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 https://tess.oerc.ox.ac.uk/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/000/000/013/original/GTNLogo1000.png?1530807559
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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

Development in Galaxy - Tool Dependencies and Conda https://tess.oerc.ox.ac.uk/materials/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 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 develop Conda recipes for use within Galaxy tools? Objectives of the tutorial: - Learn to use existing Conda recipes to enable best practice tool dependency management in Galaxy. - Learn the basics of building Conda recipes and contributing to Bioconda. - Learn to use Planemo to assist in developing Galaxy tools from existing and new Conda recipes.

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

Assembly - Unicycler Assembly https://tess.oerc.ox.ac.uk/materials/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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - How to perform an hybrid bacterial assembly with Unicycler Objectives of the tutorial: - 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 Prokka

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

ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) https://tess.oerc.ox.ac.uk/materials/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 - Perform read trimming with Trimmomatic - Align trimmed reads with BWA - Assess quality and reproducibility of experiments - Identify Tal1 binding sites with MACS2 - Determine unique/common Tal1 binding sites from G1E and Megakaryocytes - Identify unique/common Tal1 peaks occupying gene promoters - Visually inspect Tal1 peaks with Trackster

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

Development in Galaxy - Tool development and integration into Galaxy https://tess.oerc.ox.ac.uk/materials/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 tool environment? Objectives of the tutorial: - Discover what is a wrapper and its structure - Use the Planemo utilities to develop a good wrapper - Deal with the dependencies - Write functional tests - Make a tool ready for publishing in a ToolShed

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

ChIP-Seq data analysis - Identification of the binding sites of the Estrogen receptor https://tess.oerc.ox.ac.uk/materials/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 Bowtie2 - Assess the quality of an ChIP-seq experiments - Extract coverage files - Call enriched regions or peaks

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

Assembly - De Bruijn Graph Assembly https://tess.oerc.ox.ac.uk/materials/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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - What are the factors that affect genome assembly? - How does Genome assembly work? Objectives of the tutorial: - Perform an optimised Velvet assembly with the Velvet Optimiser - Compare this assembly with those we did in the basic tutorial - Perform an assembly using the SPAdes assembler.

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

Introduction to Galaxy - Extracting Workflows from Histories https://tess.oerc.ox.ac.uk/materials/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 create a workflow based on my analysis history? Objectives of the tutorial: - Learn how to extract a workflow from a Galaxy history - Learn how to change a workflow using the workflow editor

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

Development in Galaxy - Prerequisites for building software/conda packages https://tess.oerc.ox.ac.uk/materials/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 to solve common compiling and installation issues? Objectives of the tutorial: - Learn how to compile and install tools using standard procedures. - Learn needed tricks to write conda build.sh files.

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

Variant Analysis - Exome sequencing data analysis https://tess.oerc.ox.ac.uk/materials/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 tutorial: - Identification of the genetic variation using the exome sequencing - Using FreeBayes calls for variants generating - Variant analysis and GEMINI queries

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

Epigenetics - DNA Methylation data analysis https://tess.oerc.ox.ac.uk/materials/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 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? Objectives of the tutorial: - Learn how to analyse methylation data - Get a first intuition what are common pitfalls.

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

Proteomics - Metaproteomics tutorial https://tess.oerc.ox.ac.uk/materials/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 functional analysis on this metaproteomics data? Objectives of the tutorial: - A taxonomy and functional analysis of metaproteomic mass spectrometry data.

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

Resource type: Tutorial

Galaxy Server administration - Galaxy Database schema https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-galaxy-database-schema Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task 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, which can not be gathered using the given report tools - How to move from MySQL to PostgreSQL - Is there ever a need to manually change the contents of a table Objectives of the tutorial: - Learn some of the design concepts of the Galaxy database - Extract information from the Galaxy database - Get to know SchemaSpy

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

Resource type: Tutorial

Galaxy Server administration - Connecting Galaxy to a compute cluster https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-connecting-galaxy-to-a-compute-cluster Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task 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, configuring, and using Slurm - Understand all components of the Galaxy job running stack - Understand how the `job_conf.xml` file controls Galaxy's jobs subsystem - Have a strong understanding of Galaxy job destinations - Know how to map tools to job destinations - Be able to use the dynamic job runner to make arbitrary destination mappings - Understand the job resource selector config and dynamic rule creation

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

Resource type: Tutorial

Train the trainers - Creating a new tutorial - Setting up the infrastructure https://tess.oerc.ox.ac.uk/materials/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 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...

