is a method used to analyze protein interactions with DNA.

Questions of the tutorial:

  • How is raw ChIP-seq data processed and analyzed?
  • What are the binding sites of the Estrogen receptor?

Objectives of the tutorial:

  • Inspect read quality with FastQC
  • Map reads with...

Resource type: Tutorial

Data Manipulation - Collections: Rule Based Uploader

A collection of microtutorials explaining data manipulation within Galaxy

Questions of the tutorial:

  • How to use the rule based uploader to create complex collections

Objectives of the tutorial:

  • Learn about the Rule Based Uploader

Resource type: Tutorial

Introduction to Galaxy - Extracting Workflows from Histories

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • What is a workflow?
  • How can I...

Resource type: Tutorial

Slides for 'Server: Other' tutorial

The questions this addresses are:
- How to monitor a Galaxy service?

\nThe objectives are:
- Learn about different monitoring strategies.
- Setup and start the Galaxy reports app.

Keywords: admin

Resource type: slides

Hands-on for 'Protein-ligand docking' tutorial

The questions this addresses are:
- What is cheminformatics?
- What is protein-ligand docking?
- How can I perform a simple docking workflow in Galaxy?

\nThe objectives are:
- Create a small compound library using the ChEMBL database
- Dock a variety of ligands to the active site of the...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Contributing to the Galaxy Training Material - Contributing with GitHub via its interface

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Development in Galaxy - Contributing with GitHub

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How can I contribute to an open-source project with GitHub

Objectives of the tutorial:

  • Understand what...

Genome Annotation - Genome annotation with Prokka

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile...

Resource type: Tutorial

Tutorials using public Galaxy at usegalaxy.org - Using dataset collection

This tutorials cover a variety of analyses that can be performed at usegalaxy.org

Questions of the tutorial:

  • How to manipulate large numbers of datasets at once?

Objectives of the tutorial:

  • Understand and master dataset collections

Development in Galaxy - Galaxy from a developer point of view

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Development in Galaxy - Galaxy Webhooks

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What are Galaxy Webhooks?
  • How to create them?

Objectives of the tutorial:

  • Discover what Galaxy...

Resource type: Tutorial

Introduction to Galaxy Analyses - IGV Introduction

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Resource type: Tutorial

Variant Analysis - Calling very rare variants

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • What frequency of variants is so low that it is obscured by sequencing error rate?
  • What are the different types of consensus sequences produced from duplex sequencing?

Objectives of...

Resource type: Tutorial

Tutorials using public Galaxy at usegalaxy.org - Reference-based RNAseq

This tutorials cover a variety of analyses that can be performed at usegalaxy.org

Questions of the tutorial:

  • How to perform analysis of RNAseq data when reference genome is available?

Objectives of the tutorial:

  • Learns basic concepts of RNAseq analysis

Train the trainers - Creating a new tutorial - Writing content in Markdown

Train the trainers

Questions of the tutorial:

  • How to integrate a new tutorial?
  • How to write a tutorial with hands-on?

Objectives of the tutorial:

  • Creating a tutorial from scratch
  • Creating hands-on

Assembly - Introduction to Genome Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Train the trainers - Creating a new tutorial - Creating Interactive Galaxy Tours

Train the trainers

Questions of the tutorial:

  • What is a Interactive Galaxy Tour?
  • How can we create an Interactive Tour?

Objectives of the tutorial:

  • Creating a Galaxy tour from scratch
  • Deploying and running a tour

Tutorials using public Galaxy at usegalaxy.org - Understanding Galaxy history system

This tutorials cover a variety of analyses that can be performed at usegalaxy.org

Questions of the tutorial:

  • How do Galaxy histories work?

Objectives of the tutorial:

  • Gain understanding on navigating and manipulating histories

Variant Analysis - Calling variants in non-diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How does frequency of mitochondrial polymorphisms change from mother to child?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in bacteria,...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Overview of the Galaxy Training Material

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Contributing to the Galaxy Training Material - Running the Galaxy Training material website locally

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Generating PDF artefacts of the website

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

ChIP-sequencing is a method used to analyze protein interactions with DNA.

Questions of the tutorial:

  • How is raw ChIP-seq data processed and analyzed?
  • What are the binding sites of Tal1?
  • Which genes are regulated by Tal1?

Objectives of the tutorial:

  • Inspect read quality with FastQC -...

Resource type: Tutorial

Variant Analysis - Exome sequencing data analysis

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How to identify the genetic variation with the use of exome sequencing?
  • What is the pipeline of the process of finding genetic variation which caused the disease?

Objectives of the...

Resource type: Tutorial

Sequence analysis - RAD-Seq to construct genetic maps

Analyses of sequences

Questions of the tutorial:

  • How to analyze RAD sequencing data for a genetic map study?

Objectives of the tutorial:

  • SNP calling from RAD sequencing data
  • Find and correct haplotypes
  • Create input files for genetic map building software

Resource type: Tutorial

Galaxy Server administration - Galaxy Database schema

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that
  • How to extract usage information,...

Resource type: Tutorial

Development in Galaxy - Galaxy Code Architecture

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How is the Galaxy code structured?
  • What do the various other projects related to Galaxy do?
  • What...

Resource type: Slides

Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to convert LC-MS/MS raw files?
  • How to identify peptides?
  • How to identify proteins?
  • How to evaluate the results?

Objectives of the tutorial:

  • Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Galaxy Server administration - Ansible

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • Why Ansible?
  • How and when to use Ansible?
  • How to write a role?
  • How to leverage community build roles?

Objectives of the tutorial:

  • Learn Ansible basics
  • Write a simple role
  • Install a...

Resource type: Tutorial

User Interface and Features - Jupyter: Use Jupyter notebooks in Galaxy

A collection of microtutorials explaining various features of the Galaxy user interface

Questions of the tutorial:

  • How to use a Jupyter Notebook in Galaxy

Objectives of the tutorial:

  • Learn about the Jupyter Interactive Environment

Resource type: Tutorial

Epigenetics - Introduction to DNA Methylation data analysis

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • What are MS1 features?
  • How to quantify based on MS1 features?
  • How to map MS1 features to MS2 identifications?
  • How to evaluate and optimize the results?

Objectives of the tutorial:

  • MS1 feature...

Resource type: Tutorial

Proteomics - Metaproteomics tutorial

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?
  • How can I perform taxonomy analysis and visualize metaproteomics data?
  • How can I perform...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Creating a new tutorial - Creating Interactive Galaxy Tours

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Creating a new tutorial

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Creating a new tutorial - Writing content in Markdown

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How can protein N-termini be enriched for LC-MS/MS?
  • How to analyze the LC-MS/MS data?

Objectives of the tutorial:

  • Run an N-TAILS data analysis.

Resource type: Tutorial

Contributing to the Galaxy Training Material - Creating a new tutorial - Defining the technical infrastructure

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Galaxy Server administration - Deployment and Platform options

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • What options to deploy Galaxy do I have?
  • Which platforms are supported by Galaxy?
  • What requirements does Galaxy have?

Objectives of the tutorial:

  • Learn about different options about Galaxy...

Resource type: Slides

Sequence analysis - Genome annotation with Prokka

Analyses of sequences

Questions of the tutorial:

  • How to annotate a bacterial genome?
  • How to visualize annoted genomic features?

Objectives of the tutorial:

  • Load genome into Galaxy
  • Annotate genome with Prokka
  • View annotations in JBrowse

Sequence analysis - Quality Control

Analyses of sequences

Questions of the tutorial:

  • How to control quality of NGS data?
  • What are the quality parameters to check for each dataset?
  • How to improve the quality of a sequence dataset?

Objectives of the tutorial:

  • Manipulate FastQ files
  • Control quality from a FastQ file -...

Resource type: Tutorial

Development in Galaxy - Tool Dependencies and Conda

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How can I connect tools to applications and libraries?
  • What are the advantages of declaring dependencies...

Resource type: Tutorial

Assembly - Making sense of a newly assembled genome

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Variant Analysis - Introduction to Variant analysis

Exome sequencing means that all protein-coding genes in a genome are sequenced

Introduction to Galaxy - Getting data into Galaxy

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Resource type: Slides

Contributing to the Galaxy Training Material - Creating a new tutorial - Slides

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Slides

Galaxy Server administration - Upgrading Galaxy

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • What is the release cycle of Galaxy?
  • What do I need to do before updating my Galaxy server?
  • How to upgrade Galaxy to a new release?

Objectives of the tutorial:

  • Identify the challenges...

Resource type: Slides

User Interface and Features - Histories: Understanding Galaxy history system

A collection of microtutorials explaining various features of the Galaxy user interface

Questions of the tutorial:

  • How do Galaxy histories work?

Objectives of the tutorial:

  • Gain understanding on navigating and manipulating histories

Resource type: Tutorial

Variant Analysis - Calling variants in diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How to find variable sites in diploid genomes?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in human genome.

Resource type: Tutorial

Data Manipulation - Collections: Using dataset collection

A collection of microtutorials explaining data manipulation within Galaxy

Questions of the tutorial:

  • How to manipulate large numbers of datasets at once?

Objectives of the tutorial:

  • Understand and master dataset collections

Resource type: Tutorial

Galaxy Server administration - Server Monitoring and Maintenance

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • How to monitor a Galaxy service?
  • What are the best practices to maintain a Galaxy server?

Objectives of the tutorial:

  • Learn about different monitoring strategies.
  • Setup and start the...

Resource type: Tutorial

Assembly - De Bruijn Graph Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Development in Galaxy - Tool Dependencies and Containers

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What are the advantages of running my Galaxy tool inside of a container?
  • How does Galaxy find a container...

Resource type: Tutorial

Sequence analysis - RAD-Seq Reference-based data analysis

Analyses of sequences

Questions of the tutorial:

  • How to analyze RAD sequencing data using a reference genome for a population genomics study?

Objectives of the tutorial:

  • Analysis of RAD sequencing data using a reference genome
  • SNP calling from RAD sequencing data
  • Calculate population...

Resource type: Tutorial

Introduction to Galaxy Analyses - NGS data logistics

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • How to manipulate and process...

Resource type: Tutorial

Train the trainers - Creating a new tutorial - Setting up the infrastructure

Train the trainers

Questions of the tutorial:

  • How to setup the infrastructure to build training webpages?

Objectives of the tutorial:

  • Installing packages needed for rendering the webpage
  • Running the GTN website locally
  • Tracking changes to the content live in the webbrowser

Galaxy Server administration - Connecting Galaxy to a compute cluster

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • How to connect Galaxy to a compute cluster?
  • How can I configure job dependent resources, like cores, memory for my DRM?

Objectives of the tutorial:

  • Be familiar with the basics of installing,...

Resource type: Tutorial

Development in Galaxy - Tool Shed: sharing Galaxy tools

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What is a Tool Shed?
  • How to install tools and workflows from a Tool Shed into a Galaxy instance?
  • What...

Resource type: Slides

Genome Annotation - Genome Annotation

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

Resource type: Tutorial

Contributing to the Galaxy Training Material - Creating a new tutorial - Defining metadata

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Variant Analysis - Mapping and molecular identification of phenotype-causing mutations

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • What is mapping-by-sequencing?
  • How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?

Objectives of the tutorial:

  • Use joint...

Resource type: Tutorial

Development in Galaxy - Visualizations: charts plugins

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How can I make a custom plugin for Charts?

Objectives of the tutorial:

  • Learn how to add custom...

Resource type: Tutorial

Proteomics - Secretome Prediction

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to predict cellular protein localization based upon GO-terms?
  • How to combine multiple localization predictions?

Objectives of the tutorial:

  • Predict proteins in the cellular secretome by using...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Including a new topic

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Transcriptomics - Reference-based RNAseq data analysis (long)

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How to perform analysis of RNAseq data when reference genome is available?

Objectives of the tutorial:

  • Learns basic concepts of RNAseq analysis

Resource type: Tutorial

Introduction to Galaxy Analyses - From peaks to genes

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • How to use Galaxy?
  • How to get...

Resource type: Tutorial

Development in Galaxy - Prerequisites for building software/conda packages

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What does 'installing a software' means on a Linux architecture?
  • Why my compilations always fail?
  • How...

Resource type: Slides

Transcriptomics - Differential abundance testing of small RNAs

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • What small RNAs are expressed?
  • What RNA features have significantly different numbers of small RNAs targeting them between two conditions?

Objectives of the tutorial:

  • Process small RNA-seq datasets...

Resource type: Tutorial

Proteomics - Protein FASTA Database Handling

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to download protein FASTA databases of a certain organism?
  • How to download a contaminant database?
  • How to create a decoy database?
  • How to combine databases?

Objectives of the tutorial:

  • Creation of a...

Resource type: Tutorial

Transcriptomics - De novo transcriptome reconstruction with RNA-Seq

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • What genes are differentially expressed between G1E cells and megakaryocytes?
  • How can we generate a transcriptome de novo from RNA sequencing data?

Objectives of the tutorial:

  • Analysis of RNA...

Resource type: Tutorial

Metagenomics - 16S Microbial Analysis with Mothur

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Questions of the tutorial:

  • What is the effect of normal variation in the gut microbiome on host health?

Objectives of the tutorial:

  • Analyze of 16S rRNA sequencing data using the Mothur toolsuite in...

Resource type: Tutorial

Introduction to Galaxy Analyses - Options for using Galaxy

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • Which Galaxy instance should I use?

Resource type: Slides

Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Questions of the tutorial:

  • Why is a Hi-C analysis useful?
  • What is...

Resource type: Tutorial

Epigenetics - DNA Methylation data analysis

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Questions of the tutorial:

  • What is methylation and why it cannot be...

Resource type: Tutorial

Development in Galaxy - Visualizations: generic plugins

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How can visualization plugins benefit science?

Objectives of the tutorial:

  • Implement a first Galaxy...

Resource type: Tutorial

Slides for 'Running Jobs on Remote Resources with Pulsar' tutorial

The questions this addresses are:
- How does pulsar work?
- How can I deploy it?

\nThe objectives are:
- Have an understanding of what Pulsar is and how it works
- Install and configure a Pulsar server on a remote linux machine
- Be able to get Galaxy to send jobs to a remote Pulsar server

Keywords: admin, jobs

Resource type: slides

Introduction to Galaxy Analyses

Introduction to Galaxy Analyses

Slides for 'Reference Data with CVMFS' tutorial

The objectives are:
- Have an understanding of what CVMFS is and how it works
- Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
- Configure your Galaxy to use these reference genomes and indices
- Use an ansible playbook for all of the...

Keywords: admin

Resource type: slides

Slides for 'Terraform' tutorial

The questions this addresses are:
- What is Terraform?
- In which situations is it good/bad?
- How to use it for managing your VM cluster

\nThe objectives are:
- Learn Terraform basics
- Launch a VM with Terraform
- Launch and tear down a cluster with Terraform

Keywords: admin

Resource type: slides

Slides for 'Feedforward neural networks (FNN) Deep Learning - Part 1' tutorial

The questions this addresses are:
- What is a feedforward neural network (FNN)?
- What are some applications of FNN?

