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1609 materials found

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

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

The objectives are:
- Identification of genetic variations using variant calling

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

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

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

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

Keywords: visualisation

Resource type: hands-on tutorial

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

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

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

Keywords: genome-annotation

Resource type: hands-on tutorial

Hands-on for 'Visualisation with Circos' tutorial

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

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

Keywords: visualisation

Resource type: hands-on tutorial

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

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

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

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

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Maker' tutorial

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

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

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

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

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

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

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Refining Genome Annotations with Apollo (prokaryotes)' tutorial

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

Keywords: genome-annotation, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Maker (short)' tutorial

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

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

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'CRISPR screen analysis' tutorial

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

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

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

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Prokka' tutorial

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

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

Keywords: genome-annotation, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Masking repeats with RepeatMasker' tutorial

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

The objectives are:
- Use Red and RepeatMasker to soft-mask a newly assembled genome

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Funannotate' tutorial

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

The objectives are:
- Load genome into...

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

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

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

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

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Galaxy Admin Training' tutorial

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

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

Keywords: teaching

Resource type: hands-on tutorial

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

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

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

Keywords: teaching, cyoa

Resource type: hands-on tutorial

Hands-on for 'Organizing a workshop' tutorial

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

Keywords: teaching

Resource type: hands-on tutorial

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

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

The objectives are:
- Interact with Galaxy via BioBlend.

Keywords: dev, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Debugging Galaxy' tutorial

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

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

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'JavaScript plugins' tutorial

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

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

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Creating Galaxy tools from Conda Through Deployment' tutorial

The questions this addresses are:
- How do you create a conda package used as a dependency in a Galaxy tool wrapper?
- How do you create a Galaxy tool wrapper and all of its requirements?
- How do you test a Galaxy tool wrapper after it's written?
- How do you deploy a Galaxy tool wrapper?
...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Contributing a New Feature to Galaxy Core' tutorial

The questions this addresses are:
- How can I add a new feature to Galaxy that involves modifications to the database, the API, and the UI?

The objectives are:
- Learn to develop extensions to the Galaxy data model
- Learn to implement new API functionality within Galaxy
- Learn to extend...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Galaxy Webhooks' tutorial

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

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

Keywords: dev

Resource type: hands-on tutorial

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

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

The objectives are:
- Further develop your ToolFactory Skills

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Generic plugins' tutorial

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

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

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Data source integration' tutorial

The questions this addresses are:
- How can I write a tool that can import data into Galaxy from an external database?
- What are "data sources" and how do they function?
- Is there any ready-to-use example?

Keywords: dev

Resource type: hands-on tutorial

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

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

Keywords: dev

Resource type: hands-on tutorial

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

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

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

Keywords: dev

Resource type: hands-on tutorial

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

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

Keywords: dev

Resource type: hands-on tutorial

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

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

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

Keywords: synthetic-biology

Resource type: hands-on tutorial