Resource type: Slides

Development in Galaxy - Contributing with GitHub https://tess.oerc.ox.ac.uk/materials/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 is a pull request

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

Sequence analysis - RAD-Seq Reference-based data analysis https://tess.oerc.ox.ac.uk/materials/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 genomics statistics from RAD sequencing data

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

Assembly - Introduction to Genome Assembly https://tess.oerc.ox.ac.uk/materials/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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - How do we perform a very basic genome assembly from short read data? Objectives of the tutorial: - assemble some paired end reads using Velvet - examine the output of the assembly.

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

Variant Analysis - Mapping and molecular identification of phenotype-causing mutations https://tess.oerc.ox.ac.uk/materials/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 variant calling and extraction to facilitate variant comparison across samples - Perform variant linkage analyses for phenotypically selected recombinant progeny - Filter, annotate and report lists of variants

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

Introduction to Galaxy - NGS data logistics https://tess.oerc.ox.ac.uk/materials/introduction-to-galaxy-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 NGS data Objectives of the tutorial: - Learn about Fastq, SAM, and BAM.

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

Introduction to Galaxy - Using dataset collection https://tess.oerc.ox.ac.uk/materials/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 of datasets at once? Objectives of the tutorial: - Understand and master dataset collections

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

Introduction to Galaxy - Understanding Galaxy history system https://tess.oerc.ox.ac.uk/materials/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 work? Objectives of the tutorial: - Gain understanding on navigating and manipulating 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.

Resource type: Slides

Introduction to Galaxy - Getting data into Galaxy https://tess.oerc.ox.ac.uk/materials/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.

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: - First question addressed during...

Resource type: Tutorial

Introduction to Galaxy - IGV Introduction https://tess.oerc.ox.ac.uk/materials/introduction-to-galaxy-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. Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

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

Introduction to Galaxy - Options for using Galaxy https://tess.oerc.ox.ac.uk/materials/introduction-to-galaxy-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?

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: - First question addressed during...

Resource type: Tutorial

Introduction to Galaxy - Multisample Analysis https://tess.oerc.ox.ac.uk/materials/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. Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

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

Introduction to Galaxy - Introduction to Genomics and Galaxy https://tess.oerc.ox.ac.uk/materials/introduction-to-galaxy-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 ever overlap? If so, how often? Objectives of the tutorial: - Learn some of the basic concepts of genomics and bioinformatics - Familiarize yourself with the basics of 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: - How to use Galaxy? - How to get...

Resource type: Tutorial

Introduction to Galaxy - From peaks to genes https://tess.oerc.ox.ac.uk/materials/introduction-to-galaxy-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 from peak regions to a list of gene names? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work

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

Introduction to Galaxy - Galaxy 101 https://tess.oerc.ox.ac.uk/materials/introduction-to-galaxy-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 highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work

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.

Introduction to Galaxy - Introduction to Galaxy https://tess.oerc.ox.ac.uk/materials/introduction-to-galaxy-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.

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

Development in Galaxy - Galaxy Code Architecture https://tess.oerc.ox.ac.uk/materials/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 happens when I start Galaxy? Objectives of the tutorial: - Explore various aspects of the Galaxy codebase. - Understand the various top-level files and modules in Galaxy. - Understand how dependencies work in Galaxy's frontend and backend.

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

Development in Galaxy - Tool Dependencies and Containers https://tess.oerc.ox.ac.uk/materials/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 to run my tool in? - What are BioContainers and how are they related to Galaxy? Objectives of the tutorial: - Explore the differences between containerizing Galaxy and tool execution. - Discuss the advantages of containerizing tools. - Learn to build best practice tools ready to be containerized.

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

Development in Galaxy - BioBlend module, a Python library to use Galaxy API https://tess.oerc.ox.ac.uk/materials/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 familiar with BioBlend using IPython - Launch a Galaxy job / Visualize your actions with Galaxy - Launch a Galaxy workflow / Visualize your actions with 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: - How can visualization plugins benefit science? Objectives of the tutorial: - Implement a first Galaxy...