\nThe objectives are:
- Understand the inspiration for neural networks
- Learn activation functions & various problems solved by neural networks
- Discuss various...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: slides

Hands-on for 'Introduction to deep learning' tutorial

The questions this addresses are:
- What are deep learning and neural networks?
- Why is it useful?
- How to create a neural network architecture for classification?

\nThe objectives are:
- Learn basic principles of deep learning
- Learn about how to create an end-to-end neural network...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Slides for 'Image classification in Galaxy with fruit 360 dataset' tutorial

The questions this addresses are:
- How to solve an image classification problem using convolutional neural network (CNN)?

\nThe objectives are:
- Learn how to create a CNN using Galaxy's deep learning tools
- Solve an image classification problem on fruit 360 dataset using CNN in Galaxy

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: slides

Slides for 'Convolutional neural networks (CNN) Deep Learning - Part 3' tutorial

The questions this addresses are:
- What is a convolutional neural network (CNN)?
- What are some applications of CNN?

\nThe objectives are:
- Understand the inspiration behind CNN and learn the CNN architecture
- Learn the convolution operation and its parameters
- Learn how to create a...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: slides

Hands-on for 'Deep Learning (Part 3) - Convolutional neural networks (CNN)' tutorial

The questions this addresses are:
- What is a convolutional neural network (CNN)?
- What are some applications of CNN?

\nThe objectives are:
- Understand the inspiration behind CNN and learn the CNN architecture
- Learn the convolution operation and its parameters
- Learn how to create a...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Slides for 'Recurrent neural networks (RNN) Deep Learning - Part 2' tutorial

The questions this addresses are:
- What is a recurrent neural network (RNN)?
- What are some applications of RNN?

\nThe objectives are:
- Understand the difference between feedforward neural networks (FNN) and RNN
- Learn various RNN types and architectures
- Learn how to create a neural...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: slides

Slides for 'Pangeo ecosystem 101 for everyone' tutorial

The questions this addresses are:
- What are Pangeo and its ecosystem?
- Why Pangeo?
- What is the Pangeo Software Ecosystem?
- How can I use Pangeo in Galaxy?
- How to cite and support Pangeo?

\nThe objectives are:
- Understand Pangeo, its community and software ecosystem
- Learn how to...

Keywords: climate, climate

Resource type: slides

Slides for 'Dealing with Cross-Contamination in Fixed Barcode Protocols' tutorial

The questions this addresses are:
- What is cross-contamination?
- What are fixed barcodes?
- Why are plating setups important to know?
- Is it necessary to check barcodes that don't exist in a batch?

\nThe objectives are:
- How to describe a plating setup
- Proper naming conventions when...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: slides

Slides for 'Plates, Batches, and Barcodes' tutorial

The questions this addresses are:
- What is a batch when it comes to single cells?
- What’s the difference between a barcode and an index?
- What is batch effect and how do you prevent it?
- What is a lane?

\nThe objectives are:
- How to set up plates to prevent batch effect
- Proper...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: slides

Slides for 'Clustering 3K PBMCs with Scanpy' tutorial

The questions this addresses are:
- What are the main steps of scRNA-seq?
- What kind of variation can confound an analysis?

\nThe objectives are:
- Learn the main stages of an scRNA-seq analysis
- Understand the methods and concepts underlying scRNA-seq

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: slides

Hands-on for 'Understanding Barcodes' tutorial

The questions this addresses are:
- What are barcodes?
- What is their purpose?
- How are barcodes formatted?

\nThe objectives are:
- Demultiplex FASTQ data via UMI-tools
- Understand and validate the extraction of barcodes

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: hands-on tutorial

Slides for 'Visualization of RNA-Seq results with CummeRbund' tutorial

The questions this addresses are:
- How are RNA-Seq results stored?
- Why are visualization techniques needed?
- How to select our desired subjects for differential gene expression analysis?

\nThe objectives are:
- Manage RNA-Seq results
- Extract the desired subject for differential gene...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: slides

Slides for 'An introduction to scRNA-seq data analysis' tutorial

The questions this addresses are:
- How are samples compared?
- How are cells captured?
- How does bulk RNA-seq differ from scRNA-seq?
- Why is clustering important?

\nThe objectives are:
- To understand the pitfalls in scRNA-seq sequencing and amplification, and how they are overcome.
-...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, español

Resource type: slides

Slides for 'De Bruijn Graph Assembly' tutorial

The questions this addresses are:
- What are the factors that affect genome assembly?
- How does Genome assembly work?

\nThe objectives are:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an...

Keywords: assembly

Resource type: slides

Slides for 'An Introduction to Genome Assembly' tutorial

The questions this addresses are:
- How do we perform a very basic genome assembly from short read data?

\nThe objectives are:
- assemble some paired end reads using Velvet
- examine the output of the assembly.

Keywords: assembly

Resource type: slides

Slides for 'Unicycler Assembly' tutorial

The questions this addresses are:
- I have short reads and long reads. How do I assemble a genome?

\nThe objectives are:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with...

Keywords: assembly, prokaryote

Resource type: slides

Slides for 'Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads' tutorial

The questions this addresses are:
- How can a genome of interest be assembled against a background of contaminating reads from other genomes?
- How can sequencing data used to obtain an assembled genome?

\nThe objectives are:
- Know basic characteristics of SARS-CoV-2
- Understand Nanopore...

Keywords: assembly, covid19

Resource type: slides

Slides for 'An introduction to get started in genome assembly and annotation' tutorial

The questions this addresses are:
- What are the guidelines before starting a Genome Assembly and Annotation project?

Keywords: assembly

Resource type: slides

Slides for 'Deeper look into Genome Assembly algorithms' tutorial

The questions this addresses are:
- What are the main types of assembly algorithms?
- How do they perform with short and long reads?
- How to improve assemblies using other technologies?

Keywords: assembly

Resource type: slides

Slides for 'ChIP-seq data analysis' tutorial

The questions this addresses are:
- What is ChIP-seq?

\nThe objectives are:
- Identify ChIP-seq data

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: slides

Slides for 'Creating Slides' tutorial

The questions this addresses are:
- How to format slides?
- How do we add presenter notes?
- How to use the features of the slide show tool?
- What sort of content should be included in slides?

\nThe objectives are:
- Create a new set of slides
- Add presenter comments

Keywords: contributing

Resource type: slides

Slides for 'Generic plugins' tutorial

The questions this addresses are:
- How can visualization plugins benefit science?

\nThe objectives are:
- Implement a first Galaxy visualization
- Understand the client side vs. server side principle

Keywords: dev

Resource type: slides

Slides for 'Galaxy Webhooks' tutorial

The questions this addresses are:
- What are Galaxy Webhooks?
- How to create them?

\nThe objectives are:
- Discover what Galaxy Webhooks are
- Be able to create Webhooks
- Be able to add a Galaxy Webhook in a Galaxy instance

Keywords: dev

Resource type: slides

Slides for 'Galaxy Code Architecture' tutorial

The questions this addresses are:
- How is the Galaxy code structured?
- What do the various other projects related to Galaxy do?
- What happens when I start Galaxy?

\nThe objectives are:
- Explore various aspects of the Galaxy codebase.
- Understand the various top-level files and modules...

Keywords: dev

Resource type: slides

Slides for 'Tool Shed: sharing Galaxy tools' tutorial

The questions this addresses are:
- 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?

\nThe objectives are:
- Discover what is a Tool Shed
- Be able to install tools...

Keywords: dev

Resource type: slides

Hands-on for 'Introduction to Genomics and Galaxy' tutorial

The questions this addresses are:
- Do genes on opposite strands ever overlap? If so, how often?

\nThe objectives are:
- Learn some of the basic concepts of genomics and bioinformatics
- Familiarize yourself with the basics of Galaxy

Keywords: introduction

Resource type: hands-on tutorial

Slides for 'Galaxy Interactive Tours' tutorial

The questions this addresses are:
- What is a Galaxy Interactive Tour?
- How to create a Galaxy Interactive Tour?

\nThe objectives are:
- 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: dev

Resource type: slides

Slides for 'Galaxy Interactive Environments' tutorial

The questions this addresses are:
- What are Galaxy Interactive Environments (GIEs)?
- How to enable GIEs in Galaxy?
- How to develop your own GIE?

\nThe objectives are:
- Implement a Hello-World Galaxy Interactive Environment

Keywords: dev

Resource type: slides

Slides for 'Visualizations: JavaScript Plugins' tutorial

The questions this addresses are:
- How can I make a custom JavaScript plugin?

\nThe objectives are:
- Learn how to add custom JavaScript plugins using the Galaxy Charts framework

Keywords: dev

Resource type: slides

Slides for 'Scripting Galaxy using the API and BioBlend' tutorial

The questions this addresses are:
- What is a REST API?
- How to interact with Galaxy programmatically?
- Why and when should I use BioBlend?

Keywords: dev

Resource type: slides

Slides for 'Genome annotation with Prokka' tutorial

The questions this addresses are:
- How to annotate a bacterial genome?
- How to visualize annoted genomic features?

\nThe objectives are:
- Load genome into Galaxy
- Annotate genome with Prokka
- View annotations in JBrowse

Keywords: genome-annotation, prokaryote

Resource type: slides

Slides for 'Introduction to CRISPR screen analysis' tutorial

The questions this addresses are:
- What is CRISPR?
- What is a CRISPR screen?
- How is a guide RNA library created?
- What is the difference between a negative and positive screen?
- How to analyse CRISPR screen data?

\nThe objectives are:
- Describe what CRISPR screen data is
- Outline...

Keywords: genome-annotation

Resource type: slides

Slides for 'Refining Genome Annotations with Apollo' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, prokaryote

Resource type: slides

Slides for 'Essential genes detection with Transposon insertion sequencing' tutorial

The questions this addresses are:
- What is Transposon insertion Sequencing?
- How to get TA sites Coverage ?
- How to predict essential genes ?

\nThe objectives are:
- Understand the read structure of TnSeq analyses
- Predict Essential genes with Transit
- Compare gene essentiality in...

Keywords: genome-annotation, bacteria, tnseq, essential genes

Resource type: slides

Slides for 'Prerequisites for building software/conda packages' tutorial

The questions this addresses are:
- What does 'installing a software' means on a Linux architecture?
- Why my compilations always fail?
- How to solve common compiling and installation issues?

\nThe objectives are:
- Learn how to compile and install tools using standard procedures.
- Learn...

Keywords: dev

Resource type: slides

Hands-on for 'Running molecular dynamics simulations using NAMD' tutorial

The questions this addresses are:
- How do I use the NAMD engine in Galaxy?
- What is the correct procedure for performing a simple molecular dynamics simulation of a protein?

\nThe objectives are:
- Learn about the NAMD engine provided in BRIDGE

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Analysis of molecular dynamics simulations' tutorial

The questions this addresses are:
- Which analysis tools are available?

\nThe objectives are:
- Learn which analysis tools are available.
- Analyse a protein and discuss the meaning behind each analysis.

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Running molecular dynamics simulations using GROMACS' tutorial

The questions this addresses are:
- How do I use the GROMACS engine in Galaxy?
- What is the correct procedure for performing a simple molecular dynamics simulation of a protein?

\nThe objectives are:
- Learn about the GROMACS engine provided via Galaxy.
- Understand the structure of the...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring' tutorial

The questions this addresses are:
- How can candidate ligands be generated and docked to a protein in Galaxy?
- How can the poses of the docked ligands be evaluated?
- How can a workflow for drug virtual screening be constructed in Galaxy?

\nThe objectives are:
- Understand how Galaxy was...

Keywords: computational-chemistry, covid19

Resource type: hands-on tutorial

Slides for 'Circos' tutorial

The questions this addresses are:
- What is Circos?
- How can I use Circos within Galaxy?
- What are some of the different track types I can plot?

Keywords: visualisation

Resource type: slides

Hands-on for 'Setting up molecular systems' tutorial

The questions this addresses are:
- How to get started modelling a protein and a ligand?

\nThe objectives are:
- learn about the Protein Data Bank
- learn how to set up up a model protein and ligand system (with CHARMM-GUI)
- learn how to upload the system to Galaxy

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Galaxy 101' tutorial

The questions this addresses are:
- Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22?

\nThe objectives are:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
-...

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'A short introduction to Galaxy' tutorial

The questions this addresses are:
- How to get started in Galaxy

\nThe objectives are:
- Learn how to upload a file
- Learn how to use a tool
- Learn how to view results
- Learn how to view histories
- Learn how to extract and run a workflow

Keywords: introduction, español

Resource type: hands-on tutorial

Hands-on for 'How to reproduce published Galaxy analyses' tutorial

The questions this addresses are:
- How to reproduce published Galaxy results (workflows and histories)

\nThe objectives are:
- Learn how to load published data into Galaxy
- Learn how to run a published Galaxy workflow
- Learn how histories can be inspected and re-used.

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'NGS data logistics' tutorial

The questions this addresses are:
- How to manipulate and process NGS data

\nThe objectives are:
- Understand most common types of NGS-related datatypes
- Learn about how Galaxy handles NGS data using Illumina data derived from patients infected with SARS-CoV-2

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'From peaks to genes' tutorial

The questions this addresses are:
- How to use Galaxy?
- How to get from peak regions to a list of gene names?

\nThe objectives are:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
- Learn how histories work
-...

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'Data Manipulation Olympics' tutorial

The questions this addresses are:
- How can I do basic data manipulation in Galaxy?
- Which tools are available to convert, reformat, filter, sort etc my text-based data?

\nThe objectives are:
- Familiarize yourself with data manipulation tools in Galaxy
- Perform basic text manipulation...

Keywords: introduction, cyoa

Resource type: hands-on tutorial

Hands-on for 'Regional GAM' tutorial

The questions this addresses are:
- What are abundance and trends of a butterfly species?

\nThe objectives are:
- Obtain and filter/manipulate occurrence data
- Compute and visualize phenology of a species through the years
- Compute temporal abundance trends

Scientific topics: Ecology

Keywords: ecology

Resource type: hands-on tutorial

Hands-on for 'RAD-Seq de-novo data analysis' tutorial

The questions this addresses are:
- How to analyze RAD sequencing data without a reference genome for a population genomics study?

\nThe objectives are:
- Analysis of RAD sequencing data without a reference genome
- SNP calling from RAD sequencing data
- Calculate population genomics...

Scientific topics: Ecology

Keywords: ecology, RAD-seq

Resource type: hands-on tutorial

Hands-on for 'RAD-Seq to construct genetic maps' tutorial

The questions this addresses are:
- How to analyze RAD sequencing data for a genetic map study?

\nThe objectives are:
- SNP calling from RAD sequencing data
- Find and correct haplotypes
- Create input files for genetic map building software

Scientific topics: Ecology

Keywords: ecology, RAD-seq

Resource type: hands-on tutorial

Hands-on for 'Metabarcoding/eDNA through Obitools' tutorial

The questions this addresses are:
- how to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools?

\nThe objectives are:
- Deal with paired-end data to create consensus sequences
- Clean, filter and anlayse data to obtain strong results

Scientific topics: Ecology

Keywords: ecology

Resource type: hands-on tutorial

Hands-on for 'Biodiversity data exploration' tutorial

The questions this addresses are:
- How to explore biodiversity data?
- How to look at Homoscedasticity, normality or collinearity of presences-absence or abundance data?
- How to compare beta diversity taking into account space, time and species components?

