Register training material
40 materials found

Contributors: Björn Grüning  or Dr. Colin Combe 


Hands-on for 'Exome sequencing data analysis for diagnosing a genetic disease' tutorial

The questions this addresses are:
- How do you identify genetic variants in samples based on exome sequencing data?
- How do you, among the set of detected variants, identify candidate causative variants for a given phenotype/disease?

\nThe objectives are:
- Jointly call variants and...

Scientific topics: Genetic variation

Keywords: variant-analysis

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?

\nThe 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 'Galaxy Webhooks' tutorial

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

\nThe 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 'Creating Interactive Galaxy Tours' tutorial

The questions this addresses are:
- What is a Interactive Galaxy Tour?
- How can we create an Interactive Tour?

\nThe objectives are:
- Creating a Galaxy tour from scratch
- Deploying and running a tour

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Tools, Data, and Workflows for tutorials' tutorial

The questions this addresses are:
- 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...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Running the GTN website locally' tutorial

The questions this addresses are:
- How to setup the infrastructure to build training webpages?

\nThe objectives are:
- Installing packages needed for rendering the webpage
- Running the GTN material website locally
- Tracking changes to the content live in the webbrowser

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Label-free versus Labelled - How to Choose Your Quantitation Method' tutorial

The questions this addresses are:
- What are benefits and drawbacks of different quantitation methods?
- How to choose which quantitation method bests suits my need?

\nThe objectives are:
- Choose your quantitation method.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Secretome Prediction' tutorial

The questions this addresses are:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?

\nThe objectives are:
- Predict proteins in the cellular secretome by using GO-terms.
- Predict proteins in the cellular secretome by...

Scientific topics: Proteomics

Keywords: proteomics, human

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein Quantification via Stable Isotope Labelling (SIL)' tutorial

The questions this addresses are:
- What are MS1 features?
- How to quantify based on MS1 features?
- How to map MS1 features to MS2 identifications?
- How to evaluate and optimize the results?

\nThe objectives are:
- MS1 feature quantitation and mapping of quantitations to peptide and...

Scientific topics: Proteomics

Keywords: proteomics, DDA, SILAC

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using SearchGUI and PeptideShaker' tutorial

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

\nThe objectives are:
- Protein identification from LC-MS/MS raw files.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Detection and quantitation of N-termini (degradomics) via N-TAILS' tutorial

The questions this addresses are:
- How can protein N-termini be enriched for LC-MS/MS?
- How to analyze the LC-MS/MS data?

\nThe objectives are:
- Run an N-TAILS data analysis.

Scientific topics: Proteomics

Keywords: proteomics

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using OpenMS tools' tutorial

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

\nThe objectives are:
- Protein identification from LC-MS/MS raw files.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Protein FASTA Database Handling' tutorial

The questions this addresses are:
- How to download protein FASTA databases of a certain organism?
- How to download a contaminant database?
- How to create a decoy database?
- How to combine databases?

\nThe objectives are:
- Creation of a protein FASTA database ready for use with...

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Galaxy Database schema' tutorial

The questions this addresses are:
- Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that
- How to extract usage information, which can not be gathered using the given report tools
- How...

Keywords: admin

Resource type: hands-on tutorial

Hands-on for 'Connecting Galaxy to a compute cluster' tutorial

The questions this addresses are:
- How to connect Galaxy to a compute cluster?
- What are job metrics?
- What sort of information can I collect?
- Where can I find this information?

\nThe objectives are:
- Be familiar with the basics of installing, configuring, and using Slurm
-...

Keywords: admin, jobs, ansible, git-gat

Resource type: hands-on tutorial

Hands-on for 'Mapping Jobs to Destinations' tutorial

The questions this addresses are:
- How can I configure job dependent resources, like cores, memory for my DRM?
- How can I map jobs to resources and destinations

\nThe objectives are:
- Know how to map tools to job destinations
- Be able to use the dynamic job runner to make arbitrary...

Keywords: admin, ansible, jobs, git-gat

Resource type: hands-on tutorial

Hands-on for 'Galaxy Monitoring with Reports' tutorial

The questions this addresses are:
- How to monitor a Galaxy service with the Reports application?