Resource type: Tutorial

Development in Galaxy - Visualizations: generic plugins https://tess.oerc.ox.ac.uk/materials/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 visualization - Understand the client side vs. server side principle

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

Development in Galaxy - Galaxy Webhooks https://tess.oerc.ox.ac.uk/materials/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 Webhooks are - Be able to create Webhooks - Be able to add a Galaxy Webhook in a Galaxy instance

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

Development in Galaxy - Visualizations: charts plugins https://tess.oerc.ox.ac.uk/materials/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 javascript plugins to the Galaxy Charts framework

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

Development in Galaxy - Galaxy Interactive Environments https://tess.oerc.ox.ac.uk/materials/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 GIE? Objectives of the tutorial: - Implement a Hello-World Galaxy Interactive Environment

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

Development in Galaxy - Galaxy Interactive Tours https://tess.oerc.ox.ac.uk/materials/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 tutorial: - 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

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

Development in Galaxy - Tool Shed: sharing Galaxy tools https://tess.oerc.ox.ac.uk/materials/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 are the Tool Shed repository types? - How to publish with Planemo? Objectives of the tutorial: - Discover what is a Tool Shed - Be able to install tools and workflows from a Tool Shed into a Galaxy instance - Be able to publish tools with Planemo

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 from a developer point of view https://tess.oerc.ox.ac.uk/materials/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, ...

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

Metagenomics - Analyses of metagenomics data - The global picture https://tess.oerc.ox.ac.uk/materials/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 in the analyses of amplicon and shotgun data? Objectives of the tutorial: - Choosing the best approach to analyze metagenomics data - Selection of tools to analyze amplicon data or shotgun data - Visualisation of a community structure

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

Metagenomics - 16S Microbial Analysis with Mothur https://tess.oerc.ox.ac.uk/materials/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 Galaxy

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

Metagenomics - Introduction to metagenomics https://tess.oerc.ox.ac.uk/materials/metagenomics-introduction-to-metagenomics Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

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

Resource type: Tutorial

Variant Analysis - Calling very rare variants https://tess.oerc.ox.ac.uk/materials/variant-analysis-calling-very-rare-variants Exome sequencing means that all protein-coding genes in a genome are sequenced 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

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

Variant Analysis - Calling variants in diploid systems https://tess.oerc.ox.ac.uk/materials/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.

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

Variant Analysis - Calling variants in non-diploid systems https://tess.oerc.ox.ac.uk/materials/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, viruses, and organelles.

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

Variant Analysis - Microbial Variant Calling https://tess.oerc.ox.ac.uk/materials/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 reads - Visualise the SNP in context of the reads aligned to the genome - Determine the effect of those variants on genomic features - Understand if the SNP is potentially affecting the phenotype

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 - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://tess.oerc.ox.ac.uk/materials/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 'chromosome conformation capture'? - What are main steps in order to generate and plot a Hi-C contact matrix?

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.

Epigenetics - Introduction to DNA Methylation data analysis https://tess.oerc.ox.ac.uk/materials/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.

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 - Peptide and Protein Quantification via Stable Isotope Labelling (SIL) https://tess.oerc.ox.ac.uk/materials/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 quantitation and mapping of quantitations to peptide and protein IDs.

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

Proteomics - Secretome Prediction https://tess.oerc.ox.ac.uk/materials/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 GO-terms. - Predict proteins in the cellular secretome by using WolfPSORT. - Combine the results of both predictions.

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

Proteomics - Peptide and Protein ID using OpenMS tools https://tess.oerc.ox.ac.uk/materials/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.

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

Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker https://tess.oerc.ox.ac.uk/materials/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.

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

Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS https://tess.oerc.ox.ac.uk/materials/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.

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

Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method https://tess.oerc.ox.ac.uk/materials/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.

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

Proteomics - Protein FASTA Database Handling https://tess.oerc.ox.ac.uk/materials/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 protein FASTA database ready for use with database search algorithms.

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

Transcriptomics - Reference-based RNAseq data analysis (long) https://tess.oerc.ox.ac.uk/materials/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

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

Transcriptomics - Visualization of RNA-Seq results with CummeRbund https://tess.oerc.ox.ac.uk/materials/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 results - Extract the desired subject for differential gene expression analysis - Visualize information

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

Transcriptomics - Differential abundance testing of small RNAs https://tess.oerc.ox.ac.uk/materials/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 to determine quality and reproducibility. - Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets. - Differentiate between subclasses of small RNAs based on their characteristics. - Identify differently abundant small RNAs and their targets.

