Register training material
29 materials found

Authors: Jan Slifka  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

The 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

The 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?

The 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?

The 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?

The 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?

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

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'Galaxy Interactive Tools' tutorial

The objectives are:
- Understand what Galaxy Interactive Tools are and how they work
- Be aware of the security implications of Interactive Tools
- Have a basic understanding of the Interactive Tools (GxIT/GIE) Proxy, its purpose, and configuration
- Be familiar with wildcard SSL certificates...

Keywords: admin, ansible, interactive-tools

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?

The 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?

The 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?

The 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?

The 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?

The 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?

The 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?

The 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?

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

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?

The 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?

The 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?

The 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?

The 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?

The 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?

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

Keywords: admin

Resource type: slides

DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data management, Data governance

Keywords: Data managment plan, data stewardship, data management, software tools

Resource type: Video, Slides, Webinar

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data governance, Data management

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides