Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- How is raw CLIP-Seq data processed and analysed?
- How do I find binding motifs and targets for a protein (e.g., RBFOX2)?
Objectives of the tutorial:
- Remove Adapters, Barcodes and Unique Molecular...
Resource type: Tutorial
Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detectionhttp://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/clipseq/tutorial.htmlhttps://tess.elixir-europe.org/materials/transcriptomics-clip-seq-data-analysis-from-pre-processing-to-motif-detectionTraining 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 callingFlorian-H-Labdmaticzkabebatut
Resources related to configuration and maintenance of Galaxy servers
Questions of the tutorial:
- Why Ansible?
- How and when to use Ansible?
- How to write a role?
- How to leverage community build roles?
Objectives of the tutorial:
- Learn Ansible basics
- Write a simple role
- Install a...
Resource type: Tutorial
Galaxy Server administration - Ansiblehttp://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible/tutorial.htmlhttps://tess.elixir-europe.org/materials/galaxy-server-administration-ansibleResources 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 Galaxyerasche
A collection of microtutorials explaining data manipulation within Galaxy
Questions of the tutorial:
- How to use the rule based uploader to create complex collections
Objectives of the tutorial:
- Learn about the Rule Based Uploader
Resource type: Tutorial
Data Manipulation - Collections: Rule Based Uploaderhttp://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/upload-rules/tutorial.htmlhttps://tess.elixir-europe.org/materials/data-manipulation-collections-rule-based-uploaderA 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 Uploaderjmchiltonerasche
A collection of microtutorials explaining data manipulation within Galaxy
Resource type: Tutorial
Data Manipulation - Collections: Multisample Analysishttp://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/processing-many-samples-at-once/tutorial.htmlhttps://tess.elixir-europe.org/materials/data-manipulation-collections-multisample-analysisA collection of microtutorials explaining data manipulation within Galaxynekrutpajanne
A collection of microtutorials explaining data manipulation within Galaxy
Questions of the tutorial:
- How to manipulate large numbers of datasets at once?
Objectives of the tutorial:
- Understand and master dataset collections
Resource type: Tutorial
Data Manipulation - Collections: Using dataset collectionhttp://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/collections/tutorial.htmlhttps://tess.elixir-europe.org/materials/data-manipulation-collections-using-dataset-collectionA 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 collectionsnekrut
A collection of microtutorials explaining data manipulation within Galaxy
Resource type: Slides
Data Manipulation - Data: Getting data into Galaxyhttp://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/get-data/slides.htmlhttps://tess.elixir-europe.org/materials/data-manipulation-data-getting-data-into-galaxyA collection of microtutorials explaining data manipulation within Galaxypajannetnabtaf
A collection of microtutorials explaining various features of the Galaxy user interface
Questions of the tutorial:
- How to use a Jupyter Notebook in Galaxy
Objectives of the tutorial:
- Learn about the Jupyter Interactive Environment
Resource type: Tutorial
User Interface and Features - Jupyter: Use Jupyter notebooks in Galaxyhttp://galaxyproject.github.io/training-material/topics/galaxy-ui/tutorials/galaxy-intro-jupyter/tutorial.htmlhttps://tess.elixir-europe.org/materials/user-interface-and-features-jupyter-use-jupyter-notebooks-in-galaxyA 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 EnvironmentDelphine-L
A collection of microtutorials explaining various features of the Galaxy user interface
Questions of the tutorial:
- What is a workflow?
- How can I create a workflow based on my analysis history?
Objectives of the tutorial:
- Learn how to extract a workflow from a Galaxy history
- Learn how...
Resource type: Tutorial
User Interface and Features - Workflows: Extracting Workflows from Historieshttp://galaxyproject.github.io/training-material/topics/galaxy-ui/tutorials/history-to-workflow/tutorial.htmlhttps://tess.elixir-europe.org/materials/user-interface-and-features-workflows-extracting-workflows-from-historiesA 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 editortnabtaf
A collection of microtutorials explaining various features of the Galaxy user interface
Questions of the tutorial:
- How do Galaxy histories work?
Objectives of the tutorial:
- Gain understanding on navigating and manipulating histories
Resource type: Tutorial
User Interface and Features - Histories: Understanding Galaxy history systemhttp://galaxyproject.github.io/training-material/topics/galaxy-ui/tutorials/history/tutorial.htmlhttps://tess.elixir-europe.org/materials/user-interface-and-features-histories-understanding-galaxy-history-systemA 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 historiesnekrut
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Creating a new tutorialhttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorialGalaxy 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 tutorialbebatut
Statistical Analyses for omics data
Questions of the tutorial:
- How to visualize high-resolution omics data in different groups of genomic regions?