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

Transcriptomics - Reference-based RNA-Seq data analysis https://tess.oerc.ox.ac.uk/materials/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 a reference genome - Analysis of differentially expressed genes - Identification of functional enrichment among differentially expressed genes

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

Transcriptomics - De novo transcriptome reconstruction with RNA-Seq https://tess.oerc.ox.ac.uk/materials/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 sequencing data using a reference genome - Reconstruction of transcripts without reference transcriptome (de novo) - Analysis of differentially expressed genes

Training material for all kinds of transcriptomics analysis.

Transcriptomics - Introduction to Transcriptomics https://tess.oerc.ox.ac.uk/materials/transcriptomics-introduction-to-transcriptomics Training material for all kinds of transcriptomics analysis.

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

Resource type: Slides

Galaxy Server administration - Advanced customisation of a Galaxy instance https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-advanced-customisation-of-a-galaxy-instance Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

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

Resource type: Slides

Galaxy Server administration - Docker and Galaxy https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-docker-and-galaxy Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task 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 Docker (internals) - Galaxy flavours

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

Resource type: Tutorial

Galaxy Server administration - Server Monitoring and Maintenance https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-server-monitoring-and-maintenance Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task 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 Galaxy reports app.

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

Resource type: Slides

Galaxy Server administration - User, Group and Quota managment https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-user-group-and-quota-managment Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task 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 the Role Based Access Control (RBAC) of Galaxy.

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

Resource type: Slides

Galaxy Server administration - Deployment and Platform options https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-deployment-and-platform-options Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task 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 deployment. - Make an educated decision about your preferred deployment model.

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

Galaxy Server administration - Galaxy from an administrator point of view https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-galaxy-from-an-administrator-point-of-view Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

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

Resource type: Slides

Train the trainers - Good practices to run a workshop https://tess.oerc.ox.ac.uk/materials/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

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...

Resource type: Tutorial

Train the trainers - Creating a new tutorial - Building a Docker flavor for a tutorial https://tess.oerc.ox.ac.uk/materials/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 technical infrastructure is working? Objectives of the tutorial: - Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial - Testing the Galaxy Docker flavor of a tutorial

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

Resource type: Tutorial

Train the trainers - Creating a new tutorial - Creating Interactive Galaxy Tours https://tess.oerc.ox.ac.uk/materials/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

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

Variant Analysis - Introduction to Variant analysis https://tess.oerc.ox.ac.uk/materials/variant-analysis-introduction-to-variant-analysis Exome sequencing means that all protein-coding genes in a genome are sequenced

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

Resource type: Tutorial

Train the trainers - Creating a new tutorial - Defining metadata https://tess.oerc.ox.ac.uk/materials/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

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

Resource type: Tutorial

Train the trainers - Creating a new tutorial - Writing content in Markdown https://tess.oerc.ox.ac.uk/materials/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

Train the trainers

Train the trainers - Introduction to training with Galaxy https://tess.oerc.ox.ac.uk/materials/train-the-trainers-introduction-to-training-with-galaxy Train the trainers

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

ChIP-Seq data analysis - Introduction to ChIP-Seq data analysis https://tess.oerc.ox.ac.uk/materials/chip-seq-data-analysis-introduction-to-chip-seq-data-analysis ChIP-sequencing is a method used to analyze protein interactions with DNA.

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

Resource type: Tutorial

Sequence analysis - Genome annotation with Prokka https://tess.oerc.ox.ac.uk/materials/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

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

Sequence analysis - RAD-Seq to construct genetic maps https://tess.oerc.ox.ac.uk/materials/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

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

Sequence analysis - RAD-Seq de-novo data analysis https://tess.oerc.ox.ac.uk/materials/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 population genomics statistics from RAD sequencing data

Analyses of sequences Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

Resource type: Tutorial

Sequence analysis - Genome Annotation https://tess.oerc.ox.ac.uk/materials/sequence-analysis-genome-annotation Analyses of sequences Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

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

Sequence analysis - Mapping https://tess.oerc.ox.ac.uk/materials/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

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

Sequence analysis - Quality Control https://tess.oerc.ox.ac.uk/materials/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 - Use FastQC tool - Understand FastQC output - Use tools for quality correction
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