RCC and QRIScloud resources assisted a demonstration of potentially revolutionary software on Saturday, 4 November at the UQ Centre for Clinical Research.
Tania Duarte from UQ’s Institute for Molecular Bioscience demonstrated the Streamformatics software program at the RCC co-sponsored Practical Microbial Genomics Workshop with the help of RCC Systems Administrator Derek Benson.
Streamformatics develops streaming bioinformatics algorithms for rapid diagnosis of antibiotic resistant bacterial infection and for tracking infection outbreaks. These algorithms cut down the time required to identify infection from two days to a few hours, and enable health providers to rapidly identify the emergence of new outbreaks.
With Streamformatics, real-time data can be sent straight from a researcher's laptop to a high performance computer to crunch the numbers with the results produced in a dynamic, interactive data visualisation viewed via a web browser.
In the background, a Nectar virtual machine in QRIScloud, an RCC-supported cloud computer, runs the analysis.
Apart from saving researchers time, Streamformatics could save money too, enabling expensive HPC and sequencing devices to be turned off much sooner.
Another important application of the software outside of clinical pathology is in agriculture, identifying infections in plants.
Bioinformatician Michael Hall originally developed Streamformatics in 2016 as his Masters project within the “Coin Group” at IMB, led by Associate Professor Lachlan Coin. Over the past year Michael has further developed the software’s visualisation features and backend.
Streaminformatics software is freely available from GitHub under licence. A dynamic version of a Streamformatics “donut chart” can be viewed here.
RCC, UQ, QCIF, the Queensland Genomics Health Alliance and the Queensland Government all sponsored the Practical Microbial Genomics Workshop.
For more information about Streamformatics, please contact Derek Benson: d.benson@uq.edu.au