\nThe objectives are:
- Setup and start the Galaxy reports app.

Keywords: admin, ansible, monitoring, git-gat

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry imaging: Loading and exploring MSI data' tutorial

The questions this addresses are:
- Did the tryptic digestions work?
- Is there an intensity gradient in the data?
- How good is the m/z accuracy?

\nThe objectives are:
- How to upload an imzML file into Galaxy
- Getting an overview of the MSI data with the MSI quality control tool
- How...

Scientific topics: Proteomics

Keywords: proteomics, mouse, imaging

Resource type: hands-on tutorial

Hands-on for 'Galaxy 101' tutorial

The questions this addresses are:
- Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22?

\nThe objectives are:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
-...

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'From peaks to genes' tutorial

The questions this addresses are:
- How to use Galaxy?
- How to get from peak regions to a list of gene names?

\nThe objectives are:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
- Learn how histories work
-...

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'High Throughput Molecular Dynamics and Analysis' tutorial

The questions this addresses are:
- How are protein-ligand systems parameterized for molecular dynamics simulation?
- What kind of analysis can be carried out on molecular trajectories?
- How can high-throughput MD be used to study multiple ligands?

\nThe objectives are:
- Learn about...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Slides for 'Visualizations: JavaScript Plugins' tutorial

The questions this addresses are:
- How can I make a custom JavaScript plugin?

\nThe objectives are:
- Learn how to add custom JavaScript plugins using the Galaxy Charts framework

Keywords: dev

Resource type: slides

Slides for 'Tool Dependencies and Conda' tutorial

The questions this addresses are:
- How can I connect tools to applications and libraries?
- What are the advantages of declaring dependencies for my tool?
- What are Conda and Bioconda?
- What are Conda recipes and environments?
- How do I find and use existing Conda recipes?
- How do I...

Keywords: dev

Resource type: slides

Slides for 'Galaxy Code Architecture' tutorial

The questions this addresses are:
- How is the Galaxy code structured?
- What do the various other projects related to Galaxy do?
- What happens when I start Galaxy?

\nThe objectives are:
- Explore various aspects of the Galaxy codebase.
- Understand the various top-level files and modules...

Keywords: dev

Resource type: slides

Slides for 'Galaxy Webhooks' tutorial

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

\nThe 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: slides

Slides for 'Galaxy Interactive Environments' tutorial

The questions this addresses are:
- What are Galaxy Interactive Environments (GIEs)?
- How to enable GIEs in Galaxy?
- How to develop your own GIE?

\nThe objectives are:
- Implement a Hello-World Galaxy Interactive Environment

Keywords: dev

Resource type: slides

Slides for 'Galaxy Interactive Tours' tutorial

The questions this addresses are:
- What is a Galaxy Interactive Tour?
- How to create a Galaxy Interactive Tour?

\nThe objectives are:
- Discover what is a Galaxy Interactive Tour
- Be able to create a Galaxy Interactive Tour
- Be able to add a Galaxy Interactive Tour in a Galaxy instance

Keywords: dev

Resource type: slides

Slides for 'Tool development and integration into Galaxy' tutorial

The questions this addresses are:
- What is a tool for Galaxy?
- How to write a best-practice tool?
- How to deal with the tool environment?

\nThe objectives are:
- Learn what a tool is and its structure
- Use the Planemo utilities to develop a tool
- Deal with the dependencies
- Write...

Keywords: dev

Resource type: slides

Slides for 'Tool Dependencies and Containers' tutorial

The questions this addresses are:
- What are the advantages of running my Galaxy tool inside of a container?
- How does Galaxy find a container to run my tool in?
- What are BioContainers and how are they related to Galaxy?

\nThe objectives are:
- Explore the differences between...

Keywords: dev

Resource type: slides

Slides for 'Connecting Galaxy to a compute cluster' tutorial

The questions this addresses are:
- How to connect Galaxy to a compute cluster?
- How can I configure job dependent resources, like cores, memory for my DRM?

\nThe objectives are:
- Understand all components of the Galaxy job running stack
- Understand how the job_conf.xml file controls...

Keywords: admin, features

Resource type: slides