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17 materials found

Authors: erasche  or nekrut 


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...

Resource type: Tutorial

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

Resource type: Tutorial

Data Manipulation - Collections: Multisample Analysis

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Tutorial

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

Resource type: Tutorial

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

Resource type: Tutorial

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...

Resource type: Tutorial

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...

Resource type: Slides

Variant Analysis - Calling very rare variants

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

Questions of the tutorial:

  • What frequency of variants is so low that it is obscured by sequencing error rate?
  • What are the different types of consensus sequences produced from duplex sequencing?

Objectives of...

Resource type: Tutorial

Variant Analysis - Calling variants in diploid systems

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

Questions of the tutorial:

  • How to find variable sites in diploid genomes?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in human genome.

Resource type: Tutorial

Variant Analysis - Calling variants in non-diploid systems

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

Questions of the tutorial:

  • How does frequency of mitochondrial polymorphisms change from mother to child?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in bacteria,...

Resource type: Tutorial

Introduction to Galaxy Analyses - NGS data logistics

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 manipulate and process...

Resource type: Tutorial

Transcriptomics - Reference-based RNAseq data analysis (long)

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How to perform analysis of RNAseq data when reference genome is available?

Objectives of the tutorial:

  • Learns basic concepts of RNAseq analysis

Resource type: Tutorial

Assembly - Unicycler Assembly

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

Introduction to Galaxy Analyses - IGV Introduction

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.

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

Galaxy Server administration - Advanced customisation of a Galaxy instance

Resources related to configuration and maintenance of Galaxy servers

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