News

Need help with Galaxy Australia?

When Manuela Cascini from the Queensland University of Technology needed help with mitochondrial genome analysis to support her PhD, she called on QFAB’s Analysis Hotel and Galaxy Australia.

The Analysis Hotel allows students and researchers to perform data analysis embedded with the team at QFAB's office at The University of Queensland’s Institute for Molecular Bioscience (IMB). There, they can receive as much support as they need and get facilitated access to tools, platforms, data and international resources.
 
In Ms Cascini’s case, she spent a week last month with Dr Gareth Price and Mike Thang of QFAB to get the bioinformatics help required to use Galaxy Australia to conduct NGS mitochondrial genome assembly in order to provide the molecular data she needed for her thesis.
 
Galaxy Australia is a nationally-hosted service of Galaxy, a platform for accessible, reproducible, and transparent bioinformatics analysis, run by QCIF, Melbourne Bioinformatics and UQ’s Research Computing Centre.
 
“I like many things about Galaxy,” said Ms Cascini. “It's free and Web-based, so it doesn't take up all the memory on my laptop. I also like that I can rely on prompt assistance in case of problems. And it is flexible: if there's an analysis that cannot yet be made on Galaxy, the team will work to add the tool you need.”
 
She said she felt very welcome and comfortable in the QFAB office. “All the people I met there were absolutely affable and easy to approach. Working with Mike and Gareth at QFAB has been an excellent experience—they are both incredibly competent and supportive.”
 
At the Analysis Hotel, Ms Cascini wanted to check the quality of her data, troubleshoot any issues, and ensure she had all the data she required. She also wanted to save as much as possible of the whole NGS sequencing and assemble as many genomes as possible for her analyses.
 
The overall objective of Ms Cascini’s PhD is to use phylogenetic inference methods to reconstruct the origin and diversification of Australasian marsupials.
 
“I study the evolution of marsupials and I aim to clarify the when and how of their diversification. I mostly use molecular phylogenetic methods; in other words, I make "family trees" by looking at the DNA of the species. 
 
“Australia has the largest proportion of endangered mammal species and the highest rate of extinction among all continents. Predation and competition by introduced placental mammals from Eurasia seem to be the major threats to native marsupials, but the reason why they are so susceptible to introduced animals is still poorly understood. Disentangling the evolutionary process that shaped the Australian fauna means also understanding which factors could possibly undermine it. To this end, the outcome of my research could be used to make predictions about the effects of invasive species, and therefore greatly contribute to informing conservation strategies.”
 
As well as its Analysis Hotel, QFAB also operates biostatistics and bioinformatics clinics for researchers and HDR students at its member universities, i.e. UQ, QUT, Griffith, JCU, USQ and CQU. Researchers and HDR students from member universities can receive free QFAB consultations to help with research projects, publications and upcoming grant applications.
 
QFAB can provide advice related to bioinformatics, biostatistics and biodata, including:

  • advice on experimental design 
  • recommendations and coaching on analysis methods
  • analysis of data and interpretation of results 
  • access to bioinformatics resources and compute infrastructure
  • choice and use of software
  • recommendations on data management plans 
  • content and pilot analysis for grants 
  • publication revision and help with reviewer comments. 

Visit QFAB.org/member-clinics to book an appointment. Any questions? Please email the QFAB team: This email address is being protected from spambots. You need JavaScript enabled to view it.
 
Additional bioinformatics and biostatistics support may also be provided through the following institutions for its researchers: Brisbane’s Centre for Children’s Health Research, UQ’s Centre for Clinical Research, and UQ’s Diamantina Institute. 


L–R: Dr Gareth Price, Mike Thang and Manuela Cascini in QFAB's "Analysis Hotel".