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...
Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/clipseq/tutorial.html
https://tess.elixir-europe.org/materials/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 Identifiers (UMIs) from the reads
- Align trimmed reads with STAR
- De-duplicate the read library
- Inspect the read mapping and de-duplication quality
- Perform peak calling with PEAKachu
- Analyse the peaks and find potential binding motifs and targets
- Check the quality of the peak calling
Florian-H-Lab
dmaticzka
bebatut
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...
Galaxy Server administration - Ansible
http://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible/tutorial.html
https://tess.elixir-europe.org/materials/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 role from Ansible Galaxy
erasche
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
Data Manipulation - Collections: Rule Based Uploader
http://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/upload-rules/tutorial.html
https://tess.elixir-europe.org/materials/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
jmchilton
erasche
Data Manipulation - Collections: Multisample Analysis
A collection of microtutorials explaining data manipulation within Galaxy
Data Manipulation - Collections: Multisample Analysis
http://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/processing-many-samples-at-once/tutorial.html
https://tess.elixir-europe.org/materials/data-manipulation-collections-multisample-analysis
A collection of microtutorials explaining data manipulation within Galaxy
nekrut
pajanne
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
Data Manipulation - Collections: Using dataset collection
http://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/collections/tutorial.html
https://tess.elixir-europe.org/materials/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
nekrut
Data Manipulation - Data: Getting data into Galaxy
A collection of microtutorials explaining data manipulation within Galaxy
Data Manipulation - Data: Getting data into Galaxy
http://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/get-data/slides.html
https://tess.elixir-europe.org/materials/data-manipulation-data-getting-data-into-galaxy
A collection of microtutorials explaining data manipulation within Galaxy
pajanne
tnabtaf
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
User Interface and Features - Jupyter: Use Jupyter notebooks in Galaxy
http://galaxyproject.github.io/training-material/topics/galaxy-ui/tutorials/galaxy-intro-jupyter/tutorial.html
https://tess.elixir-europe.org/materials/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
Delphine-L
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...
User Interface and Features - Workflows: Extracting Workflows from Histories
http://galaxyproject.github.io/training-material/topics/galaxy-ui/tutorials/history-to-workflow/tutorial.html
https://tess.elixir-europe.org/materials/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 to change a workflow using the workflow editor
tnabtaf
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
User Interface and Features - Histories: Understanding Galaxy history system
http://galaxyproject.github.io/training-material/topics/galaxy-ui/tutorials/history/tutorial.html
https://tess.elixir-europe.org/materials/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
nekrut
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...
Contributing to the Galaxy Training Material - Creating a new tutorial
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial/tutorial.html
https://tess.elixir-europe.org/materials/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 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 integrate a new tutorial?
- How to make a tutorial robust and reproducible?
Objectives of the tutorial:
- Create a tutorial from scratch
- Link a tutorial to a topic
- Create hands-on
- Add technical support for a tutorial
bebatut
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...
Statistics - Interval-Wise Testing for omics data
http://galaxyproject.github.io/training-material/topics/statistics/tutorials/iwtomics/tutorial.html
https://tess.elixir-europe.org/materials/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 significant effects unfold?
Objectives of the tutorial:
- Pre-process high-resolution omics data
- Create pointwise boxplots corresponding to different groups of genomic regions
- Perform the Interval-Wise Testing between two groups of genomic regions
- Visualize and inspect test results
- Detect relevant locations and scales
marziacremona
fabio-cumbo
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...
Assembly - Making sense of a newly assembled genome
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/ecoli_comparison/tutorial.html
https://tess.elixir-europe.org/materials/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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- I just assembled a genome. How does it compare with already sequenced genomes?
- How do I find rearranged, inserted, or deleted regions?
Objectives of the tutorial:
- Identification of the most closely related genome to my new assembly
- Perform sequence comparison to locate rearrangements
- Identify genes located in deletions
nekrut
delphine-l
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
https://tess.elixir-europe.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
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...
Genome Annotation - Genome annotation with Prokka
http://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html
https://tess.elixir-europe.org/materials/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 elements.
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
annasyme
tseemann
slugger70
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.
Genome Annotation - Genome Annotation
http://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/genome-annotation/tutorial.html
https://tess.elixir-europe.org/materials/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.
joachimwolff
erxleben
bgruening
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...
Contributing to the Galaxy Training Material - Contributing with GitHub via its interface
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/github-interface-contribution/tutorial.html
https://tess.elixir-europe.org/materials/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 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 I contribute to an open-source project with GitHub and its interface
Objectives of the tutorial:
- Edit a file via GitHub interface
- Create a pull request
- Update a pull request
bebatut
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...
Contributing to the Galaxy Training Material - Set up a Galaxy for Training
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/setup-galaxy-for-training/tutorial.html
https://tess.elixir-europe.org/materials/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 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 do I prepare my Galaxy instance to support a training module?
- How can I generate a Docker Galaxy instance for my topic?
Objectives of the tutorial:
- Use ephemeris to install the training requirements to a Galaxy instance
- Create a docker image for a training topic
shiltemann
bebatut
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...
Contributing to the Galaxy Training Material - Good practices to run a workshop
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/good-practices/slides.html
https://tess.elixir-europe.org/materials/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 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 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
bebatut
bgruening
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
https://tess.elixir-europe.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 - 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...
Contributing to the Galaxy Training Material - Generating PDF artefacts of the website
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/generating-pdf/tutorial.html
https://tess.elixir-europe.org/materials/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 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 generate PDF of the different tutorials and slides?
Objectives of the tutorial:
- Generating PDFs
bebatut
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...
Contributing to the Galaxy Training Material - Including a new topic
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-topic/tutorial.html
https://tess.elixir-europe.org/materials/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 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 include a new topic?
Objectives of the tutorial:
- Create a new topic
- Set up the metadata for a topic
bebatut
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
https://tess.elixir-europe.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
https://tess.elixir-europe.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 - 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...
Contributing to the Galaxy Training Material - Creating a new tutorial - Defining metadata
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-metadata/tutorial.html
https://tess.elixir-europe.org/materials/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 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 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
bebatut
bgruening
shiltemann
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...
Contributing to the Galaxy Training Material - Contributing with GitHub via command-line
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/github-command-line-contribution/tutorial.html
https://tess.elixir-europe.org/materials/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 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 I contribute to an open-source project with GitHub?
- What is the GitHub flow?
Objectives of the tutorial:
- Fork a repository on GitHub
- Clone a remote repository locally
- Create a branch
- Commit changes
- Push changes to a remote repository
- Create a pull request
- Update a pull request
cmonjeau
bebatut
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
https://tess.elixir-europe.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
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 - Overview of the Galaxy Training Material
http://galaxyproject.github.io/training-material/topics/contributing/slides/introduction.html
https://tess.elixir-europe.org/materials/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 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.
bebatut
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...
Introduction to Galaxy - Rule Based Uploader
http://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-rules/tutorial.html
https://tess.elixir-europe.org/materials/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 uploader to create complex collections
Objectives of the tutorial:
- Learn about the Rule Based Uploader
jmchilton
erasche
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...
Galaxy Server administration - Upgrading Galaxy
http://galaxyproject.github.io/training-material/topics/admin/tutorials/upgrading/slides.html
https://tess.elixir-europe.org/materials/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 involved in the Galaxy upgrade process.
- Complete the upgrade to a new release.
martenson
afgane
nsoranzo
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 Analysis - Mapping and molecular identification of phenotype-causing mutations
http://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html
https://tess.elixir-europe.org/materials/variant-analysis-mapping-by-sequencing
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
wm75
