Simon Gladman reports from a recent visit to the Canadian Integrated Rapid Infectious Disease Analysis project (IRIDA) where they are building an open source, end-to-end platform for infectious disease genomics epidemiology. Simon worked with the team to incorporate the PHAC’s IRIDA system into the GVL and test out it’s functionality. A working example. This is […]
Torsten Seemann leads this group
|Melbourne Bioinformatics||LEAD INSTITUTE|
|University of Melbourne||MEMBER INSTITUTE|
|University of Queensland||SUBSCRIBER|
|Peter Doherty Institute for Infection and Immunity||SUBSCRIBER|
Several grants support this group
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The Microbial Genomics Group contributes specialist expertise and leadership to national collaborative projects, develops platforms for more efficient research data storage, analysis and sharing, and develop a wide range of training activities. Co-located with the Microbial Diagnostic Unit of the Public Health Laboratory at the Doherty Institute, the Microbial Genomics team works with researchers and public health authorities around the world to implement a new ‘gold standard’ in public health outbreak investigations, using the refined analytical tools now available to microbiologists through next generation sequencing technologies. As well as developing our own novel tools to share with the bioinformatics community, we work to continually upgrade the the Australian-made GVL to make genomic data analysis more accessible to microbiologists in Australia and now our public health colleagues around the world.
- Hear ‘How bioinformatics and genomics is transforming Australian public health and clinical microbiology’ from Torsten (53min recorded presentation to BC Centre for Disease Control, Canada, June 2017)
- Genomics Virtual Laboratory
- The history of the GVL project at Nectar
- Galaxy in public health – the microbial genomics virtual laboratory.
Assoc Prof Torsten Seemann (Lead Bioinformatician for Microbial Genomics. Lead Bioinformatician at MDU PHL and Doherty Applied Microbial Genomics)
Dr Dieter Bulach (Senior Research Scientist)
Mr Simon Gladman (Research Scientist)
Dr Anna Syme (Bioinformatician)
A 2-day COMBINE workshop was held at UWA over 22/23 November 2016, facilitated by VLSCI’s Simon Gladman and Anna Syme. This workshop covered Nectar resources, Galaxy, genome assembly and annotation, variant calling and RNA-Seq analysis. Of the 31 participants, all were very pleased with the whole course: I thought this was an excellent workshop, I […]
Funded in 2016, this three-year NHMRC partnership grant is led out of ANU by Assoc Prof Martyn Kirk, with collaborators from public agencies and institutions around Australia and New Zealand. UNDERSTANDING THE SOURCES OF CAMPYLOBACTER IN AUSTRALIA Campylobacter is a key cause of food-borne disease globally, with Australian rates of reported illness amongst the highest […]
25 October 2017 Thanks to the global efforts of over 250 contributors, including our own Simon Gladman, bioinformaticians and life scientists now have access to ‘Bioconda’, a software-package building and management system designed for bioinformatics. This work is now documented at BioRxiv. A common problem in computing and data science especially […]
With growing antibiotic resistance spreading through our communities, finding new ways to stop illness and death from Methicillin resistant Staphylococcus aureus (MRSA or golden staph) has become a significant challenge for health systems the world over. Understanding MRSA’s vulnerabilities, through knowledge of its genome, offers new technologies for researchers, and our microbial genomics experts are contributing to this work […]
Simon Gladman has now published a new version of the mGVL. It’s now at 0.11-1 and is based on GVL 4.1. Following loads of testing while at the Galaxy conference (#GCC2016) it now has: the newest version of Galaxy – including embedded JBrowse (as a tool) some image updates a new GVL extension system (for […]
VLSCI announces Australian-made Microbial Genomics Virtual Laboratory (microGVL) being installed for CLIMB project in UK.