Project Description

Dr Igor Makunin

Research Computing Centre
The University of Queensland

An introduction to Galaxy with the NeCTAR Genomics Virtual Laboratory


Wednesday 3 July 2019

Igor has extensive experience in analysis of nextGen sequencing data, comparative genomics, genetics and molecular biology. He provides support for biologists working with nextGen sequencing data on the Galaxy platform.

Igor has worked as a scientist at the Queensland Institute of Medical Research, The University of Queensland, Institute of Cytology and Genetics (Novosibirsk, Russia), the University of Geneva and the University of Cambridge.

The Galaxy platform is one of the world’s most popular and fastest growing bioinformatics web-based interfaces. With Galaxy, biologists can access a huge range of bioinformatics tools, using user-friendly and intuitive graphical interfaces. Galaxy also captures and records analysis pipelines to provide full reproducibility, and simplifies sharing of data and analyses between colleagues.

The NeCTAR*-supported Genomics Virtual Laboratory project has adopted Galaxy as one of its major platforms to bring the power of the national research cloud to bench biologists. Through the GVL and NeCTAR, Australian researchers and their collaborators have free access to high performance bioinformatics computing resources.

This workshop will focus on a hands-on introduction to using Galaxy on the research cloud. Participants will learn where and how they can access a Galaxy instance, how to upload and access data, running basic analysis pipelines, and using both integrated and plug-in functions to visualise genomic data.

We will introduce histories and workflows, and explore how they can be used to run reproducible analysis pipelines and to share analyses with colleagues. We will also discuss how to extend the standard Galaxy build to add new tools and custom reference genomes.

Galaxy Australia: advanced bioinformatics within a biologist-friendly interface

Getting started with bioinformatic software

Friday 5 July 2019

Galaxy Australia is a national service designed for the analysis of genome scale data, with an emphasis on high throughput sequencing. Galaxy Australia provides preinstalled bioinformatic tools and public data, such as reference genomes. The Galaxy web interface does not require knowledge of Unix or programming skills, all analyses can be triggered with a mouse click. The interface also means that the service can be accessed from any web-connected device providing users with flexibility and convenience of a virtual laboratory. For new users we offer step-by-step tutorials covering various topics ranging from basic operations in Galaxy to complex analysis, such as RNA-Seq (differential gene expression analysis with high throughput sequencing data), genome assembly and variant calling. After a simple registration process, users get access to an ample amount of storage, compute resources and diverse public datasets. There is no wait time on registration and users can start data analysis immediately after uploading their data. Galaxy provides easy connections to external services for direct data import from public repositories and visualisation of user data on public servers such as UCSC Genome Browser. Raw data, analysis results or chain tool execution (tool workflow) can be shared with other users or made public. Galaxy workflows are one of the most powerful features of the service, allowing users to perform a series of tasks reproducibly on one or many files. Galaxy workflows record not only parameters for tools, but also tool version, providing a reproducible robustness to data analysis and also providing a historical record of the methodology applied to input data. With over 3,000 registered users Galaxy Australia is actively used for research and training. The talk will provide overview of Galaxy Australia and will be of interest for both researchers and educators.