\nThe objectives are:
- Explore...

Scientific topics: Ecology

Keywords: ecology

Resource type: hands-on tutorial

Hands-on for 'Rule Based Uploader' tutorial

The questions this addresses are:
- How to use the rule based uploader to create complex collections

\nThe objectives are:
- Learn about the Rule Based Uploader

Keywords: galaxy-interface, collections, tags

Resource type: hands-on tutorial

Hands-on for 'Use Jupyter notebooks in Galaxy' tutorial

The questions this addresses are:
- How to use a Jupyter Notebook in Galaxy

\nThe objectives are:
- Learn about the Jupyter Interactive Environment

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'InterMine integration with Galaxy' tutorial

The questions this addresses are:
- How to export your query results from your InterMine of choice to Galaxy?
- How to export a list of identifiers from Galaxy to your InterMine of choice?

\nThe objectives are:
- Learn how to import/export data from/to InterMine instances
- Understand the...

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Creating, Editing and Importing Galaxy Workflows' tutorial

The questions this addresses are:
- How can you construct Galaxy workflows from scratch?
- How can you label outputs?
- How can you include workflows in workflows?
- How can you tag workflows?
- How can you manage tool versions?
- How can you manage workflow versions?

\nThe objectives...

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'RStudio in Galaxy' tutorial

The questions this addresses are:
- How can I manipulate data using R in Galaxy?

\nThe objectives are:
- Launch RStudio in Galaxy

Keywords: galaxy-interface, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Group tags for complex experimental designs' tutorial

The questions this addresses are:
- What are group tags?
- How can I use group tags to perform multi-factor analyses with collections

\nThe objectives are:
- Learn how to set group tags
- Learn how to select group tags in tools

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Submitting raw sequencing reads to ENA' tutorial

The questions this addresses are:
- How do you submit raw viral sequence reads to the European Nucleotide Archive?

\nThe objectives are:
- Add ENA Webin credentials to your Galaxy user information
- Use Galaxy's 'ENA upload tool' to interactively generate metadata
- Use a metadata template...

Keywords: galaxy-interface, covid19

Resource type: hands-on tutorial

Hands-on for 'Using dataset collections' tutorial

The questions this addresses are:
- How to manipulate large numbers of datasets at once?

\nThe objectives are:
- Understand and master dataset collections

Keywords: galaxy-interface, collections

Resource type: hands-on tutorial

Hands-on for 'Automating Galaxy workflows using the command line' tutorial

The questions this addresses are:
- How can I schedule and run tens or hundreds of Galaxy workflows easily?
- How can I automate my analyses when large amounts of data are being produced daily?

\nThe objectives are:
- Learn to use the planemo run subcommand to run workflows from the...

Keywords: galaxy-interface, workflows, variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis' tutorial

The questions this addresses are:
- How can I search SRA SARS-CoV-2 metadata from within Galaxy?
- How can I import SRA aligned read files and extract the data in my format of choice?
- How can I import vcf files into Galaxy that have been generated for these Runs?

\nThe objectives are:
-...

Keywords: galaxy-interface, ncbi, covid19

Resource type: hands-on tutorial

Hands-on for 'Extracting Workflows from Histories' tutorial

The questions this addresses are:
- What is a workflow?
- How can I create a workflow based on my analysis history?

\nThe objectives are:
- Learn how to extract a workflow from a Galaxy history
- Learn how to change a workflow using the workflow editor

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'Workflow Reports' tutorial

The questions this addresses are:
- What are workflow reports?
- How can I view a workflow report?
- How can I customize a workflow report?
- How can I share a workflow report with others?

\nThe objectives are:
- Understanding, viewing and creating workflow reports

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'Rule Based Uploader: Advanced' tutorial

The questions this addresses are:
- How to use the rule based uploader to create complex collections

\nThe objectives are:
- Learn even more about the Rule Based Uploader

Keywords: galaxy-interface, collections, tags

Resource type: hands-on tutorial

Hands-on for 'JupyterLab in Galaxy' tutorial

The questions this addresses are:
- How can I manipulate data using JupyterLab in Galaxy?
- How can I start a notebook in JupyterLab?
- How can I import/export dataset from/to my history to/from the notebook?
- How can I save my notebook to my history?

\nThe objectives are:
- Launch...

Keywords: galaxy-interface, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Downloading and Deleting Data in Galaxy' tutorial

The questions this addresses are:
- How can I efficiently download my data from Galaxy once I've completed my analyses?
- How do I delete old data to make more room in my quota?

\nThe objectives are:
- Have a greater knowledge of how Galaxy handles data downloads and deletions
- Be able to...

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry: LC-MS analysis' tutorial

The questions this addresses are:
- What are the main steps of untargeted LC-MS data processing for metabolomic analysis?
- How to conduct metabolomic data analysis from preprocessing to annotation using Galaxy?

\nThe objectives are:
- To comprehend the diversity of LC-MS metabolomic data...

Scientific topics: Metabolomics

Keywords: metabolomics

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry : GC-MS analysis with metaMS package' tutorial

The questions this addresses are:
- What are the main steps of GC-MS datas processing for metabolomic analysis ?
- How te be able to annotate the maximum of unknowns using Galaxy ?

\nThe objectives are:
- To be sure you have already comprehend the diversity of MS pre-processing analysis.
-...

Scientific topics: Metabolomics

Keywords: metabolomics

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry imaging: Finding differential analytes' tutorial

The questions this addresses are:
- Can N-linked glycans from FFPE tissues be detected by MALDI imaging?
- Can potential N-linked glycans be identified by an additional LC-MS/MS experiment?
- Do specific kidney compartments have different N-linked glycan compositions?

\nThe objectives are:
...

Scientific topics: Metabolomics

Keywords: metabolomics

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry imaging: Loading and exploring MSI data' tutorial

The questions this addresses are:
- Did the tryptic digestions work?
- Is there an intensity gradient in the data?
- How good is the m/z accuracy?

\nThe objectives are:
- How to upload an imzML file into Galaxy
- Getting an overview of the MSI data with the MSI quality control tool
- How...

Scientific topics: Proteomics

Keywords: proteomics, mouse, imaging

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry: LC-MS preprocessing with XCMS' tutorial

The questions this addresses are:
- What are the main steps of untargeted LC-MS data preprocessing for metabolomic analyses?
- How to conduct metabolomic data preprocessing using Galaxy?

\nThe objectives are:
- To comprehend the diversity of steps necessary to perform untargeted LC-MS...

Scientific topics: Metabolomics

Keywords: metabolomics

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry: LC-MS data processing' tutorial

The questions this addresses are:
- Why should one consider performing data processing steps when dealing with Metabolomics data?
- How to conduct LCMS-based untargeted metabolomic data processing using Galaxy?

\nThe objectives are:
- To comprehend the key role of data processing
- To...

Scientific topics: Metabolomics

Keywords: metabolomics

Resource type: hands-on tutorial

Hands-on for 'Python - Lists & Strings & Dictionaries' tutorial

The questions this addresses are:
- How can I store multiple values?

\nThe objectives are:
- Explain why programs need collections of values.
- Write programs that create flat lists, index them, slice them, and modify them through assignment and method calls.

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Advanced Python' tutorial

The questions this addresses are:
- How can I analyze data using Python with Numpy and Pandas?

\nThe objectives are:
- Use the scientific libraries pandas and numpy to explore tabular datasets
- Calculate basic statistics about datasets and columns

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Introduction to 'Synthetic Biology'

Slides for Synthetic Biology

Resource type: slides

Hands-on for 'Object tracking using CellProfiler' tutorial

The questions this addresses are:
- How to segment and track objects in fluorescence time-lapse microscopy images?

\nThe objectives are:
- Segment fluorescent objects using CellProfiler in Galaxy
- Track objects over multiple frames using CellProfiler in Galaxy

Keywords: imaging

Resource type: hands-on tutorial

Hands-on for 'Introduction to Python' tutorial

The questions this addresses are:
- How can I run Python programs?

\nThe objectives are:
- Learn the fundamentals of programming in Python

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Advanced SQL' tutorial

The questions this addresses are:
- How can I calculate sums, averages, and other summary values?
- How can I combine data from multiple tables?
- How should I format data in a database, and why?
- How can I create, modify, and delete tables and data?
- How can I access databases from...

Keywords: data-science, SQL, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Basics of using Git from the Command Line' tutorial

The questions this addresses are:
- How can I start tracking my changes with git?
- How do I commit changes?
- How can I undo a mistake?

\nThe objectives are:
- Create a repository
- Commit a file
- Make some changes
- Use the log to view the diff
- Undo a bad change

Keywords: data-science

Resource type: hands-on tutorial

Hands-on for 'R basics in Galaxy' tutorial

The questions this addresses are:
- What are the basic features and objects of the R language?

\nThe objectives are:
- Know advantages of analyzing data using R within Galaxy.
- Compose an R script file containing comments, commands, objects, and functions.
- Be able to work with objects...

Keywords: data-science, interactive-tools, R

Resource type: hands-on tutorial

Hands-on for 'Plotting in Python' tutorial

The questions this addresses are:
- How can I create plots using Python in Galaxy?

\nThe objectives are:
- Use the scientific library matplolib to explore tabular datasets

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Introductory Graduation' tutorial

The questions this addresses are:
- What all did I learn up until now?

\nThe objectives are:
- Recap all previous modules.
- Use exercises to ensure that all previous knowledge is sufficiently covered.

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Introduction to 'Development in Galaxy'

Slides for Development in Galaxy

Resource type: slides

Hands-on for 'Python - Math' tutorial

The questions this addresses are:
- How do I do math in Python?

\nThe objectives are:
- Understand the fundamentals of object assignment and math in python and can write simple statements and execute calcualtions in order to be able to summarize the results of calculations and classify valid...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Functions' tutorial

The questions this addresses are:
- How do I write functions in Python?
- What is a function?
- What do they look like?
- Fill in the missing part of a function

\nThe objectives are:
- Understand the structure of a "function" in order to be able to construct their own functions and predict...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Loops' tutorial

The questions this addresses are:
- How can I make a program do many things?

\nThe objectives are:
- Explain what for loops are normally used for.
- Trace the execution of a simple (unnested) loop and correctly state the values of variables in each iteration.
- Write for loops that use the...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Files & CSV' tutorial

The questions this addresses are:
- How can I read from a file?
- How can I parse a CSV file?
- How can I write results out

\nThe objectives are:
- Read data from a file
- Write new data to a file
- Use with to ensure the file is closed properly.
- Use the CSV module to parse comma and...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Try & Except' tutorial

The questions this addresses are:
- How do I try to execute code, knowing it might fail?
- What are some situations where this is important?
- How can I write my own exceptions.

\nThe objectives are:
- catch an exception
- raise your own exception

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Make & Snakemake' tutorial

The questions this addresses are:
- What is Make & Snakemake
- What is a Makefile/Snakefile
- How do these improve pipelines over simple scripts?
- Why is Snakemake better for scientific research and how can I use it
- How do I use conda envs with Snakemake?

\nThe objectives are:
-...

Keywords: data-science

Resource type: hands-on tutorial

Hands-on for 'Python - Argparse' tutorial

The questions this addresses are:
- How do I make a proper command line script
- How do I use argparse?
- What problems does it solve?

\nThe objectives are:
- Learn how sys.argv works
- Write a simple command line program that sums some numbers
- Use argparse to make it nicer.

Keywords: data-science

Resource type: hands-on tutorial

Hands-on for 'SQL with R' tutorial

The questions this addresses are:
- How can I access databases from programs written in R?

\nThe objectives are:
- Write short programs that execute SQL queries.
- Trace the execution of a program that contains an SQL query.
- Explain why most database applications are written in a...

Keywords: data-science, SQL, R, rmarkdown-notebook, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Flow Control' tutorial

The questions this addresses are:
- How can my programs do different things based on data values?

\nThe objectives are:
- Write conditional statements including if, elif, and else branches.
- Correctly evaluate expressions containing and and or.

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Subprocess' tutorial

The questions this addresses are:
- How can I run another program?

\nThe objectives are:
- Run a command in a subprocess.
- Learn about check_call and check_output and when to use each of these.
- Read it's output.

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'CLI Educational Game - Bashcrawl' tutorial

The questions this addresses are:
- How can I move around on my computer?
- How can I see what files and directories I have?
- How can I specify the location of a file or directory on my computer?
- How can I create, copy, and delete files and directories?
- How can I edit files?

\nThe...

Keywords: data-science, game, bash, jupyter-notebook

Resource type: hands-on tutorial

Slides for 'Options for using Galaxy' tutorial

The questions this addresses are:
- Which Galaxy instance should I use?

Keywords: introduction

Resource type: slides

Hands-on for 'Python - Globbing' tutorial

The questions this addresses are:
- How can I collect a list of files.

\nThe objectives are:
- Use glob to collect a list of files
- Learn about the potential pitfalls of glob

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Managing Galaxy on Kubernetes' tutorial

The questions this addresses are:
- How do I change Galaxy configs?
- How can I upgrade to a new version?
- How do I rollback my changes?
- How do I scale Galaxy?

\nThe objectives are:
- Have an understanding of how to modify Galaxy configuration
- Be able to upgrade and scale galaxy

Keywords: admin, kubernetes

Resource type: hands-on tutorial

Hands-on for 'Galaxy Tool Management with Ephemeris' tutorial

The questions this addresses are:
- How to install, update, and maintain Galaxy tools?
- How to extract a list of tools from a workflow or Galaxy instance?

\nThe objectives are:
- Learn about Ephemeris
- Extract a list of tools from a workflow
- Install these tools on a given Galaxy

Keywords: admin, tools, git-gat

Resource type: hands-on tutorial

Hands-on for 'Galaxy Monitoring with Telegraf and Grafana' tutorial

The questions this addresses are:
- How to monitor Galaxy with Telegraf
- How do I set up InfluxDB
- How can I make graphs in Grafana?
- How can I best alert on important metrics?

\nThe objectives are:
- Setup InfluxDB
- Setup Telegraf
- Setup Grafana
- Create several charts

Keywords: admin, ansible, monitoring, git-gat

Resource type: hands-on tutorial

Hands-on for 'Galaxy Monitoring with gxadmin' tutorial

The questions this addresses are:
- What is gxadmin
- What can it do?
- How to write a query?

\nThe objectives are:
- Learn gxadmin basics
- See some queries and learn how they help debug production issues

Keywords: admin, monitoring, ansible, git-gat

Resource type: hands-on tutorial

Hands-on for 'External Authentication' tutorial

The questions this addresses are:
- How can I connect Galaxy with CAS, SAML, etc.

\nThe objectives are:
- be familiar with configuring Galaxy to use an upstream (proxy) authentication provider
- be able to log in to your Galaxy server with a file-configured user.

Keywords: admin, authentication

Resource type: hands-on tutorial

Hands-on for 'Running Jobs on Remote Resources with Pulsar' tutorial

The questions this addresses are:
- How does pulsar work?
- How can I deploy it?

