Register training material
34 materials found

Authors: David Wishart  or Simon Gladman 


Hands-on for 'M. tuberculosis Variant Analysis' tutorial

The questions this addresses are:
- How do we detect differences between a set of reads from M. tuberculosis (Mtb) and the Mtb reference genome

\nThe objectives are:
- How should we filter those variants
- How can we predict drug resistance from those variants
- How do we annotate those...

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Microbial Variant Calling' tutorial

The questions this addresses are:
- How do we detect differences between a set of reads from a microorganism and a reference genome

\nThe objectives are:
- Find variants between a reference genome and a set of reads
- Visualise the SNP in context of the reads aligned to the genome
-...

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

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?

\nThe 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 'Unicycler Assembly' tutorial

The questions this addresses are:
- I have short reads and long reads. How do I assemble a genome?

\nThe objectives are:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with...

Keywords: assembly, prokaryote

Resource type: hands-on tutorial

Hands-on for 'An Introduction to Genome Assembly' tutorial

The questions this addresses are:
- How do we perform a very basic genome assembly from short read data?

\nThe objectives are:
- assemble some paired end reads using Velvet
- examine the output of the assembly.

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'De Bruijn Graph Assembly' tutorial

The questions this addresses are:
- What are the factors that affect genome assembly?
- How does Genome assembly work?

\nThe objectives are:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an...

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'Reference Data with CVMFS without Ansible' tutorial

The objectives are:
- Have an understanding of what CVMFS is and how it works
- Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
- Configure your Galaxy to use these reference genomes and indices

Keywords: admin

Resource type: hands-on tutorial

Hands-on for 'Upgrading Galaxy' tutorial

The questions this addresses are:
- How can I find which version of Galaxy I'm running?
- How do I upgrade the Galaxy server to the latest version?

\nThe objectives are:
- Understand how to find the current Galaxy server version you are using
- How to find the latest release version
- How...

Keywords: admin, ansible

Resource type: hands-on tutorial

Hands-on for 'Reference Data with CVMFS' tutorial

The objectives are:
- Have an understanding of what CVMFS is and how it works
- Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
- Configure your Galaxy to use these reference genomes and indices
- Use an Ansible playbook for all of the...

Keywords: admin, ansible, git-gat

Resource type: hands-on tutorial

Hands-on for 'Running Jobs on Remote Resources with Pulsar' tutorial

The questions this addresses are:
- How does pulsar work?
- How can I deploy it?

\nThe objectives are:
- Have an understanding of what Pulsar is and how it works
- Install and configure a RabbitMQ message queueing server
- Install and configure a Pulsar server on a remote linux machine
-...

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 'Downloading and Deleting Data in Galaxy' tutorial

The questions this addresses are:
- How can I efficiently download my data from Galaxy once I've completed my analyses?
- How do I delete old data to make more room in my quota?

\nThe objectives are:
- Have a greater knowledge of how Galaxy handles data downloads and deletions
- Be able to...

Keywords: galaxy-interface

Resource type: hands-on tutorial

Slides for 'Genome annotation with Prokka' tutorial

The questions this addresses are:
- How to annotate a bacterial genome?
- How to visualize annoted genomic features?

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

Keywords: genome-annotation, prokaryote

Resource type: slides

Slides for 'Deeper look into Genome Assembly algorithms' tutorial

The questions this addresses are:
- What are the main types of assembly algorithms?
- How do they perform with short and long reads?
- How to improve assemblies using other technologies?

Keywords: assembly

Resource type: slides

Slides for 'Unicycler Assembly' tutorial

The questions this addresses are:
- I have short reads and long reads. How do I assemble a genome?

\nThe objectives are:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with...

Keywords: assembly, prokaryote

Resource type: slides

Slides for 'An Introduction to Genome Assembly' tutorial

The questions this addresses are:
- How do we perform a very basic genome assembly from short read data?

\nThe objectives are:
- assemble some paired end reads using Velvet
- examine the output of the assembly.

Keywords: assembly

Resource type: slides

Slides for 'De Bruijn Graph Assembly' tutorial

The questions this addresses are:
- What are the factors that affect genome assembly?
- How does Genome assembly work?

\nThe objectives are:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an...

Keywords: assembly

Resource type: slides

Slides for 'Reference Data with CVMFS' tutorial

The objectives are:
- Have an understanding of what CVMFS is and how it works
- Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
- Configure your Galaxy to use these reference genomes and indices
- Use an ansible playbook for all of the...

Keywords: admin

Resource type: slides

Slides for 'Galaxy Installation with Ansible' tutorial

The questions this addresses are:
- How does it all connect?
- What steps will we go through?

\nThe objectives are:
- Get a high-level overview of a Galaxy server setup

Keywords: admin

Resource type: slides

Slides for 'Running Jobs on Remote Resources with Pulsar' tutorial

The questions this addresses are:
- How does pulsar work?
- How can I deploy it?

\nThe objectives are:
- Have an understanding of what Pulsar is and how it works
- Install and configure a Pulsar server on a remote linux machine
- Be able to get Galaxy to send jobs to a remote Pulsar server

Keywords: admin, jobs

Resource type: slides

Slides for 'Galaxy Monitoring with Telegraf and Grafana' tutorial

The questions this addresses are:
- How to monitor Galaxy with Telegraf
- How do I set up InfluxDB
- How can I make graphs in Grafana?
- How can I best alert on important metrics?

\nThe objectives are:
- Setup InfluxDB
- Setup Telegraf
- Setup Grafana
- Create several charts

Keywords: admin

Resource type: slides

Slides for 'Galaxy Monitoring with gxadmin' tutorial

The questions this addresses are:
- What is gxadmin
- What can it do?
- How to write a query?

\nThe objectives are:
- Learn gxadmin basics
- See some queries and learn how they help debug production issues

Keywords: admin

Resource type: slides

Slides for 'Server: Other' tutorial

The questions this addresses are:
- How to monitor a Galaxy service?

\nThe objectives are:
- Learn about different monitoring strategies.
- Setup and start the Galaxy reports app.

Keywords: admin

Resource type: slides

Slides for 'Galaxy Tool Management with Ephemeris' tutorial

The questions this addresses are:
- How are tools configured on a Galaxy instance?
- What is the Galaxy Tool Shed?
- How are Galaxy tools installed?
- What is ephemeris and how can it be used to manage tools on a Galaxy instance?

Keywords: admin

Resource type: slides

Slides for 'Server Maintenance and Backups' tutorial

The questions this addresses are:
- How do I maintain a Galaxy server?
- What happens if I lose everything?

\nThe objectives are:
- Learn about different maintenance steps
- Learn what to back up and how to recover

Keywords: admin

Resource type: slides

Informatics and Statistics for Metabolomics 2018 Module 6-Future of Metabolomics

Course covers many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomics databases, and exploring chemical databases.

Informatics and Statistics for Metabolomics 2018 Module 3-Databases for Chemical, Spectral, and Biological Data

Course covers many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomics databases, and exploring chemical databases.

Informatics and Statistics for Metabolomics 2018 Module 2-Metabolite Identification and Annotation

Course covers many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomics databases, and exploring chemical databases.

Informatics and Statistics for Metabolomics 2018 Module 1-Introduction to Metabolomics

Course covers many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomics databases, and exploring chemical databases.

Informatics and Statistics for Metabolomics 2017 Module 6-Future of Metabolomics

Course covers many topics ranging from understanding metabolomics technologies, data collection and analysis, conducting univariate and multivariate statistics, working with metabolomic databases, and exploring chemical databases.