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Bioinformatics First Community of Practice Meeting

29 September 2021
1:00pm - 2:30pm

Meet the specialists supporting researchers working on Bioinformatics at Pawsey, while they present about resources, tools and services available at the Centre for the community.

This event is being hosted by the Pawsey Supercomputing Research Centre, with the support of the Australian BioCommons, ABACBS and COMBINE Australia.

Register here

The session will be followed by a Q&A for the participants. We have a stellar lineup of speakers from the Pawsey Supercomputing Research Centre, Australian BioCommons, ABACBS and COMBINE Australia.

Event schedule:

  • Pawsey Supercomputing Centre overview
    • Introduction to Pawsey, systems and the future
  • AusBiocommons overview
    • About AusBiocommons
    • Bioinformatics and HPC
    • Tools and resources
    • Why Pawsey?
  • ABACBS overview
    • About ABACBS
    • Bioinformatics and HPC
    • Tools and resources
    • Why Pawsey?
  • COMBINE overview
    • About COMBINE
    • Tools and resources
  • Pawsey and bioinformatics
    • Tools available
    • Pawsey visualisation services
    • Accessing Pawsey: Nimbus & Setonix
    • Bioinformaticians HPC pathways
      • How do you know when your laptop can no longer do what you need it to do for your research? When is it best to use cloud resources? When is it best to use supercomputing resources? When do I need both (or neither)?
  • Q&A (30 minutes)

Register here

If you are an Australia Bioinformatics practitioner and have not yet joined the Community of Practice, join the slack channel to discover what is there, register for upcoming events, organise your own events, share your most recent papers and publications, ask your peers questions and discover what they are working on.

To read more about the space read Building a Bioinformatics HPC Community in Australia.

Speakers

Dr Jeff Christiansen, Australian BioCommons

Jeff leads the Community Engagement, Training and Comms teams at the Australian BioCommons, who collectively aim to ensure that appropriate infrastructure is established at a national level to support Australian life research communities, and that researchers are upskilled to use this infrastructure to support their research. 

Jeff has a PhD in Biochemistry from the University of Queensland, and started his career conducting research in the fields of cancer, molecular genetics and embryo development. He has since held many community facing roles in the UK and Australia, all focussed on developing computational infrastructure to support health and life science research – at the UK Medical Research Council (MRC), Australian National Data Service (ANDS), Intersect Australia, University of Queensland’s Research Computing Centre, Queensland Cyber Infrastructure Foundation (QCIF), and the EMBL-Australia Bioinformatics Resource (EMBL-ABR). 

Dr Nicola Armstrong, ABACBS

Nicola recently started at Curtin University as an Associate Professor in Data Science. She is a statistical bioinformatician who completed her doctoral studies in Statistics at the University of California, Berkeley. After graduating with her PhD, she spent several years in the Netherlands as a postdoc at Eurandom and the Vrije Universiteit before moving to the Netherlands Cancer Institute in Amsterdam as a senior statistician. 

Nicola’s work focuses on human disease, developing and applying statistical methods for the analysis and integration of high-throughput genomic and epigenomic data to understand how the development of complex diseases and ageing processes vary between individuals. 

Dr Sarah Beecroft, Pawsey Supercomputing Research Centre

Sarah obtained a PhD in Medicine from UWA in 2020. She has a background both laboratory and computational based genetics research, specifically focussing on disease gene discovery in neuromuscular disorders. She now works to support bioinformatics development and optimisation at Pawsey 

Audrey Stott, Pawsey Supercomputing Research Centre

Having completed a Bachelor of Podiatric Medicine and a Master of Biomedical Science (Human Biology), Audrey has experience in both clinical and research settings. Her interest lies in the area of bioinformatics, where crossover from bench to bedside is taken place. With her strong background in biology, she joins the Pawsey Team to work on accessibility of HPC for bioinformatics. 

Ali Zamani, Pawsey Supercomputing Research Centre

Ali is a Visualisation Specialist with an engineering background and specialises in visualising scientific data. With extensive exposure to VTK technology and script visualisation this puts him in good stead to supply researchers with an in-depth insight into their simulation, resulting in an integrated time-efficient workflow. 

Dr Pascal Elahi, Pawsey Supercomputing Research Centre

Pascal obtained a PhD in Astrophysics from Queen’s University, Kingston Ontario, Canada. His background is in numerical astrophysics, where he explored the physics governing the Universe through complex virtual universes. At Pawsey, he is responsible for assisting researchers to efficiently parallelise their codes and port them onto the infrastructure operated at the centre. Pascal undertakes technical assessment of parallelised applications for performance on supercomputers and assists research groups in scaling their research applications and simulations from hundreds to thousands of processors.