Register training material
30 materials found

Authors: Manuel Corpas  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

BioJS

Introduction to BioJS a standard for visualisation of biological data in JavaScript

Keywords: Biojs, Javascript, Software, Standards

GOBLET Training portal

Presention

Keywords: Goblet

Presentation About GOBLET Portal

This is a presentation I gave at the Jornadas de Bioinformática in Seville, Spain (24/09/14)

Keywords: Goblet, Training portal

Training Bioinformatics in the Cloud

I present the points of view, the challenges and advantages of developing training materials through the cloud.

Keywords: Advanced bioinformatics training, Cloud computing, Training

RNA-seq analysis

I give an overview of the analysis of gene expression in plants using RNA-seq data. This course provides a foundation on the tuxedo software suite: TopHat, Cufflinks, CummeRbund.