\nThe objectives are:
- Have an understanding of what Pulsar is and how it works
- Install and configure a RabbitMQ message queueing server
- Install and configure a Pulsar server on a remote linux machine
-...

Keywords: admin, ansible, jobs, git-gat

Resource type: hands-on tutorial

Hands-on for 'Connecting Galaxy to a compute cluster' tutorial

The questions this addresses are:
- How to connect Galaxy to a compute cluster?
- What are job metrics?
- What sort of information can I collect?
- Where can I find this information?

\nThe objectives are:
- Be familiar with the basics of installing, configuring, and using Slurm
-...

Keywords: admin, jobs, ansible, git-gat

Resource type: hands-on tutorial

Hands-on for 'Galaxy Monitoring with Reports' tutorial

The questions this addresses are:
- How to monitor a Galaxy service with the Reports application?

\nThe objectives are:
- Setup and start the Galaxy reports app.

Keywords: admin, ansible, monitoring, git-gat

Resource type: hands-on tutorial

Hands-on for 'Automation with Jenkins' tutorial

The questions this addresses are:
- What sort of tasks should be automated?
- What are my options for automation?
- How can I automate repetitive tasks?

\nThe objectives are:
- Setup Jenkins
- Setup a simple job
- Automate running of the Galaxy playbook
- Secure Jenkins

Keywords: admin, ansible, automation

Resource type: hands-on tutorial

Hands-on for 'Upgrading Galaxy' tutorial

The questions this addresses are:
- How can I find which version of Galaxy I'm running?
- How do I upgrade the Galaxy server to the latest version?

\nThe objectives are:
- Understand how to find the current Galaxy server version you are using
- How to find the latest release version
- How...

Keywords: admin, ansible

Resource type: hands-on tutorial

Hands-on for 'Deploying a compute cluster in OpenStack via Terraform' tutorial

The questions this addresses are:
- What is Terraform?
- In which situations is it good/bad?
- How to use it for managing your VM cluster

\nThe objectives are:
- Learn Terraform basics
- Launch a VM with Terraform
- Launch and tear down a cluster with Terraform

Keywords: admin, terraform, deploying, cloud

Resource type: hands-on tutorial

Hands-on for 'Performant Uploads with TUS' tutorial

The objectives are:
- Setup TUSd
- Configure Galaxy to use it to process uploads

Keywords: admin

Resource type: hands-on tutorial

Hands-on for 'Data Libraries' tutorial

The questions this addresses are:
- How do data libraries work?
- What are they good for?
- How can I use them?
- How can I setup permissions for them?

\nThe objectives are:
- Setup a data library
- Manage permissions
- Import data from disk

Keywords: admin, ansible, storage, git-gat

Resource type: hands-on tutorial

Hands-on for 'Training Infrastructure as a Service (TIaaS)' tutorial

The questions this addresses are:
- How to deploy EU's TIaaS

\nThe objectives are:
- Setup TIaaS
- Request and manage trainings
- Join a training

Keywords: admin, ansible, training, jobs, git-gat

Resource type: hands-on tutorial

Hands-on for 'How I learned to stop worrying and love the systemd' tutorial

The questions this addresses are:
- Unix is supposed to be about FILES™
- What is this systemd stuff?
- Why should I love it?
- I have so many worries!

\nThe objectives are:
- Have an objective understanding of systemd allowing the user to obtain the benefits of this new system
- Realise...

Keywords: admin, ansible, systemd

Resource type: hands-on tutorial

Hands-on for 'Reference Data with CVMFS' tutorial

The objectives are:
- Have an understanding of what CVMFS is and how it works
- Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
- Configure your Galaxy to use these reference genomes and indices
- Use an Ansible playbook for all of the...

Keywords: admin, ansible, git-gat

Resource type: hands-on tutorial

Hands-on for 'Reference Data with CVMFS without Ansible' tutorial

The objectives are:
- Have an understanding of what CVMFS is and how it works
- Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
- Configure your Galaxy to use these reference genomes and indices

Keywords: admin

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein Quantification via Stable Isotope Labelling (SIL)' tutorial

The questions this addresses are:
- What are MS1 features?
- How to quantify based on MS1 features?
- How to map MS1 features to MS2 identifications?
- How to evaluate and optimize the results?

\nThe objectives are:
- MS1 feature quantitation and mapping of quantitations to peptide and...

Scientific topics: Proteomics

Keywords: proteomics, DDA, SILAC

Resource type: hands-on tutorial

Hands-on for 'Clustering in Machine Learning' tutorial

The questions this addresses are:
- How to use clustering algorithms to categorize data in different clusters

\nThe objectives are:
- Learn clustering background
- Learn hierarchical clustering algorithm
- Learn k-means clustering algorithm
- Learn DBSCAN clustering algorithm
- Apply...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Regression in Machine Learning' tutorial

The questions this addresses are:
- How to use regression techniques to create predictive models from biological datasets?

\nThe objectives are:
- Learn regression background
- Apply regression based machine learning algorithms
- Learn ageing biomarkers and predict age from DNA methylation...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Enable upload via FTP' tutorial

The questions this addresses are:
- How can I setup FTP to be easy for my users?
- Can I authenticate ftp users with Galaxy credentials?

\nThe objectives are:
- Configure galaxy and install a FTP server.
- Use an Ansible playbook for this.

Keywords: admin, data, git-gat

Resource type: hands-on tutorial

Hands-on for 'Distributed Object Storage' tutorial

The questions this addresses are:
- How does Galaxy locate data?
- How can I have Galaxy use multiple storage locations?

\nThe objectives are:
- Setup Galaxy with both the Hierarachical and Distributed Object Storages

Keywords: admin, ansible, storage

Resource type: hands-on tutorial

Hands-on for '16S Microbial Analysis with mothur (short)' tutorial

The questions this addresses are:
- What is the effect of normal variation in the gut microbiome on host health?

\nThe objectives are:
- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
- Using a mock community to assess the error rate of your sequencing experiment
-...

Scientific topics: Metagenomics

Keywords: metagenomics

Resource type: hands-on tutorial

Hands-on for '16S Microbial analysis with Nanopore data' tutorial

The questions this addresses are:
- How can we analyse the health status of the soil?
- How do plants modify the composition of microbial communities?

\nThe objectives are:
- Use Nanopore data for studying soil metagenomics
- Analyze and preprocess Nanopore reads
- Use Kraken2 to assign a...

Scientific topics: Metagenomics

Keywords: metagenomics, nanopore

Resource type: hands-on tutorial

Hands-on for 'Analyses of metagenomics data - The global picture' tutorial

The questions this addresses are:
- How to analyze metagenomics data?
- What information can be extracted of metagenomics data?
- What is the difference between amplicon and shotgun data?
- What are the difference in the analyses of amplicon and shotgun data?

\nThe objectives are:
-...

Scientific topics: Metagenomics

Keywords: metagenomics

Resource type: hands-on tutorial

Hands-on for 'Galaxy Database schema' tutorial

The questions this addresses are:
- Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that
- How to extract usage information, which can not be gathered using the given report tools
- How...

Keywords: admin

Resource type: hands-on tutorial

Hands-on for 'Use Singularity containers for running Galaxy jobs' tutorial

The objectives are:
- Configure your Galaxy to use Singularity and BioContainers for running jobs

Keywords: admin, jobs, ansible, git-gat

Resource type: hands-on tutorial

Hands-on for '16S Microbial Analysis with mothur (extended)' tutorial

The questions this addresses are:
- What is the effect of normal variation in the gut microbiome on host health?

\nThe objectives are:
- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
- Using a mock community to assess the error rate of your sequencing experiment
-...

Scientific topics: Metagenomics

Keywords: metagenomics

Resource type: hands-on tutorial

Hands-on for 'Metatranscriptomics analysis using microbiome RNA-seq data' tutorial

The questions this addresses are:
- How to analyze metatranscriptomics data?
- What information can be extracted of metatranscriptomics data?
- How to assign taxa and function to the identified sequences?

\nThe objectives are:
- Choose the best approach to analyze metatranscriptomics data
...

Scientific topics: Metagenomics

Keywords: metagenomics, metatranscriptomics

Resource type: hands-on tutorial

Hands-on for 'Visualize Climate data with Panoply netCDF viewer' tutorial

The questions this addresses are:
- How to start Panoply interactive environment in Galaxy?
- How to inspect netCDF data?
- How to make a plot with Panoply?
- Where to save your plots in Panoply?
- How to customize plots in Panoply?
- How to generate animation in Panoply?

\nThe objectives...

Keywords: climate, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Functionally Assembled Terrestrial Ecosystem Simulator (FATES)' tutorial

The questions this addresses are:
- How to run CLM-FATES with the CLM-FATES Galaxy tool?
- How to upload input data for running CLM-FATES?
- How to customize your runs?
- How to analyze your model outputs?
- How to create a workflow?
- How to share your workflow?

\nThe objectives are:
-...

Keywords: climate, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using OpenMS tools' tutorial

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

\nThe objectives are:
- Protein identification from LC-MS/MS raw files.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Antibiotic resistance detection' tutorial

The questions this addresses are:
- How do I assemble a genome with Nanopore data?
- How do I get more information about the structure of the genomes?
- How do I get more information about the antimicrobial resistance genes?

\nThe objectives are:
- Perform Quality control on your reads
-...

Scientific topics: Metagenomics

Keywords: metagenomics, nanopore, plasmids, assembly, amr

Resource type: hands-on tutorial

Hands-on for 'Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools' tutorial

The questions this addresses are:
- What Xarray Galaxy Tools can I use in Galaxy and what for?
- What is an Xarray?
- How do I use Xarray in Galaxy?
- How to get metadata information?
- How to make a selection?
- How to visualize?
- How to filter?
- How to make reduction operations...

Keywords: climate, pangeo

Resource type: hands-on tutorial

Hands-on for 'Getting your hands-on climate data' tutorial

The questions this addresses are:
- What is climate?
- What type of data is available?

\nThe objectives are:
- Learn about the terminology
- Learn about the different source of climate data
- Learn about climate observations, reanalysis, climate predictions and climate projections

Keywords: climate

Resource type: hands-on tutorial

Hands-on for 'Metaproteomics tutorial' tutorial

The questions this addresses are:
- How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?
- How can I perform taxonomy analysis and visualize metaproteomics data?
- How can I perform functional analysis on this metaproteomics...

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Protein FASTA Database Handling' tutorial

The questions this addresses are:
- How to download protein FASTA databases of a certain organism?
- How to download a contaminant database?
- How to create a decoy database?
- How to combine databases?

\nThe objectives are:
- Creation of a protein FASTA database ready for use with...

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'EncyclopeDIA' tutorial

The questions this addresses are:
- How to perform quantitative analysis using DIA data with the help of EncyclopeDIA?
- How to perform quantitation with or without Chromatogram Libraries?

\nThe objectives are:
- Understand the difference between DDA and DIA methods
- Performing...

Scientific topics: Proteomics

Keywords: proteomics, DIA

Resource type: hands-on tutorial

Hands-on for 'Pangeo Notebook in Galaxy - Introduction to Xarray' tutorial

The questions this addresses are:
- What is Pangeo notebook?
- How to start Pangeo Notebook in Galaxy?
- What are the main software components of the Pangeo ecosystem?
- What is Xarray?
- How to manipulate Xarrays?
- How to print metadata information?
- How to make a selection?
- How to...

Keywords: climate, pangeo, interactive-tools, jupyter-notebook, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Detection and quantitation of N-termini (degradomics) via N-TAILS' tutorial

The questions this addresses are:
- How can protein N-termini be enriched for LC-MS/MS?
- How to analyze the LC-MS/MS data?

\nThe objectives are:
- Run an N-TAILS data analysis.

Scientific topics: Proteomics

Keywords: proteomics

Resource type: hands-on tutorial

Hands-on for 'Machine Learning Modeling of Anticancer Peptides' tutorial

The questions this addresses are:
- Which machine learning (ML) algorithm is superior in classifying anticancer peptides (ACPs) and non-anticancer peptides (non-ACPs)?

\nThe objectives are:
- Learn, how to calculate peptide descriptor
- Learn, how to create training data set from features?
...

Scientific topics: Proteomics

Keywords: proteomics, ML, cancer

Resource type: hands-on tutorial

Hands-on for 'Proteogenomics 3: Novel peptide analysis' tutorial

The questions this addresses are:
- How to verify the spectra of novel proteoforms?
- How to assign genomic allocation to these novel proteoforms?

\nThe objectives are:
- How to assign and visualize the genomic localization of these identified novel proteoforms?

Scientific topics: Proteomics

Keywords: proteomics, proteogenomics

Resource type: hands-on tutorial

Hands-on for 'Statistical analysis of DIA data' tutorial

The questions this addresses are:
- How to perform statistical analysis on DIA mass spectrometry data?
- How to detect and quantify differentially abundant proteins in a HEK-Ecoli Benchmark DIA datatset?

\nThe objectives are:
- Statistical analysis of a HEK-Ecoli Benchmark DIA dataset
-...

Scientific topics: Proteomics

Keywords: proteomics, DIA

Resource type: hands-on tutorial

Hands-on for 'DIA Analysis using OpenSwathWorkflow' tutorial

The questions this addresses are:
- How to analyze data independent acquisition (DIA) mass spectrometry (MS) data using OpenSwathWorkflow?
- How to detect different Spike-in amounts of Ecoli in a HEK-Ecoli Benchmark DIA dataset?

\nThe objectives are:
- Analysis of HEK-Ecoli Spike-in DIA data...

Scientific topics: Proteomics

Keywords: proteomics, DIA

Resource type: hands-on tutorial

Hands-on for 'Label-free data analysis using MaxQuant' tutorial

The questions this addresses are:
- How to perform label-free analysis in Maxquant?
- Which are the most abundant proteins in serum?
- How successful was the depletion of those in our experiment?

\nThe objectives are:
- Analysis of human serum proteome samples with label-free quantification...

Scientific topics: Proteomics

Keywords: proteomics, DDA, label-free

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 2: Function' tutorial

The questions this addresses are:
- How do I look at differentially expressed proteins?
- How do I get top 5 or 10 function present in the sample?
- How can I visualize my results?

\nThe objectives are:
- A functional and quantitational analysis of metaproteomic mass spectrometry data.

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Peptide Library Data Analysis' tutorial

The questions this addresses are:
- How to utilize quantitative properties of amino acids and peptide sequence to analyse peptide data?

\nThe objectives are:
- Calculate descriptors
- Quantitative analysis of peptide sequence properties

Scientific topics: Proteomics

Keywords: proteomics

Resource type: hands-on tutorial

Hands-on for 'Proteogenomics 2: Database Search' tutorial

The questions this addresses are:
- How to identify variant proteoforms in MS data by searching with the customized Protein database?

\nThe objectives are:
- A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides.

Scientific topics: Proteomics

Keywords: proteomics, proteogenomics

Resource type: hands-on tutorial

Hands-on for 'Proteogenomics 1: Database Creation' tutorial

The questions this addresses are:
- How to create a customized Protein Database from RNAseq data?

\nThe objectives are:
- Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences.