- How to evaluate differences in high-resolution omics data between groups of genomic regions?
- How to detect locations and scales at which the...
Resource type: Tutorial
Statistics - Interval-Wise Testing for omics datahttp://galaxyproject.github.io/training-material/topics/statistics/tutorials/iwtomics/tutorial.htmlhttps://tess.elixir-europe.org/materials/statistics-interval-wise-testing-for-omics-dataStatistical 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 scalesmarziacremonafabio-cumbo
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 - Making sense of a newly assembled genomehttp://galaxyproject.github.io/training-material/topics/assembly/tutorials/ecoli_comparison/tutorial.htmlhttps://tess.elixir-europe.org/materials/assembly-making-sense-of-a-newly-assembled-genomeDNA 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 deletionsnekrutdelphine-l
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Slides
Contributing to the Galaxy Training Material - Creating a new tutorial - Slideshttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-slides/slides.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-slidesGalaxy 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 commentseraschebebatutshiltemann
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile...
Resource type: Tutorial
Genome Annotation - Genome annotation with Prokkahttp://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.htmlhttps://tess.elixir-europe.org/materials/genome-annotation-genome-annotation-with-prokkaGenome 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 JBrowseannasymetseemannslugger70
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Resource type: Tutorial
Genome Annotation - Genome Annotationhttp://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/genome-annotation/tutorial.htmlhttps://tess.elixir-europe.org/materials/genome-annotation-genome-annotationGenome 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.joachimwolfferxlebenbgruening
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Contributing with GitHub via its interfacehttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/github-interface-contribution/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-contributing-with-github-via-its-interfaceGalaxy 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 requestbebatut
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Set up a Galaxy for Traininghttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/setup-galaxy-for-training/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-set-up-a-galaxy-for-trainingGalaxy 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 topicshiltemannbebatut
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Slides
Contributing to the Galaxy Training Material - Good practices to run a workshophttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/good-practices/slides.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-good-practices-to-run-a-workshopGalaxy 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 workshopbebatutbgrueningshiltemann
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Running the Galaxy Training material website locallyhttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/running-jekyll/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-running-the-galaxy-training-material-website-locallyGalaxy 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 webbrowserbebatutbgrueningshiltemann
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Generating PDF artefacts of the websitehttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/generating-pdf/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-generating-pdf-artefacts-of-the-websiteGalaxy 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 PDFsbebatut
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Including a new topichttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-topic/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-including-a-new-topicGalaxy 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 topicbebatut
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Creating a new tutorial - Creating Interactive Galaxy Tourshttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-tours/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-creating-interactive-galaxy-toursGalaxy 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 tourbebatutbgrueningshiltemann
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Creating a new tutorial - Defining the technical infrastructurehttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-defining-the-technical-infrastructureGalaxy 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 tutorialbebatutbgrueningshiltemann
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Creating a new tutorial - Defining metadatahttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-metadata/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-defining-metadataGalaxy 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 objectivesbebatutbgrueningshiltemann
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Contributing with GitHub via command-linehttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/github-command-line-contribution/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-contributing-with-github-via-command-lineGalaxy 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 requestcmonjeaubebatut
Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...
Resource type: Tutorial
Contributing to the Galaxy Training Material - Creating a new tutorial - Writing content in Markdownhttp://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-content/tutorial.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-writing-content-in-markdownGalaxy 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 boxesbebatutbgrueningshiltemann
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 Materialhttp://galaxyproject.github.io/training-material/topics/contributing/slides/introduction.htmlhttps://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-overview-of-the-galaxy-training-materialGalaxy 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
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Questions of the tutorial:
- How to use the rule based...
Resource type: Tutorial
Introduction to Galaxy - Rule Based Uploaderhttp://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-rules/tutorial.htmlhttps://tess.elixir-europe.org/materials/introduction-to-galaxy-rule-based-uploaderGalaxy 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 Uploaderjmchiltonerasche
Resources related to configuration and maintenance of Galaxy servers
Questions of the tutorial:
- What is the release cycle of Galaxy?
- What do I need to do before updating my Galaxy server?
- How to upgrade Galaxy to a new release?
Objectives of the tutorial:
- Identify the challenges...
Resource type: Slides
Galaxy Server administration - Upgrading Galaxyhttp://galaxyproject.github.io/training-material/topics/admin/tutorials/upgrading/slides.htmlhttps://tess.elixir-europe.org/materials/galaxy-server-administration-upgrading-galaxyResources 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.martensonafganensoranzo
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 mutationshttp://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.htmlhttps://tess.elixir-europe.org/materials/variant-analysis-mapping-by-sequencingExome 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 variantswm75
