Workshops
Introduction to High Performance Computing
Using High Performance Computing (HPC) resources such as Melbourne Bioinformatics in an effective and efficient manner is key to modern research. This workshop will introduce you to HPC environments and assist you to get on with your research.
In particular you will learn:
- What is HPC?
- Loading software modules
- Submitting jobs
- Selecting job queues
- Monitoring your job’s progress
- What resources can I request?
- Selecting appropriate resources
Prerequisites: You will need a basic understanding of Unix, or you should have attended an ‘Introduction to Unix’ workshop in the past. All participants are required to bring their own laptop computers.
Workshops
Introduction to Unix
Knowledge of the Unix operating system is fundamental to being productive on HPC systems such as those offered by Melbourne Bioinformatics. This workshop will introduce you to the fundamental Unix concepts by way of a series of hands-on exercises.
In particular you will learn how to do the following things:
- Log into a Unix machine remotely
- Organise your files into directories
- Change file permissions to improve security and safety
- Create and edit files with a text editor
- Copy files between directories
- Use command line programs to manipulate files
- Automate your workflow using shell scripts
The workshop is facilitated by experienced Unix users who will be able to guide you through the exercises and offer assistance where needed. The workshop is intended for beginners with no prior experience in Unix. Attendees are required to bring their own laptop computers.
Workshops
Introduction to Unix
Knowledge of the Unix operating system is fundamental to being productive on HPC systems such as those offered by Melbourne Bioinformatics. This workshop will introduce you to the fundamental Unix concepts by way of a series of hands-on exercises.
Workshops
Introduction to High Performance Computing
Using High Performance Computing (HPC) resources such as Melbourne Bioinformatics in an effective and efficient manner is key to modern research. This workshop will introduce you to HPC environments and assist you to get on with your research.
Workshops
Introduction to Galaxy and the GVL
Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows. It also captures run information so that any user can repeat and understand a complete computational analysis. Finally, it allows users to share and publish analyses via the web.
This beginners workshop will introduce Galaxy’s interface, tool use, histories, and workflows and get new users of the Genomics Virtual Laboratory up and running.
This is a hands-on workshop and attendees should bring their own laptops.
Workshops
RNA-Seq Differential Gene Expression Analysis using Galaxy and the GVL
In this tutorial we will cover the concepts of RNA-Seq differential gene expression (DGE) analysis using Galaxy: an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
Participants with no previous Galaxy experience are strongly recommended to attend the “Introduction to Galaxy” workshop first.
Attendees are required to bring their own laptop computers.
Workshops
Variant Calling with Galaxy & the GVL for beginners
In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22. The tutorial is designed to introduce the tools, datatypes and workflow of variant detection. We will align reads to the genome, look for differences between reads and reference genome sequence, and filter the detected genomic variation manually to understand the computational basis of variant calling.
Workshops
Containerised Bioinformatics: Docker and other tools for reproducible analysis
Containerisation is a method of bundling an application or pipeline with all its dependencies, from language runtimes like Python and R to the operating system itself. This technology has already revolutionised web development by providing a simple way to run web applications a in precisely controlled environment, regardless of which computer system they are running on. This workshop will explain how these advantages can be easily applied to bioinformatics analysis, to ensure 100% reproducibility of your work, along with easy distribution of your pipelines to other users without the need for complex installation.
This workshop will teach you:
- What containerisation is, and why you might use it in bioinformatics
- What some common containerisation tools are, and when to use each of them
- How to find and run containers built by other people
- How to run containers on HPC systems (like Melbourne Bioinformatics)
- How to build your own application into a container (containerisation)
- How to use containers as elements of a bioinformatics pipeline
- How to distribute your container online
This workshop is aimed at anyone with basic Unix command-line experience.
Attendees are required to bring their own laptop computers.
Workshops
Open source science with Git and GitHub
Learn how to keep a record your code’s evolution over time using the git version control system, used by companies and open-source projects worldwide. Git allows you to easily maintain snapshots of your code as you make changes, keep multiple parallel versions of your code, and collaborate with others.
Workshops
Introduction to long-read genome assembly
New genome sequencing technologies are producing much longer reads. This workshop combines an introductory presentation to introduce the theory of de novo genome assembly with hands-on practice. It will cover long-read technologies and data types, and provide an overview of genome assembly methods. You will use command-line tools to perform long-read assembly and short-read polishing of bacterial genome data.
Prerequisites:
This workshop requires a familiarity with Unix and genomics concepts.
Workshop attendees must bring a laptop.