Scientific topics: Proteomics

Keywords: proteomics, proteogenomics

Resource type: hands-on tutorial

Hands-on for 'Label-free versus Labelled - How to Choose Your Quantitation Method' tutorial

The questions this addresses are:
- What are benefits and drawbacks of different quantitation methods?
- How to choose which quantitation method bests suits my need?

\nThe objectives are:
- Choose your quantitation method.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Secretome Prediction' tutorial

The questions this addresses are:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?

\nThe objectives are:
- Predict proteins in the cellular secretome by using GO-terms.
- Predict proteins in the cellular secretome by...

Scientific topics: Proteomics

Keywords: proteomics, human

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 1: Data creation' tutorial

The questions this addresses are:
- How do I perform functional and taxonomy analysis on metaproteomics data?
- How can I perform quantitation on metaproteomics data?
- How do I create inputs that can be used in metaquantome to examine differentially expressed proteins?

\nThe objectives...

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 3: Taxonomy' tutorial

The questions this addresses are:
- How do I look at differentially expressed taxa?
- Can we get top 5 or 10 taxa present in the sample?
- How can I visualize my results?

\nThe objectives are:
- A taxonomy and quantitational analysis of metaproteomic mass spectrometry data.

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Biomarker candidate identification' tutorial

The questions this addresses are:
- How to mine public databases to retrieve info?
- How to build a selection strategy by applying successive biochemical/cellular criteria to a list of gene/protein?
- How to select biomarkers candidates using experimental information (transcriptomics &...

Scientific topics: Proteomics

Keywords: proteomics, DDA, human

Resource type: hands-on tutorial

Hands-on for 'Image classification in Galaxy with fruit 360 dataset' tutorial

The questions this addresses are:
- How to solve an image classification problem using convolutional neural network (CNN)?

\nThe objectives are:
- Learn how to create a CNN using Galaxy's deep learning tools
- Solve an image classification problem on fruit 360 dataset using CNN in Galaxy

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Basics of machine learning' tutorial

The questions this addresses are:
- What is machine learning?
- Why is it useful?
- What are its different approaches?

\nThe objectives are:
- Provide the basics of machine learning and its variants.
- Learn how to do classification using the training and test data.
- Learn how to use...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Introduction to Machine Learning using R' tutorial

The questions this addresses are:
- What are the main categories in Machine Learning algorithms?
- How can I perform exploratory data analysis?
- What are the main part of a clustering process?
- How can a create a decision tree?
- How can I assess a linear regression model?

\nThe...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'MaxQuant and MSstats for the analysis of TMT data' tutorial

The questions this addresses are:
- How to analyze tandem-mass-tag (TMT) labelled shotgun (DDA) data analysis in MaxQuant and MSstats?
- Which proteins are differentially abundant between KMT9α knock-down and control cells?

\nThe objectives are:
- Learn how to use MaxQuant and MSstats for...

Scientific topics: Proteomics

Keywords: proteomics, DDA, TMT

Resource type: hands-on tutorial

Hands-on for 'Machine learning: classification and regression' tutorial

The questions this addresses are:
- what are classification and regression techniques?
- How they can be used for prediction?
- How visualizations can be used to analyze predictions?

\nThe objectives are:
- Explain the types of supervised machine learning - classification and regression.
-...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Classification in Machine Learning' tutorial

The questions this addresses are:
- What is classification and how we can use classification techniques?

\nThe objectives are:
- Learn classification background
- Learn what a quantitative structure-analysis relationship (QSAR) model is and how it can be constructed in Galaxy
- Learn to...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis' tutorial

The questions this addresses are:
- How to predict aberrant pathway activity in The Cancer Genome Atlas (TCGA) using Machine learning approaches?

\nThe objectives are:
- Learn to predict aberrant pathway activity using RNA-Seq data, mutational status and copy number variation data from TCGA.
...

Scientific topics: Statistics and probability

Keywords: statistics, Machine learning, Pan-cancer, cancer biomarkers, oncogenes and tumor suppressor genes

Resource type: hands-on tutorial

Hands-on for 'Age prediction using machine learning' tutorial

The questions this addresses are:
- How to use machine learning to create predictive models from biological datasets (RNA-seq and DNA methylation)?

\nThe objectives are:
- Learn ageing biomarkers from RNA-seq and DNA methylation datasets
- Apply regression based machine learning algorithms
...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Text-mining with the SimText toolset' tutorial

The questions this addresses are:
- How can I automatically collect PubMed data for a set of biomedical entities such as genes?
- How can I analyze similarities among biomedical entities based on PubMed data on large-scale?

\nThe objectives are:
- Learn how to use the SimText toolset
-...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with CummeRbund' tutorial

The questions this addresses are:
- How are RNA-Seq results stored?
- Why are visualization techniques needed?
- How to select genes for visualizing meaningful results of differential gene expression analysis?

\nThe objectives are:
- Manage RNA-Seq results
- Extract genes for producing...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'De novo transcriptome reconstruction with RNA-Seq' tutorial

The questions this addresses are:
- What genes are differentially expressed between G1E cells and megakaryocytes?
- How can we generate a transcriptome de novo from RNA sequencing data?

\nThe objectives are:
- Analysis of RNA sequencing data using a reference genome
- Reconstruction of...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Tree thinking for tuberculosis evolution and epidemiology' tutorial

The questions this addresses are:
- What information can I get from a phylogenetic tree?
- How do I estimate a phylogeny?

\nThe objectives are:
- Understand the basic concepts behind phylogenetic trees, as applied to Mycobacterium tuberculosis
- Be able to read and interrogate a phylogeny...

Keywords: evolution, prokaryotes, phylogenetics, evolution, work-in-progress

Resource type: hands-on tutorial

Hands-on for 'RNA Seq Counts to Viz in R' tutorial

The questions this addresses are:
- How can I create neat visualizations of the data?

\nThe objectives are:
- Describe the role of data, aesthetics, geoms, and layers in ggplot functions.
- Customize plot scales, titles, subtitles, themes, fonts, layout, and orientation.

Scientific topics: Transcriptomics

Keywords: transcriptomics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Bulk RNA Deconvolution with MuSiC' tutorial

The questions this addresses are:
- How do we infer cell type proportions from bulk RNA-seq data?
- How are these cell types grouped together?

\nThe objectives are:
- Construct Bulk and scRNA Expression Set Objects
- Inspect these objects for various properties
- Measure the abundance of...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, mouse, human, deconvolution, bulk

Resource type: hands-on tutorial

Hands-on for 'Reference-based RNAseq data analysis (long)' tutorial

The questions this addresses are:
- How to perform analysis of RNAseq data when reference genome is available?

\nThe objectives are:
- Learns basic concepts of RNAseq analysis

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Small Non-coding RNA Clustering using BlockClust' tutorial

The questions this addresses are:
- What do the read profiles of small non-coding RNAs represent?
- How to cluster the read profiles based on some intrinsic features?

\nThe objectives are:
- Difference between mRNA-seq and smallRNA-seq
- Unsupervised grouping of the adjacent reads into read...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Downstream Single-cell RNA analysis with RaceID' tutorial

The questions this addresses are:
- What is normalisation and why is it necessary?
- How many types of unwanted variation are there?
- How are biological phenotypes clustered?
- What is the difference between PCA and tSNE?
- What is the difference between cell trajectory and cell...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: hands-on tutorial

Hands-on for 'Single-cell quality control with scater' tutorial

The questions this addresses are:
- How to ensure the quality of single-cell RNA-seq data?
- What are the confounding factors that may affect the interpretation of downstream analyses?

\nThe objectives are:
- Examine scRNA-seq data for low-quality cells
- Visualise data with various types...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with heatmap2' tutorial

The questions this addresses are:
- How to generate heatmaps from RNA-seq data?

\nThe objectives are:
- Create heatmaps of RNA-seq data

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Running the GTN website online using GitPod' tutorial

The questions this addresses are:
- How can I get a preview of the GTN website using GitPod?

\nThe objectives are:
- Preview the GTN website online via GitPod
- Make changes to the GTN website and preview those changes

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Generating a single cell matrix using Alevin' tutorial

The questions this addresses are:
- I have some single cell FASTQ files I want to analyse. Where do I start?

\nThe objectives are:
- Repeat matrix generation for any droplet-based single cell sequencing data
- Apply data combination and metadata editing for particular experimental designs
-...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, español

Resource type: hands-on tutorial

Hands-on for 'Analysis of plant scRNA-Seq Data with Scanpy' tutorial

The questions this addresses are:
- Can we reclaim cell markers using a different analysis method?
- Are highly variable genes paramount to the analysis?

\nThe objectives are:
- Perform filtering, dimensionality reduction, and clustering
- Generate a DotPlot emulating the original paper...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, plants, paper-replication

Resource type: hands-on tutorial

Hands-on for 'Differential abundance testing of small RNAs' tutorial

The questions this addresses are:
- What small RNAs are expressed?
- What RNA features have significantly different numbers of small RNAs targeting them between two conditions?

\nThe objectives are:
- Process small RNA-seq datasets to determine quality and reproducibility.
- Filter out...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Pre-processing of Single-Cell RNA Data' tutorial

The questions this addresses are:
- What is single-cell?
- How do we process a batch?
- How do we process multiple batches?
- How do we check for cross-contamination?

\nThe objectives are:
- Demultiplex FASTQ data via UMI-tools
- Understand and validate the extraction of barcodes
-...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: hands-on tutorial

Hands-on for '1: RNA-Seq reads to counts' tutorial

The questions this addresses are:
- How to convert RNA-seq reads into counts?
- How to perform quality control (QC) of RNA-seq reads?
- How to do this analysis efficiently in Galaxy?

\nThe objectives are:
- Learn how RNA-seq reads are converted into counts
- Understand QC steps that can be...

Scientific topics: Transcriptomics

Keywords: transcriptomics, collections, mouse, QC

Resource type: hands-on tutorial

Hands-on for 'GO Enrichment Analysis' tutorial

The questions this addresses are:
- How can I functionally interpret a list of genes of interest that I obtained from my experiment?

\nThe objectives are:
- How to perform a GO Enrichment Analysis
- How to interpret and simplify the results

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with Volcano Plot' tutorial

The questions this addresses are:
- How to generate a volcano plot from RNA-seq data?

\nThe objectives are:
- Create a volcano plot of RNA-seq data to visualize significant genes

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Creating a new tutorial' tutorial

The questions this addresses are:
- How to integrate a new tutorial?
- How to make a tutorial robust and reproducible?

\nThe objectives are:
- Create a tutorial from scratch
- Link a tutorial to a topic
- Create hands-on
- Add technical support for a tutorial

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for '3: RNA-seq genes to pathways' tutorial

The questions this addresses are:
- What are the differentially expressed pathways in the mammary gland of pregnant versus lactating mice?

\nThe objectives are:
- Identification of differentially expressed pathways

Scientific topics: Transcriptomics

Keywords: transcriptomics, mouse

Resource type: hands-on tutorial

Hands-on for 'Pre-processing of 10X Single-Cell RNA Datasets' tutorial

The questions this addresses are:
- What is 10X?
- What is STARsolo and what is Cell Ranger?
- What are BCL and MTX files?
- What is an HDF5 file, and why is it important?

\nThe objectives are:
- Demultiplex single-cell FASTQ data from 10X Genomics
- Learn about transparent matrix...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with Volcano Plot in R' tutorial

The questions this addresses are:
- How to customise Volcano plot output in R?

\nThe objectives are:
- Learn how to use R to edit Volcano plot colours, points, labels and categories

Scientific topics: Transcriptomics

Keywords: transcriptomics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Updating diffs in admin training' tutorial

The questions this addresses are:
- How does it work?

\nThe objectives are:
- Update some text in an earlier commit

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Running the GTN website locally' tutorial

The questions this addresses are:
- How to setup the infrastructure to build training webpages?

\nThe objectives are:
- Installing packages needed for rendering the webpage
- Running the GTN material website locally
- Tracking changes to the content live in the webbrowser

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Including a new topic' tutorial

The questions this addresses are:
- How to include a new topic?

\nThe objectives are:
- Create a new topic
- Set up the metadata for a topic

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Adding Quizzes to your Tutorial' tutorial

The questions this addresses are:
- How to make a quiz?

\nThe objectives are:
- Create a quiz

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Network analysis with Heinz' tutorial

The questions this addresses are:
- Which pathways are potentially contributing to dental caries?

\nThe objectives are:
- Network Analysis of metatranscriptomics data using Heinz in Galaxy to pinpoint the optimal scoring subnetwork.

Scientific topics: Transcriptomics

Keywords: transcriptomics, metatranscriptomics, network analysis

Resource type: hands-on tutorial

Hands-on for 'Trajectory Analysis using Python (Jupyter Notebook) in Galaxy' tutorial

The questions this addresses are:
- How can I infer lineage relationships between single cells based on their RNA, without a time series?

\nThe objectives are:
- Execute multiple plotting methods designed to maintain lineage relationships between cells
- Interpret these plots

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Contributing with GitHub via its interface' tutorial

The questions this addresses are:
- How can I contribute to an open-source project with GitHub and its interface

\nThe objectives are:
- Edit a file via GitHub interface
- Create a pull request
- Update a pull request

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Contributing with GitHub via command-line' tutorial

The questions this addresses are:
- How can I contribute to an open-source project with GitHub?
- What is the GitHub flow?

\nThe objectives are:
- Fork a repository on GitHub
- Clone a remote repository locally
- Create a branch
- Commit changes
- Push changes to a remote repository
-...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Adding auto-generated video to your slides' tutorial

The questions this addresses are:
- How can we add auto-generated video?
- How does it work?
- What do I need to do to make it optimal for viewers?

\nThe objectives are:
- Adding a video to a set of slides

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Creating Interactive Galaxy Tours' tutorial

The questions this addresses are:
- What is a Interactive Galaxy Tour?
- How can we create an Interactive Tour?

\nThe objectives are:
- Creating a Galaxy tour from scratch
- Deploying and running a tour

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'GTN Metadata' tutorial

The questions this addresses are:
- What metadata is required or possible to set in a Tutorial, Slide, Topic, or FAQ

\nThe objectives are:
- Know where to find all of the available metadata, so you can reference it later.

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Generating PDF artefacts of the website' tutorial

The questions this addresses are:
- How to generate PDF of the different tutorials and slides?

\nThe objectives are:
- Generating PDFs

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'De Bruijn Graph Assembly' tutorial

The questions this addresses are:
- What are the factors that affect genome assembly?
- How does Genome assembly work?

\nThe objectives are:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an...

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'Hi-C analysis of Drosophila melanogaster cells using HiCExplorer' tutorial

The questions this addresses are:
- Why is a Hi-C analysis useful?
- What is 'chromosome conformation capture'?
- What are main steps in order to generate and plot a Hi-C contact matrix?

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: hands-on tutorial

Hands-on for 'Creating content in Markdown' tutorial

The questions this addresses are:
- How to write a tutorial with hands-on?
- What are the different boxes?
- How can I add a caption to an image?

\nThe objectives are:
- Create hands-on
- Use the different boxes

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Unicycler Assembly' tutorial

The questions this addresses are:
- I have short reads and long reads. How do I assemble a genome?

\nThe objectives are:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with...

