Informatics for RNA-Seq Analysis 2018 Module 4-Reference Free Alignment
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Informatics for RNA-Seq Analysis 2018 Module 4-Reference Free Alignment
https://bioinformaticsdotca.github.io/rnaseq_2018
http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2018-module-4-reference-free-alignment
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Malachi Griffith
Researchers
Post-Doctoral Fellows
Biologists, Genomicists, Computer Scientists
Graduate Students
Informatics for RNA-Seq Analysis 2018 Module 1-Introduction to RNA Sequencing Analysis
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Informatics for RNA-Seq Analysis 2018 Module 1-Introduction to RNA Sequencing Analysis
https://bioinformaticsdotca.github.io/rnaseq_2018
http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2018-module-1-introduction-to-rna-sequencing-analysis
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Malachi Griffith
Researchers
Biologists, Genomicists, Computer Scientists
Graduate students
Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 5-Isoform Discovery and Alternative Expression
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Informatics for RNA-Seq Analysis 2017 Module 5-Isoform Discovery and Alternative Expression
https://bioinformaticsdotca.github.io/rnaseq_2017
http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-5-isoform-discovery-and-alternative-expression
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Malachi Griffith
Researchers
Graduate students
Biologists, Genomicists, Computer Scientists
Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 4-Reference Free Alignment
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Informatics for RNA-Seq Analysis 2017 Module 4-Reference Free Alignment
https://bioinformaticsdotca.github.io/rnaseq_2017
http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-4-reference-free-alignment
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Malachi Griffith
Researchers
Graduate Students
Biologists, Genomicists, Computer Scientists
Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 1-Introduction to RNA Sequencing Analysis
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Informatics for RNA-Seq Analysis 2017 Module 1-Introduction to RNA Sequencing Analysis
https://bioinformaticsdotca.github.io/rnaseq_2017
http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-1-introduction-to-rna-sequencing-analysis
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.
Malachi Griffith
Researchers
Graduate students
Post-Doctoral Fellows
Biologists, Genomicists, Computer Scientists
High-Throughput Biology 2017 Module 11-Isoform Discovery and Alternative Expression
Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.
High-Throughput Biology 2017 Module 11-Isoform Discovery and Alternative Expression
https://bioinformaticsdotca.github.io/high-throughput_biology_2017
http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-11-isoform-discovery-and-alternative-expression
Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.
Malachi Griffith
Graduate Students
Researchers
Biologists, Genomicists, Computer Scientists
Post-Doctoral Fellows
High-Throughput Biology 2017 Module 10-Reference Free Alignment
Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.
High-Throughput Biology 2017 Module 10-Reference Free Alignment
https://bioinformaticsdotca.github.io/high-throughput_biology_2017
http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-10-reference-free-alignment
Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.
Malachi Griffith
Graduate students
Researchers
Biologists, Genomicists, Computer Scientists
Post-Doctoral Fellows
High-Throughput Biology 2017 Module 7-Introduction to RNA Sequencing Analysis
Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.
High-Throughput Biology 2017 Module 7-Introduction to RNA Sequencing Analysis
https://bioinformaticsdotca.github.io/high-throughput_biology_2017
http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-7-introduction-to-rna-sequencing-analysis
Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.
Malachi Griffith
Graduate students
Researchers
Biologists, Genomicists, Computer Scientists
Post-Doctoral Fellows
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...
Contributing to the Galaxy Training Material - Creating a new tutorial - Slides
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-slides/slides.html
http://tess.elixir-uk.org/materials/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 accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy.
Questions of the tutorial:
- 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?
Objectives of the tutorial:
- Create a new set of slides
- Add presenter comments
erasche
bebatut
shiltemann
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...
Contributing to the Galaxy Training Material - Running the Galaxy Training material website locally
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/running-jekyll/tutorial.html
http://tess.elixir-uk.org/materials/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 accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy.
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 material website locally
- Tracking changes to the content live in the webbrowser
bebatut
bgruening
shiltemann
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...
Contributing to the Galaxy Training Material - Creating a new tutorial - Creating Interactive Galaxy Tours
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-tours/tutorial.html
http://tess.elixir-uk.org/materials/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 accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy.
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
bebatut
bgruening
shiltemann
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...
Contributing to the Galaxy Training Material - Creating a new tutorial - Defining the technical infrastructure
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.html
http://tess.elixir-uk.org/materials/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 accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy.
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?
- How can we make an existing Galaxy instance able to run a tutorial?
Objectives of the tutorial:
- Extracting the technical description for a tutorial
- Populating an existing instance with the needed tools, data and workflows for a tutorial
- Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial
- Testing the Galaxy Docker flavor of a tutorial
bebatut
bgruening
shiltemann
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...
Contributing to the Galaxy Training Material - Creating a new tutorial - Writing content in Markdown
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html
http://tess.elixir-uk.org/materials/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 accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy.
Questions of the tutorial:
- How to write a tutorial with hands-on?
- What are the different boxes?
- How can I add a caption to an image?
Objectives of the tutorial:
- Create hands-on
- Use the different boxes
bebatut
bgruening
shiltemann
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...
Development in Galaxy - Visualizations: generic plugins
http://galaxyproject.github.io/training-material/topics/dev/tutorials/visualization-generic/tutorial.html
http://tess.elixir-uk.org/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
shiltemann
yhoogstrate
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...
Development in Galaxy - Galaxy Interactive Environments
http://galaxyproject.github.io/training-material/topics/dev/tutorials/interactive-environments/slides.html
http://tess.elixir-uk.org/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
shiltemann
bgruening
erasche
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...
Development in Galaxy - Visualizations: charts plugins
http://galaxyproject.github.io/training-material/topics/dev/tutorials/visualization-charts/tutorial.html
http://tess.elixir-uk.org/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
shiltemann
yhoogstrate
bgruening
guerler
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...
Introduction to Galaxy Analyses - Galaxy 101
http://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-101/tutorial.html
http://tess.elixir-uk.org/materials/galaxy-introduction-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
shiltemann
nsoranzo
blankclemens
nekrut
bgruening
pajanne
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.
Introduction to Galaxy Analyses - Introduction to Galaxy
http://galaxyproject.github.io/training-material/topics/introduction/slides/introduction.html
http://tess.elixir-uk.org/materials/galaxy-introduction-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.
bagnacan
bebatut
shiltemann
pajanne
nsoranzo
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...
Metagenomics - Analyses of metagenomics data - The global picture
http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html
http://tess.elixir-uk.org/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
shiltemann
bebatut
Metagenomics - Introduction to metagenomics
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Metagenomics - Introduction to metagenomics
http://galaxyproject.github.io/training-material/topics/metagenomics/slides/introduction.html
http://tess.elixir-uk.org/materials/metagenomics-introduction
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
bebatut
shiltemann
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...
Metagenomics - 16S Microbial Analysis with Mothur
http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
http://tess.elixir-uk.org/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
shiltemann
bebatut
