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25 materials found

Authors: Janick Mathys  or bgruening 


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.

Resource type: Tutorial

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...

Resource type: Tutorial

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...

Resource type: Tutorial

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...

Resource type: Tutorial

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...

Resource type: Tutorial

Galaxy Server administration - Connecting Galaxy to a compute cluster

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • How to connect Galaxy to a compute cluster?
  • How can I configure job dependent resources, like cores, memory for my DRM?

Objectives of the tutorial:

  • Be familiar with the basics of installing,...

Resource type: Tutorial

Galaxy Server administration - User, Group and Quota managment

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • How does Galaxy manage users and groups?
  • How can I assign Quotas to specific users/groups?

Objectives of the tutorial:

  • Learn the Galaxy user/group management and assign Quotas.
  • Understand...

Resource type: Slides

Proteomics - Peptide and Protein ID using OpenMS tools

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to convert LC-MS/MS raw files?
  • How to identify peptides?
  • How to identify proteins?
  • How to evaluate the results?

Objectives of the tutorial:

  • Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How can protein N-termini be enriched for LC-MS/MS?
  • How to analyze the LC-MS/MS data?

Objectives of the tutorial:

  • Run an N-TAILS data analysis.

Resource type: Tutorial

Development in Galaxy - Galaxy Code Architecture

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How is the Galaxy code structured?
  • What do the various other projects related to Galaxy do?
  • What...

Resource type: Slides

Development in Galaxy - Galaxy Webhooks

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What are Galaxy Webhooks?
  • How to create them?

Objectives of the tutorial:

  • Discover what Galaxy...

Resource type: Tutorial

Development in Galaxy - Galaxy Interactive Environments

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What are Galaxy Interactive Environments (GIEs)?
  • How to enable GIEs in Galaxy?
  • How to develop your own...

Resource type: Slides

Development in Galaxy - Visualizations: charts plugins

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How can I make a custom plugin for Charts?

Objectives of the tutorial:

  • Learn how to add custom...

Resource type: Tutorial

Development in Galaxy - Galaxy Interactive Tours

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What is a Galaxy Interactive Tour?
  • How to create a Galaxy Interactive Tour?

Objectives of the...

Resource type: Slides

Variant Analysis - Exome sequencing data analysis

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How to identify the genetic variation with the use of exome sequencing?
  • What is the pipeline of the process of finding genetic variation which caused the disease?

Objectives of the...

Resource type: Tutorial

Galaxy Server administration - Advanced customisation of a Galaxy instance

Resources related to configuration and maintenance of Galaxy servers

Resource type: Slides

Galaxy Server administration - Galaxy Database schema

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • 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,...

Resource type: Tutorial

Galaxy Server administration - Docker and Galaxy

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • Why Docker? What is it?
  • How to use Docker?
  • How to integrate Galaxy in Docker to facilitate its deployment?

Objectives of the tutorial:

  • Docker basics
  • Galaxy Docker image (usage)
  • Galaxy...

Resource type: Slides

Introduction to Galaxy Analyses - Galaxy 101

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • Which coding exon has the...

Resource type: Tutorial

Introduction to Galaxy Analyses - From peaks to genes

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 Galaxy?
  • How to get...

Resource type: Tutorial

Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • 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?

Objectives of the tutorial:

  • MS1 feature...

Resource type: Tutorial

Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to convert LC-MS/MS raw files?
  • How to identify peptides?
  • How to identify proteins?
  • How to evaluate the results?

Objectives of the tutorial:

  • Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Secretome Prediction

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to predict cellular protein localization based upon GO-terms?
  • How to combine multiple localization predictions?

Objectives of the tutorial:

  • Predict proteins in the cellular secretome by using...

Resource type: Tutorial

Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • What are benefits and drawbacks of different quantitation methods?
  • How to choose which quantitation method bests suits my need?

Objectives of the tutorial:

  • Choose your quantitation method.

Resource type: Tutorial

Proteomics - Protein FASTA Database Handling

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • 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?

Objectives of the tutorial:

  • Creation of a...

Resource type: Tutorial