Keywords: assembly, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Making sense of a newly assembled genome' tutorial

The questions this addresses are:
- I just assembled a genome. How does it compare with already sequenced genomes?
- How do I find rearranged, inserted, or deleted regions?

\nThe objectives are:
- Identification of the most closely related genome to my new assembly
- Perform sequence...

Keywords: assembly, prokaryote

Resource type: hands-on tutorial

Hands-on for 'VGP assembly pipeline - short version' tutorial

The questions this addresses are:
- what combination of tools can produce the highest quality assembly of vertebrate genomes?
- How can we evaluate how good it is?

\nThe objectives are:
- Learn the tools necessary to perform a de novo assembly of a vertebrate genome
- Evaluate the quality...

Keywords: assembly, pacbio, eukaryote, VGP

Resource type: hands-on tutorial

Hands-on for 'Genome assembly using PacBio data' tutorial

The questions this addresses are:
- How to perform a genome assembly with PacBio data ?
- How to check assembly quality ?

\nThe objectives are:
- Assemble a Genome with PacBio data
- Assess assembly quality

Keywords: assembly, assembly, pacbio

Resource type: hands-on tutorial

Hands-on for 'VGP assembly pipeline' tutorial

The questions this addresses are:
- what combination of tools can produce the highest quality assembly of vertebrate genomes?
- How can we evaluate how good it is?

\nThe objectives are:
- Learn the tools necessary to perform a de novo assembly of a vertebrate genome
- Evaluate the quality...

Keywords: assembly, pacbio, eukaryote, VGP

Resource type: hands-on tutorial

Slides for 'A Short Introduction to Galaxy' tutorial

The questions this addresses are:
- What is Galaxy?
- Why should I use Galaxy?
- How do I use Galaxy?
- How can I connect with the Galaxy Community?

Keywords: introduction

Resource type: slides

Hands-on for 'An Introduction to Genome Assembly' tutorial

The questions this addresses are:
- How do we perform a very basic genome assembly from short read data?

\nThe objectives are:
- assemble some paired end reads using Velvet
- examine the output of the assembly.

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'Chloroplast genome assembly' tutorial

The questions this addresses are:
- How can we assemble a chloroplast genome?

\nThe objectives are:
- Assemble a chloroplast genome from long reads
- Polish the assembly with short reads
- Annotate the assembly and view
- Map reads to the assembly and view

Keywords: assembly, plants, nanopore

Resource type: hands-on tutorial

Hands-on for 'DNA Methylation data analysis' tutorial

The questions this addresses are:
- What is methylation and why it cannot be recognised by a normal NGS procedure?
- Can a different methylation influence the expression of a gene? How?
- Which tools you can use to analyse methylation data?

\nThe objectives are:
- Learn how to analyse...

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: hands-on tutorial

Hands-on for 'Genome Assembly of MRSA using Oxford Nanopore MinION Data' tutorial

The questions this addresses are:
- How to check the quality of the MinION data?
- How to perform an assembly with MinION data?
- What species do I have and what is its sequence type?
- Which resistance genes are on my genome?
- Where are the genes located on my genome?

\nThe objectives...

Keywords: assembly, nanopore, assembly, amr

Resource type: hands-on tutorial

Hands-on for 'Infinium Human Methylation BeadChip' tutorial

The questions this addresses are:
- Which DNA regions and positions are diffrentialy methylated in pre MAPKi treatment and post MAPKi resistance Melanomas GSE65183?
- How to analyse and visualise Infinium Human Methylation BeadChip's?

\nThe objectives are:
- Learn how to perform reproducible...

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: hands-on tutorial

Hands-on for 'Designing plasmids encoding predicted pathways by using the BASIC assembly method' tutorial

The questions this addresses are:
- How to design plasmids encoding predicted pathways using BASIC assembly method ?
- How to generate scripts enabling the automatic build of plasmids ?

\nThe objectives are:
- Annotate the SBML pathway using Selenzy tool.
- Design plasmids encoding...

Keywords: synthetic-biology

Resource type: hands-on tutorial

Hands-on for 'ToolFactory: Generating Tools From Simple Scripts' tutorial

The questions this addresses are:
- What options exist for new-to-Galaxy developers to convert functioning command line scripts into Galaxy tools?
- Can any command line script I've written be wrapped as a Galaxy tool?
- Can I make a tool from a script developed in a Galaxy Interactive...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Contributing to BioBlend as a developer' tutorial

The questions this addresses are:
- How to get started making contributions to BioBlend?

\nThe objectives are:
- Learn the basics behind BioBlend and the Galaxy API from a developer perspective.
- Learn how to implement a simple method in BioBlend.
- Learn how to run the BioBlend test suite.

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Writing Automated Tests for Galaxy' tutorial

The objectives are:
- Learn about the different types of automated tests in Galaxy
- Learn to write API tests
- Learn to write unit tests

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools' tutorial

The questions this addresses are:
- Which heterologous pathways are candidates to produce a compound in a chassis?

\nThe objectives are:
- Define what data are required to run RetroSynthesis analysis.
- Understanding how to run the tools to search heterologous pathways.

Keywords: synthetic-biology

Resource type: hands-on tutorial

Hands-on for 'ToolFactory: Generating Tools From More Complex Scripts' tutorial

The questions this addresses are:
- What else can I do with the ToolFactory?

\nThe objectives are:
- Further develop your ToolFactory Skills

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'JavaScript plugins' tutorial

The questions this addresses are:
- How can I make a custom visualization plugin for Galaxy?

\nThe objectives are:
- Learn how to add JavaScript plugins to Galaxy using the Charts visualization framework

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Debugging Galaxy' tutorial

The questions this addresses are:
- How do I debug Galaxy?

\nThe objectives are:
- Fix a broken branch
- Interpret the results of failed tests on GitHub
- Run individual tests locally
- Fix errors identified by failing tests
- Debug simple runtime errors using the Python debugger
- Write...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'CRISPR screen analysis' tutorial

The questions this addresses are:
- What are the steps to process CRISPR screen data?
- How to identify essential genes across experimental conditions?

\nThe objectives are:
- Apply appropriate analysis and quality control steps for CRISPR screen data
- Identify differentially enriched...

Keywords: genome-annotation, genome editing, CRISPR, essential genes, cell line

Resource type: hands-on tutorial

Hands-on for 'Generic plugins' tutorial

The questions this addresses are:
- How can visualization plugins benefit science?

\nThe objectives are:
- Implement a first Galaxy visualization
- Understand the client side vs. server side principle

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Galaxy Webhooks' tutorial

The questions this addresses are:
- What are Galaxy Webhooks?
- How to create them?

\nThe objectives are:
- Discover what Galaxy Webhooks are
- Be able to create Webhooks
- Be able to add a Galaxy Webhook in a Galaxy instance

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Organizing a workshop' tutorial

The questions this addresses are:
- What should we think about when we organize a workshop?
- Have we done everything necessary for organising a great workshop?

Keywords: instructors

Resource type: hands-on tutorial

Hands-on for 'Training Infrastructure as a Service' tutorial

The questions this addresses are:
- Is this service appropriate for my event?

\nThe objectives are:
- Identify if it is appropriate
- Interact with the service administrators to arrange for infrastructure

Keywords: instructors, cyoa

Resource type: hands-on tutorial

Hands-on for 'Galaxy Admin Training' tutorial

The questions this addresses are:
- How do I organise a Galaxy Admin Training (GAT)
- What do I need to set up?
- What should I know during the training?

\nThe objectives are:
- Interact with the UseGalaxy.eu admins to arrange for infrastructure
- Run a great training!

Keywords: instructors

Resource type: hands-on tutorial

Hands-on for 'Set up a Galaxy for Training' tutorial

The questions this addresses are:
- How do I prepare my Galaxy instance to support a training module?
- How can I generate a Docker Galaxy instance for my topic?

\nThe objectives are:
- Use ephemeris to install the training requirements to a Galaxy instance
- Create a docker image for a...

Keywords: instructors

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Funannotate' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome with Funannotate?
- How to perform functional annotation?
- How to evaluate and visualize annotated genomic features?
- How to format the annotation for submission at NCBI?

\nThe objectives are:
- Load genome into...

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Masking repeats with RepeatMasker' tutorial

The questions this addresses are:
- How to mask repeats in a genome?
- What is the difference between hard and soft masking?

\nThe objectives are:
- Use RepeatMasker to soft mask a newly assmbled genome

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Prokka' tutorial

The questions this addresses are:
- How can we annotate a bacterial genome?
- How can we visualize annotated genomic features?

\nThe objectives are:
- Load genome into Galaxy
- Annotate genome with Prokka
- View annotations in JBrowse

Keywords: genome-annotation, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Scripting Galaxy using the API and BioBlend' tutorial

The questions this addresses are:
- What is a REST API?
- How to interact with Galaxy programmatically?
- Why and when should I use BioBlend?

\nThe objectives are:
- Interact with Galaxy via BioBlend.

Keywords: dev, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Maker' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome?
- How to evaluate and visualize annotated genomic features?

\nThe objectives are:
- Load genome into Galaxy
- Annotate genome with Maker
- Evaluate annotation quality with BUSCO
- View annotations in JBrowse

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Functional annotation of protein sequences' tutorial

The questions this addresses are:
- How to perform functional annotation on protein sequences?

\nThe objectives are:
- Perform functional annotation using EggNOG-mapper and InterProScan

Keywords: genome-annotation, eukaryote, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Essential genes detection with Transposon insertion sequencing' tutorial

The questions this addresses are:
- What is Transposon insertion Sequencing?
- How to get TA sites Coverage ?
- How to predict essential genes ?

\nThe objectives are:
- Understand the read structure of TnSeq analyses
- Predict Essential genes with Transit
- Compare gene essentiality in...

Keywords: genome-annotation, bacteria, tnseq, essential genes

Resource type: hands-on tutorial

Hands-on for 'From small to large-scale genome comparison' tutorial

The questions this addresses are:
- How can we run pairwise genome comparisons using Galaxy?
- How can we run massive chromosome comparisons in Galaxy?
- How can we quickly visualize genome comparisons in Galaxy?

\nThe objectives are:
- Learn the basics of pairwise sequence comparison
-...

Keywords: genome-annotation

Resource type: hands-on tutorial

Hands-on for 'Visualisation with Circos' tutorial

The questions this addresses are:
- What can the Circos Galaxy tool be used for?
- How can I visualise common genomic datasets using Circos?

\nThe objectives are:
- Create a number of Circos plots using the Galaxy tool
- Familiarise yourself with the various different track types

Keywords: visualisation

Resource type: hands-on tutorial

Hands-on for 'Genomic Data Visualisation with JBrowse' tutorial

The questions this addresses are:
- How can I visualise features or blast data?
- How can I visualise sequencing data in a workflow

\nThe objectives are:
- Build several visualisations in JBrowse
- Have basic familiarity with moving around JBrowse, and loading several data tracks

Keywords: visualisation

Resource type: hands-on tutorial

Hands-on for 'Refining Genome Annotations with Apollo' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Microbial Variant Calling' tutorial

The questions this addresses are:
- How do we detect differences between a set of reads from a microorganism and a reference genome

\nThe objectives are:
- Find variants between a reference genome and a set of reads
- Visualise the SNP in context of the reads aligned to the genome
-...

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'M. tuberculosis Variant Analysis' tutorial

The questions this addresses are:
- How do we detect differences between a set of reads from M. tuberculosis (Mtb) and the Mtb reference genome

\nThe objectives are:
- How should we filter those variants
- How can we predict drug resistance from those variants
- How do we annotate those...

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Calling variants in non-diploid systems' tutorial

The questions this addresses are:
- How does frequency of mitochondrial polymorphisms change from mother to child?

\nThe objectives are:
- Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Calling variants in diploid systems' tutorial

The questions this addresses are:
- How to find variable sites in diploid genomes?

\nThe objectives are:
- Identification of genetic variations using variant calling

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Exome sequencing data analysis for diagnosing a genetic disease' tutorial

The questions this addresses are:
- How do you identify genetic variants in samples based on exome sequencing data?
- How do you, among the set of detected variants, identify candidate causative variants for a given phenotype/disease?

\nThe objectives are:
- Jointly call variants and...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis' tutorial

The questions this addresses are:
- Learn how to get and use data from the Sequence Read Archive in Galaxy.

\nThe objectives are:
- Understand how Galaxy and the Sequence Read Archive interact.
- Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to...

Scientific topics: Genetic variation

Keywords: variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'Mapping and molecular identification of phenotype-causing mutations' tutorial

The questions this addresses are:
- What is mapping-by-sequencing?
- How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?

\nThe objectives are:
- Use joint variant calling and extraction to facilitate variant comparison across samples
-...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Quality Control' tutorial

The questions this addresses are:
- How to perform quality control of NGS raw data?
- What are the quality parameters to check for a dataset?
- How to improve the quality of a dataset?

\nThe objectives are:
- Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
- Assess long reads...

Keywords: sequence-analysis

Resource type: hands-on tutorial

Slides for 'Mapping' tutorial

The questions this addresses are:
- What is mapping (alignment)?
- What is the BAM format?
- How can we view aligned sequences?

\nThe objectives are:
- Understand the basic concept of mapping
- Learn about factors influencing alignment
- See a genome browser used to better understand your...

Keywords: sequence-analysis

Resource type: slides

Hands-on for 'Mapping' tutorial

The questions this addresses are:
- What is mapping?
- What two things are crucial for a correct mapping?
- What is BAM?

\nThe objectives are:
- You will learn what mapping is
- A genome browser is shown that helps you to understand your data

Keywords: sequence-analysis

Resource type: hands-on tutorial

Introduction to 'Introduction to Galaxy Analyses'

Slides for Introduction to Galaxy Analyses

Resource type: slides

Introduction to 'Metabolomics'

Slides for Metabolomics

Scientific topics: Metabolomics

Resource type: slides

Introduction to 'Galaxy Server administration'

Slides for Galaxy Server administration

Resource type: slides

Introduction to 'Metagenomics'

Slides for Metagenomics

Scientific topics: Metagenomics

Resource type: slides

Introduction to 'Climate'

Slides for Climate

Resource type: slides

Introduction to 'Contributing to the Galaxy Training Material'

Slides for Contributing to the Galaxy Training Material

Resource type: slides

Slides for 'Nucleoli Segmentation <br> & <br> Feature Extraction <br> using CellProfiler' tutorial

The questions this addresses are:
- How do I run an image analysis pipeline on public data using CellProfiler?
- How do I analyse the DNA channel of fluorescence siRNA screens?
- How do I download public image data into my history?
- How do I segment and label cell nuclei?
- How do I...

Keywords: imaging

Resource type: slides

Slides for 'Server Maintenance and Backups' tutorial

The questions this addresses are:
- How do I maintain a Galaxy server?
- What happens if I lose everything?

\nThe objectives are:
- Learn about different maintenance steps
- Learn what to back up and how to recover

Keywords: admin

Resource type: slides

Slides for 'Ansible' tutorial

The questions this addresses are:
- Why Ansible?
- How and when to use Ansible?
- How to write a role?
- How to leverage community build roles?

