Genomic Virtual Lab (GVL) as a bioinformatics training platform
Peter Tsai, PhD Candidate, Dr Thierry Jean Lints, Professional Teaching Fellow, Professor Cristin Print, Department of Molecular Medicine and Pathology; Dr William Schierding, Research Fellow, Liggins Institute.
Introduction
The ability to analyse large-scale next-generation sequencing data is now an essential skill in modern biology. There is an increasing demand within the Faculty of Medical Health Sciences at the University in bioinformatics training to better understand how to analyse RNA (ribonucleic acid) 1 – Sequencing data, rather than using out-of-shelf end-to-end black box solutions.
The training workshop
The week-long RNA-Sequencing workshop initiated by Professor Cristin Print from Faculty of Medical and Health Sciences, with a team effort from William Schierding, Peter Tsai and Thierry Lints, was held on the 19th February this year. It aims to provide an intensive step-by-step training to help researchers to understand how sequencing data needs to be analysed. The workshop on the analysis of RNA-sequencing data will include hands-on analysis of a real dataset, taking participants through a complete analysis pipeline from raw sequencing data to output graphics and spreadsheets, it covers:
- Sequencing platforms and terminology
- Gene expression and transcriptomics
- Exploring public data sources
- Pathway analysis
Genomics Virtual Laboratory (GVL)2
With the significant inputs from Sean Matheny from Centre for eResearch, the workshop uses the GVL training platform running on Nectar3.
GVL is a web portal provides a growing suite of genomics analysis tools, the biologists can start working immediately with no setup required. Date can be analysed easily on the Nectar research cloud. A workbench for reproducible results, a command line interface to support bioinformaticians, and tutorials to help biologists learn analysis techniques.
An example of multiple layers that can be built on Nectar (opensgtack) for research applications.
It is normally time consuming and sometimes difficult process to set up a bioinformatics analysis system. The pre-configured GVL eliminated the need to set up the system from scratch. The demand for the workshop amongst researchers has been overwhelming, and another week-long workshop has been planned for the end of November 2018 for those researchers who could not attend the first workshop. We hope the workshop will provide a good understanding of the tools and processes used, and enable researchers to analyse simple RNA-sequencing datasets themselves.