\nThe objectives are:
- Learn Ansible basics.
- Write a simple role.
- Install a role from Ansible Galaxy.

Keywords: admin

Resource type: slides

Slides for 'Galaxy Monitoring with Telegraf and Grafana' tutorial

The questions this addresses are:
- How to monitor Galaxy with Telegraf
- How do I set up InfluxDB
- How can I make graphs in Grafana?
- How can I best alert on important metrics?

\nThe objectives are:
- Setup InfluxDB
- Setup Telegraf
- Setup Grafana
- Create several charts

Keywords: admin

Resource type: slides

Slides for 'Galaxy Monitoring with gxadmin' tutorial

The questions this addresses are:
- What is gxadmin
- What can it do?
- How to write a query?

\nThe objectives are:
- Learn gxadmin basics
- See some queries and learn how they help debug production issues

Keywords: admin

Resource type: slides

Slides for 'Docker and Galaxy' tutorial

The questions this addresses are:
- Why Docker? What is it?
- How to use Docker?
- How to integrate Galaxy in Docker to facilitate its deployment?

\nThe objectives are:
- Docker basics
- Galaxy Docker image (usage)
- Galaxy Docker (internals)
- Galaxy flavours

Keywords: admin

Resource type: slides

Slides for 'Galaxy Interactive Tools' tutorial

The objectives are:
- Learn the differences between Galaxy Interactive Environments and Galaxy Interactive Tools
- Have an understanding of what Galaxy Interactive Tools are and how they work

Keywords: admin

Resource type: slides

Hands-on for 'Ansible' tutorial

The questions this addresses are:
- Why Ansible?
- How and when to use Ansible?
- How to write a role?
- How to leverage community build roles?

\nThe objectives are:
- Learn Ansible basics
- Write a simple role
- Install a role from Ansible Galaxy

Keywords: admin, ansible

Resource type: hands-on tutorial

Slides for 'Galaxy Installation with Ansible' tutorial

The questions this addresses are:
- How does it all connect?
- What steps will we go through?

\nThe objectives are:
- Get a high-level overview of a Galaxy server setup

Keywords: admin

Resource type: slides

Hands-on for 'Galaxy Installation with Ansible' tutorial

The questions this addresses are:
- How does the Galaxy Ansible module work internally?
- How can I install a Galaxy server with Ansible

\nThe objectives are:
- Have an understanding of how Galaxy's Ansible roles are structured and interact with one another
- Be able to use an Ansible...

Keywords: admin, ansible, deploying, git-gat

Resource type: hands-on tutorial

Slides for 'User, Role, Group and Quota managment' tutorial

The questions this addresses are:
- How does Galaxy manage users and groups?
- How can I assign Quotas to specific users/groups?

\nThe objectives are:
- Learn the Galaxy user/group management and assign Quotas.
- Understand the Role Based Access Control (RBAC) of Galaxy.

Keywords: admin

Resource type: slides

Slides for 'Connecting Galaxy to a compute cluster' tutorial

The questions this addresses are:
- How to connect Galaxy to a compute cluster?
- How can I configure job dependent resources, like cores, memory for my DRM?

\nThe objectives are:
- Understand all components of the Galaxy job running stack
- Understand how the job_conf.xml file controls...

Keywords: admin, features

Resource type: slides

Slides for 'Introduction to metatranscriptomics' tutorial

The questions this addresses are:
- How to analyze metatranscriptomics data?
- What information can be extracted of metatranscriptomics data?
- How to assign taxa and function to the identified sequences?

Scientific topics: Metagenomics

Keywords: metagenomics

Resource type: slides

Slides for 'Storage Management' tutorial

The questions this addresses are:
- How does Galaxy locate data?
- How can I have Galaxy use multiple storage locations?

\nThe objectives are:
- Setup Galaxy with both the Hierarachical and Distributed Object Storages

Keywords: admin

Resource type: slides

Hands-on for 'Deep Learning (Part 1) - Feedforward neural networks (FNN)' tutorial

The questions this addresses are:
- What is a feedforward neural network (FNN)?
- What are some applications of FNN?

\nThe objectives are:
- Understand the inspiration for neural networks
- Learn various activation functions, and classification/regression problems solved by neural networks
...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Deep Learning (Part 2) - Recurrent neural networks (RNN)' tutorial

The questions this addresses are:
- What is a recurrent neural network (RNN)?
- What are some applications of RNN?

\nThe objectives are:
- Understand the difference between feedforward neural networks (FNN) and RNN
- Learn various RNN types and architectures
- Learn how to create a neural...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Slides for 'Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies' tutorial

The questions this addresses are:
- What is the Semantic Web and how can it help integrating and querying data?
- How can AskOmics help benefiting from Semantic Web technologies without having to write RDF or SPARQL code?

\nThe objectives are:
- Understand the basics of RDF and SPARQL
-...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: slides

Slides for 'Network Analysis with Heinz' tutorial

The questions this addresses are:
- What is metatranscriptomics
- Which pathways are potentially contributing to dental caries?

\nThe objectives are:
- Learn some background knowledge about microbiome
- Understand metatranscriptomics
- Familiarize yourself with KEGG terminology
-...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: slides

Slides for 'Contributing with GitHub via command-line' tutorial

The questions this addresses are:
- How can I contribute to an open-source project with GitHub?
- What is the GitHub flow?

\nThe objectives are:
- Fork a repository on GitHub
- Clone a remote repository locally
- Create a branch
- Commit changes
- Push changes to a remote repository
-...

Keywords: contributing

Resource type: slides

Slides for 'Introduction to the ToolFactory tutorial.' tutorial

The objectives are:
- This session introduces the ToolFactory and explains how it might be useful for programmers new to Galaxy

Keywords: dev

Resource type: slides

Hands-on for 'RAD-Seq Reference-based data analysis' tutorial

The questions this addresses are:
- How to analyze RAD sequencing data using a reference genome for a population genomics study?

\nThe objectives are:
- Analysis of RAD sequencing data using a reference genome
- SNP calling from RAD sequencing data
- Calculate population genomics statistics...

Scientific topics: Ecology

Keywords: ecology, RAD-seq

Resource type: hands-on tutorial

Slides for 'Tool development and integration into Galaxy' tutorial

The questions this addresses are:
- What is a tool for Galaxy?
- How to write a best-practice tool?
- How to deal with the tool environment?

\nThe objectives are:
- Learn what a tool is and its structure
- Use the Planemo utilities to develop a tool
- Deal with the dependencies
- Write...

Keywords: dev

Resource type: slides

Slides for 'High Performance Computing for Pairwise Genome Comparison' tutorial

The questions this addresses are:
- What is sequence comparison and why does it matter?
- What are the challenges and how can we use High Performance Computing to overcome them?
- How can we use Galaxy for large scale sequence comparison?

\nThe objectives are:
- Learn the basics of genome...

Keywords: genome-annotation

Resource type: slides

Hands-on for 'High Throughput Molecular Dynamics and Analysis' tutorial

The questions this addresses are:
- How are protein-ligand systems parameterized for molecular dynamics simulation?
- What kind of analysis can be carried out on molecular trajectories?
- How can high-throughput MD be used to study multiple ligands?

\nThe objectives are:
- Learn about...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Protein target prediction of a bioactive ligand with Align-it and ePharmaLib' tutorial

The questions this addresses are:
- What is a pharmacophore model?
- How can I perform protein target prediction with a multi-step workflow or the one-step Zauberkugel workflow?

\nThe objectives are:
- Create an SMILES file of a bioactive ligand.
- Screen the query ligand against a...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Galaxy 101 for everyone' tutorial

The questions this addresses are:
- What are the differences between the Iris species?

\nThe objectives are:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to tag datasets
- Learn how to run tools
- Learn how histories work
-...

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'Compute and analyze biodiversity metrics with PAMPA toolsuite' tutorial

The questions this addresses are:
- How to evaluate properly populations and communities biological state with abundance data?
- How does trawl exploited populations of Baltic sea, Southern Atlantic and Scotland are doing over time?
- How to compute and analyze biodiversity metrics from...

Scientific topics: Ecology

Keywords: ecology

Resource type: hands-on tutorial

Hands-on for 'Understanding Galaxy history system' tutorial

The questions this addresses are:
- How do Galaxy histories work?

\nThe objectives are:
- Gain understanding on navigating and manipulating histories

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Searching Your History' tutorial

The questions this addresses are:
- How can you find your datasets?
- How to search by file type?
- What filters are available to you?

\nThe objectives are:
- Feel confident in searching your history

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Name tags for following complex histories' tutorial

The questions this addresses are:
- What are name tags or hash tags?
- How can I use them to keep track of my data?

\nThe objectives are:
- Learn how to set name tags
- Learn how they are propagated

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Using Workflow Parameters' tutorial

The questions this addresses are:
- What are Workflow Parameters
- How can I define and use Workflow Parameters
- How can I read Parameters from Datasets

\nThe objectives are:
- Learn how to use Workflow Parameters to improve your Workflows

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'Removal of human reads from SARS-CoV-2 sequencing data' tutorial

The questions this addresses are:
- How can you remove traces of human sequence data from a sequenced viral sample?

\nThe objectives are:
- Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources
- Organize the data into a collection
- Preprocess and map...

Keywords: sequence-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry imaging: Examining the spatial distribution of analytes' tutorial

The questions this addresses are:
- What is the typical mass range of VOCs?
- In which compartments of the chilli are the measured VOCs located?
- In which compartment of the chilli is the capsaicin located?

\nThe objectives are:
- Plot average mass spectra and overlaid mass spectra of...

Scientific topics: Metabolomics

Keywords: metabolomics

Resource type: hands-on tutorial

Hands-on for 'dplyr & tidyverse for data processing' tutorial

The questions this addresses are:
- How can I load tabular data into R?
- How can I slice and dice the data to ask questions?

\nThe objectives are:
- Read data with the built-in read.csv
- Read data with dplyr's read_csv
- Use dplyr and tidyverse functions to cleanup data.

Keywords: data-science, R, rmarkdown-notebook, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Advanced R in Galaxy' tutorial

The questions this addresses are:
- How can I manipulate data using R in Galaxy?
- How do I get started with tabular data from Galaxy in R?

\nThe objectives are:
- Be able to load and explore the shape and contents of a tabular dataset using base R functions.
- Understand factors and how...

Keywords: data-science, R

Resource type: hands-on tutorial

Hands-on for 'Introduction to SQL' tutorial

The questions this addresses are:
- How can I get data from a database?
- How can I sort a query's results?
- How can I remove duplicate values from a query's results?
- How can I select subsets of data?
- How can I calculate new values on the fly?
- How do databases represent missing...

Keywords: data-science, SQL, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Advanced CLI in Galaxy' tutorial

The questions this addresses are:
- How can I combine existing commands to do new things?
- How can I perform the same actions on many different files?
- How can I find files?
- How can I find things in files?

\nThe objectives are:
- Redirect a command's output to a file.
- Process a file...

Keywords: data-science, bash, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Basic Types & Type Conversion' tutorial

The questions this addresses are:
- What kinds of data do programs store?
- How can I convert one type to another?

\nThe objectives are:
- Explain key differences between integers and floating point numbers.
- Explain key differences between numbers and character strings.
- Use built-in...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'SQL with Python' tutorial

The questions this addresses are:
- How can I access databases from programs written in Python?

\nThe objectives are:
- Write short programs that execute SQL queries.
- Trace the execution of a program that contains an SQL query.
- Explain why most database applications are written in a...

Keywords: data-science, SQL, Python, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Variant Calling Workflow' tutorial

The questions this addresses are:
- How do I find sequence variants between my sample and a reference genome?

\nThe objectives are:
- Understand the steps involved in variant calling.
- Describe the types of data formats encountered during variant calling.
- Use command line tools to...

Keywords: data-science

Resource type: hands-on tutorial

Hands-on for 'Galaxy Installation on Kubernetes' tutorial

The questions this addresses are:
- How do I deploy Galaxy on Kubernetes using Helm?
- How can I create a simple replica of usegalaxy.org?

\nThe objectives are:
- Have an understanding of how to use Galaxy's Helm chart
- Be able to use Helm to install different flavors of Galaxy for...

Keywords: admin, kubernetes

Resource type: hands-on tutorial

Hands-on for 'Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab' tutorial

The questions this addresses are:
- Why and when using Galaxy Climate JupyterLab for CLM-FATES?
- How to start Galaxy Climate JupyterLab in Galaxy?
- How to upload input data for running CLM-FATES?
- How to create CLM-FATES case in Galaxy Climate JupyterLab?
- How to customize your run?
-...

Keywords: climate, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'MaxQuant and MSstats for the analysis of label-free data' tutorial

The questions this addresses are:
- How to perform label-free shotgun (DDA) data analysis in MaxQuant and MSstats?
- Which proteins are differentially abundant in the two types of cutaneous squamous cell carcinomas?

\nThe objectives are:
- Learn how to use MaxQuant and MSstats for the...

Scientific topics: Proteomics

Keywords: proteomics, label-free

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using SearchGUI and PeptideShaker' tutorial

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

\nThe objectives are:
- Protein identification from LC-MS/MS raw files.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Annotating a protein list identified by LC-MS/MS experiments' tutorial

The questions this addresses are:
- How to filter out technical contaminants?
- How to check for tissue-specificity?
- How to perform enrichment analysis?
- How to map your protein list to pathways (Reactome)?
- How to compare your proteome with other studies?

\nThe objectives are:
-...

Scientific topics: Proteomics

Keywords: proteomics, DDA, human

Resource type: hands-on tutorial

Hands-on for 'Contributing a New Feature to Galaxy Core' tutorial

The questions this addresses are:
- How can I add a new feature to Galaxy that involves modifications to the database, the API, and the UI?

\nThe objectives are:
- Learn to develop extensions to the Galaxy data model
- Learn to implement new API functionality within Galaxy
- Learn to extend...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Identifying tuberculosis transmission links: from SNPs to transmission clusters' tutorial

The objectives are:
- Create a SNP alignment
- Calculate pairwise SNP distances between MTB samples
- Identify transmission clusters based on SNP distances
- Study the emergence and spread of drug resistance based on transmission analysis.

Keywords: evolution

Resource type: hands-on tutorial

Hands-on for 'Filter, Plot and Explore Single-cell RNA-seq Data' tutorial

The questions this addresses are:
- Is my single cell dataset a quality dataset?
- How do I generate and annotate cell clusters?
- How do I pick thresholds and parameters in my analysis? What's a "reasonable" number, and will the world collapse if I pick the wrong one?

\nThe objectives are:
...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, interactive-tools, español

Resource type: hands-on tutorial

Hands-on for '2: RNA-seq counts to genes' tutorial

The questions this addresses are:
- What are the differentially expressed genes in the mammary gland of pregnant versus lactating mice?
- How to analyze RNA count data using limma-voom?
- How to perform quality control (QC) of RNA-seq count data?

\nThe objectives are:
- Analysis of RNA-seq...

Scientific topics: Transcriptomics

Keywords: transcriptomics, limma-voom, mouse, QC

Resource type: hands-on tutorial

Hands-on for 'CLIP-Seq data analysis from pre-processing to motif detection' tutorial

The questions this addresses are:
- How is raw CLIP-Seq data processed and analysed?
- How do I find binding motifs and targets for a protein (e.g., RBFOX2)?

\nThe objectives are:
- Remove Adapters, Barcodes and Unique Molecular Identifiers (UMIs) from the reads
- Align trimmed reads with...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Whole transcriptome analysis of Arabidopsis thaliana' tutorial

The questions this addresses are:
- Which miRNAs are upregulated in response to brassinosteroids?
- Which genes are potential target of brassinosteroid-induced miRNAs?

\nThe objectives are:
- Perform miRNA differential expression analysis
- Understand the quasi-mapping-based Salmon method...

Scientific topics: Transcriptomics

Keywords: transcriptomics, miRNA, plants

Resource type: hands-on tutorial

Hands-on for 'RNA-Seq analysis with AskOmics Interactive Tool' tutorial

The questions this addresses are:
- How to integrate RNA-Seq results with other datasets using AskOmics?
- How to query these datasets to answer a biological question?
- How to exploit a distant SPARQL endpoint to retrieve information?

\nThe objectives are:
- Launch an AskOmics Interactive...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Genome Assembly of MRSA using Illumina MiSeq Data' tutorial

The questions this addresses are:
- How to check the quality of the MiSeq data?
- How to perform an assembly with MiSeq data?
- What species do I have and what is its sequence type?
- Which resistance genes are on my genome?
- Where are the genes located on my genome?

\nThe objectives...

Keywords: assembly, illumina, assembly, amr

Resource type: hands-on tutorial

Hands-on for 'Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads' tutorial

The questions this addresses are:
- How can a genome of interest be assembled against a background of contaminating reads from other genomes?
- How can sequencing data from public sources be turned into assembly-ready polished datasets?

\nThe objectives are:
- Obtain viral (SARS-CoV-2)...

Keywords: assembly, covid19

Resource type: hands-on tutorial

Hands-on for 'Formation of the Super-Structures on the Inactive X' tutorial

The questions this addresses are:
- Histone modification?
- How is a raw set of ChIP-seq data processed and analyzed?
- Where are the enriched regions for H3K27me3, H3K4me3 and CTCF on the chrX?

\nThe objectives are:
- Inspect the read quality
- Trim low quality bases
- Map reads on a...

Scientific topics: Epigenomics

Keywords: epigenetics, ChIP-seq

Resource type: hands-on tutorial

Hands-on for 'Data source integration' tutorial

The questions this addresses are:
- How can I write a tool that can import data into Galaxy from an external database?
- What are "data sources" and how do they function?
- Is there any ready-to-use example?

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Maker (short)' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome?
- How to evaluate and visualize annotated genomic features?

\nThe objectives are:
- Load genome into Galaxy
- Annotate genome with Maker
- Evaluate annotation quality with BUSCO
- View annotations in JBrowse

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Calling very rare variants' tutorial

The questions this addresses are:
- What frequency of variants is so low that it is obscured by sequencing error rate?
- What are the different types of consensus sequences produced from duplex sequencing?

\nThe objectives are:
- Processing raw duplex sequencing data into consensus...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Trio Analysis using Synthetic Datasets from RD-Connect GPAP' tutorial

The questions this addresses are:
- How do you import data from the EGA?
- How to download files with HTSGET in Galaxy?
- How do you pre-process VCFs?
- How do you identify causative variants?

\nThe objectives are:
- Requesting DAC access and importing data from the EGA.
- Pre-process...

Scientific topics: Genetic variation

Keywords: variant-analysis, cancer, cyoa

Resource type: hands-on tutorial

Slides for 'The Pangeo ecosystem' tutorial

The questions this addresses are:
- What is Pangeo?
- What is the Pangeo Software Ecosystem?
- What is ARCO (Analysis Ready, Cloud Optimized) Data?
- What is Pangeo forge?
- What is STAC?
- Why and how to use STAC?
- How do Pangeo forge and STAC relate to each other?
- How can I use...

Keywords: climate, climate

Resource type: slides

Slides for 'Quality Control' tutorial

The questions this addresses are:
- How to control quality of NGS data?
- What are the quality parameters to check for each dataset?
- How to improve the quality of a sequence dataset?

\nThe objectives are:
- Manipulate FASTQ files
- Control quality from a FASTQ file for short and long...

Keywords: sequence-analysis

Resource type: slides

Slides for 'Getting data into Galaxy' tutorial

The questions this addresses are:
- How do I get my data into Galaxy?
- How do I get public data into Galaxy?

Keywords: galaxy-interface

Resource type: slides

Slides for 'Submitting SARS-CoV-2 sequences to ENA' tutorial

The objectives are:
- Introduce the European Nucleotide Archive (ENA)
- Learn the requirements to submit raw SARS-CoV-2 sequences to ENA in Galaxy
- Overview ENA's metadata model and how metadata objects are linked

Keywords: galaxy-interface

Resource type: slides

Slides for 'Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2' tutorial

The questions this addresses are:
- What is the SRA Aligned Read Format
- How can I use it?

\nThe objectives are:
- Understand which data and metadata types are available for SARS-CoV-2 SRA runs in the cloud.
- Understand what SRA Aligned Read Format is and what can you do with it.
-...

Keywords: galaxy-interface, ncbi, covid19

Resource type: slides

Slides for 'Galaxy Tool Management with Ephemeris' tutorial

The questions this addresses are:
- How are tools configured on a Galaxy instance?
- What is the Galaxy Tool Shed?
- How are Galaxy tools installed?
- What is ephemeris and how can it be used to manage tools on a Galaxy instance?

Keywords: admin

Resource type: slides

Slides for 'External Authentication' tutorial

The questions this addresses are:
- How can I connect Galaxy with CAS, SAML, etc.

\nThe objectives are:
- be familiar with configuring Galaxy to use an upstream (proxy) authentication provider
- be able to log in to your Galaxy server with a file-configured user.

Keywords: admin

Resource type: slides

Slides for 'Tool Dependencies and Containers' tutorial

The questions this addresses are:
- What are the advantages of running my Galaxy tool inside of a container?
- How does Galaxy find a container to run my tool in?
- What are BioContainers and how are they related to Galaxy?

\nThe objectives are:
- Explore the differences between...

Keywords: dev

Resource type: slides

Slides for 'Tool Dependencies and Conda' tutorial

The questions this addresses are:
- How can I connect tools to applications and libraries?
- What are the advantages of declaring dependencies for my tool?
- What are Conda and Bioconda?
- What are Conda recipes and environments?
- How do I find and use existing Conda recipes?
- How do I...

Keywords: dev

Resource type: slides

Hands-on for 'Species distribution modeling' tutorial

The questions this addresses are:
- How to build &amp; evaluate a niche model, visualize and project it ?

\nThe objectives are:
- Find and download occurrences data from GBIF
- Find and download environmental data
- Process both occurrences and environmental
- Partition occurrence data
-...

Scientific topics: Ecology

Keywords: ecology, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Introduction to image analysis using Galaxy' tutorial

The questions this addresses are:
- How do I use Galaxy with imaging data?
- How do I convert images using Galaxy?
- How do I display images in Galaxy?
- How do I filter images in Galaxy?
- How do I segment simple images in Galaxy?

\nThe objectives are:
- How to handle images in Galaxy.
...

Keywords: imaging

Resource type: hands-on tutorial

Hands-on for 'Nucleoli segmentation and feature extraction using CellProfiler' tutorial

The questions this addresses are:
- How do I run an image analysis pipeline on public data using CellProfiler?
- How do I analyse the DNA channel of fluorescence siRNA screens?
- How do I download public image data into my history?
- How do I segment and label cell nuclei?
- How do I...

Keywords: imaging

Resource type: hands-on tutorial

Hands-on for 'Analyse HeLa fluorescence siRNA screen' tutorial

The questions this addresses are:
- How do I analyze a HeLa fluorescence siRNA screen?
- How do I segment cell nuclei?
- How do I extract features from segmentations?
- How do I filter segmentations by morphological features?
- How do I apply a feature extraction workflow to a screen?
-...

Keywords: imaging

Resource type: hands-on tutorial

Hands-on for 'SQL Educational Game - Murder Mystery' tutorial

The questions this addresses are:
- Who did the crime?

\nThe objectives are:
- Explore SQL City and discover who committed the murder
- Reinforce your experiences with SQL such as querying, filtering, and joining data.

Keywords: data-science, game, SQL, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'CLI basics' tutorial

The questions this addresses are:
- What is a command shell and why would I use one?
- How can I move around on my computer?
- How can I see what files and directories I have?
- How can I specify the location of a file or directory on my computer?
- How can I create, copy, and delete files...

Keywords: data-science, bash, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Version Control with Git' tutorial

The questions this addresses are:
- What is version control and why should I use it?
- How do I get set up to use Git?
- Where does Git store information?
- How do I record changes in Git?
- How do I check the status of my version control repository?
- How do I record notes about what...

Keywords: data-science

Resource type: hands-on tutorial

Hands-on for 'Mapping Jobs to Destinations' tutorial

The questions this addresses are:
- How can I configure job dependent resources, like cores, memory for my DRM?
- How can I map jobs to resources and destinations

\nThe objectives are:
- Know how to map tools to job destinations
- Be able to use the dynamic job runner to make arbitrary...

Keywords: admin, ansible, jobs, git-gat

Resource type: hands-on tutorial

Hands-on for 'Metatranscriptomics analysis using microbiome RNA-seq data (short)' tutorial

The questions this addresses are:
- How to analyze metatranscriptomics data?"
- What information can be extracted of metatranscriptomics data?
- How to assign taxa and function to the identified sequences?

\nThe objectives are:
- Choose the best approach to analyze metatranscriptomics data
...

Scientific topics: Metagenomics

Keywords: metagenomics, metatranscriptomics

Resource type: hands-on tutorial

Hands-on for 'Library Generation for DIA Analysis' tutorial

The questions this addresses are:
- How does the peptide identification work in data independent acquisition (DIA) mass spectrometry (MS) data?
- What is a spectral library and how to generate a spectral library using Maxquant, diapysef and OpenSwath tools?

\nThe objectives are:
- Generating...

Scientific topics: Proteomics

Keywords: proteomics, DIA

Resource type: hands-on tutorial

Hands-on for 'Interval-Wise Testing for omics data' tutorial

The questions this addresses are:
- How to visualize high-resolution omics data in different groups of genomic regions?
- How to evaluate differences in high-resolution omics data between groups of genomic regions?
- How to detect locations and scales at which the significant effects...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy' tutorial

The questions this addresses are:
- How to use Jupyterlab and it several features?
- How to use it for creating input datasets and writing artificial intelligence (AI) algorithms?

\nThe objectives are:
- Learn to use Jupyterlab - an online Python editor designed for developing AI algorithms
...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools, machine-learning, deep-learning, jupyter-lab, image-segmentation, protein-3D-structure

Resource type: hands-on tutorial

Hands-on for 'Reference-based RNA-Seq data analysis' tutorial

The questions this addresses are:
- What are the steps to process RNA-Seq data?
- How to identify differentially expressed genes across multiple experimental conditions?
- What are the biological functions impacted by the differential expression of genes?

\nThe objectives are:
- Check a...

Scientific topics: Transcriptomics

Keywords: transcriptomics, bulk, rna-seq, collections, drosophila, QC, cyoa

Resource type: hands-on tutorial

Hands-on for 'Clustering 3K PBMCs with Scanpy' tutorial

The questions this addresses are:
- What are the steps to prepare single-cell RNA-Seq data for clustering?
- How to cluster cells in single-cell RNA-Seq data?
- How cell type annotation can be assigned to cell clusters?

\nThe objectives are:
- Describe an AnnData object to store single-cell...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x

Resource type: hands-on tutorial

Hands-on for 'De novo transcriptome assembly, annotation, and differential expression analysis' tutorial

The questions this addresses are:
- Which biological questions are addressed by the tutorial?
- Which bioinformatics techniques are important to know for this type of data?

\nThe objectives are:
- The learning objectives are the goals of the tutorial
- They will be informed by your audience...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'RNA-RNA interactome data analysis' tutorial

The questions this addresses are:
- What are the difficulties in mapping chimeric reads from RNA interactome data?
- How multi mapping is a big problem in these datasets?
- How to filter for meaningful results from large analysis output files?

\nThe objectives are:
- Quality control and...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Tools, Data, and Workflows for tutorials' tutorial

The questions this addresses are:
- How can we define the technical infrastructure for a tutorial?
- How to define the tools needed for a tutorial?
- How to add the needed data directly in an instance?
- How to add the workflows related to a tutorial?
- How can we check the technical...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)' tutorial

The questions this addresses are:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of TAL1?
- Which genes are regulated by TAL1?

\nThe objectives are:
- Inspect read quality with FastQC
- Perform read trimming with Trimmomatic
- Align trimmed reads with BWA
...

Scientific topics: Epigenomics

Keywords: epigenetics, ChIP-seq

Resource type: hands-on tutorial

Hands-on for 'Identification of the binding sites of the Estrogen receptor' tutorial

The questions this addresses are:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of the Estrogen receptor?

\nThe objectives are:
- Inspect read quality with FastQC
- Map reads with Bowtie2
- Assess the quality of an ChIP-seq experiments
- Extract coverage...

Scientific topics: Epigenomics

Keywords: epigenetics, ChIP-seq, work-in-progress

Resource type: hands-on tutorial

Hands-on for 'ATAC-Seq data analysis' tutorial

The questions this addresses are:
- Which DNA regions are accessible in the human lymphoblastoid cell line GM12878?
- How to analyse and visualise ATAC-Seq data?

\nThe objectives are:
- Apply appropriate analysis and quality control steps for ATAC-Seq
- Generate a heatmap of transcription...

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: hands-on tutorial

Hands-on for 'Creating Galaxy tools from Conda Through Deployment' tutorial

The questions this addresses are:
- How do you create a conda package used as a dependency in a Galaxy tool wrapper?
- How do you create a Galaxy tool wrapper and all of its requirements?
- How do you test a Galaxy tool wrapper after it's written?
- How do you deploy a Galaxy tool wrapper?
...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Galaxy Interactive Tools' tutorial

The questions this addresses are:
- What is an Interactive Tool on Galaxy (GxIT)?
- How to set up a GxIT?

\nThe objectives are:
- Discover what Galaxy Interactive Tools (GxIT) are
- Understand how GxITs are structured
- Understand how GxITs work
- Be able to dockerise a basic web...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data' tutorial

The questions this addresses are:
- How can we extract annotated allelic variants in SARS-Cov-2 sequences in Galaxy?
- Which tools and workflows can we use to identify SARS-CoV-2 lineages in Galaxy?

\nThe objectives are:
- Repeat SARS-CoV-2 data preparation
- Select and run workflow to...

Scientific topics: Genetic variation

Keywords: variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'Identification of somatic and germline variants from tumor and normal sample pairs' tutorial

The questions this addresses are:
- What are the specific challenges in somatic variant calling that set it apart from regular diploid variant calling?
- How can you call variants and classify them according to their presence/absence in/from tumor and normal tissue of the same individual?
-...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Found 0 upcoming events. Found 7 past events. View all results.