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2016 Winter School Program 2016 Winter School in Mathematical & Computational Biology 4-8 July 2016 Auditorium Queensland Bioscience Precinct The University of Queensland Brisbane, Australia Program Hosted by: IMB 2016 Winter School in Mathematical and Computational Biology 4-­‐8 July 2016 http://bioinformatics.org.au/ws16 Queensland Bioscience Precinct (Building #80) The University of Queensland Brisbane, Australia MONDAY 4 JULY 2016 08:00 Registration desk open NEXT GENERATION SEQUENCING & BIOINFORMATICS 09:00 – 09:05 Welcome and introduction Dr Nicholas Hamilton Research Computing Centre and Institute for Molecular Bioscience The University of Queensland 09:05 – 09:45 Next-­‐generation sequencing overview (Game of Thrones Edition) Dr Ken McGrath Australian Genome Research Facility Ltd, Brisbane 09:45 – 10:30 NGS mapping, errors and quality control Dr Felicity Newell Queensland University of Technology, Brisbane 10:30 – 11:00 Morning Tea 11:00 – 11:45 Mutation detection in -­‐ whole genome sequencing Dr Ann-­‐Marie Patch QIMR Berghofer Medical Research Institute, Brisbane 11:45 – 12:30 De novo genome assembly A/Professor Torsten Seemann Victorian Life Sciences Computation , Initiative The University of Melbourne 12:30 – 13:30 Lunch 13:30 – 14:30 Long-­‐read sequencing: an overview of technologies and applications Dr Mathieu Bourgey Montréal Node, McGill University and Genome Québec Innovation Centre, Canada 14:30 – 15:15 Genomics resources -­‐ feeding your inner bioinformatician A/Professor Mik Black University of Otago, Dunedin, New Zealand 15:15 – 15:45 Afternoon Tea 15:45 – 16:30 Defensive NGS informatics -­‐ what can go wrong and how do you know when to throw in the towel? Mr John Pearson QIMR Berghofer Medical Research Institute, Brisbane 16:30 – 17:15 The current and upcoming challenges and opportunities in bioinformatics Dr Annette McGrath DATA61 | CSIRO, Canberra 17:15 – 17:30 Resource talk: what the Australian Bioinformatics and Computational Biology Society can do for you Professor David Lovell, Queensland University of Technology, Brisbane 17:45 Social BBQ Venue: Auditorium foyer i TUESDAY 5 JULY 2016 NEXT GENERATION SEQUENCING & BIOINFORMATICS 09:00 – 09:45 Analysing RNA-­‐seq data: differential expression and beyond Dr Alicia Oshlack Murdoch Childrens Research Institute, Melbourne 09:45 – 10:30 MicroRNAs -­‐ sequencing, analysis ... and then what? Dr Pamela Mukhopadhyay QIMR Berghofer Medical Research Institute, Brisbane 10:30 – 11:00 Morning Tea TUESDAY 5 JULY 2016 BIOINFORMATICS METHODS, MODELS AND APPLICATIONS TO DISEASE 11:00 – 11:45 Evolution teaches protein prediction Professor Burkhard Rost Technische Universität München (TUM), Munich, Germany 11:45 – 12:45 Lunch 12:45 – 13:30 Personalised health: harnessing the power of diversity Professor Burkhard Rost Technische Universität München (TUM), Munich, Germany 13:30 -­‐ 14:15 The predictive power of machine learning techniques in data-­‐driven biomedical knowledge discovery Dr Jiangning , Song Monash University 14:15 – 15:00 Personalised medicine: d iscriminating disease-­‐causing from n eutral g enetic v ariations Professor Yaoqi Zhou Griffith University, Brisbane 15:00 – 15:30 Afternoon Tea 15:30 – 16:15 Processing, integrating and analysing chromatin immunoprecipitation followed by sequencing (ChIP-­‐seq) data Ms Alexandra Essebier, The University of Queensland 16:15 – 17:00 VariantSpark: applying -­‐ Spark based machine learning methods to genomic information Dr Denis Bauer CSIRO Health Program, Sydney 17:00 – 17:15 Resource talk: h ow QCIF enables research Ms Belinda Weaver e-­‐Research Analyst Team , Manager Queensland Cyber Infrastructure Foundation, Brisbane ii WEDNESDAY 6 JULY 2016 BIOINFORMATICS METHODS, MODELS AND APPLICATIONS TO DISEASE 09:00 – 09:45 The role of common genetic variations in complex diseases and pharmacogenomics studies Dr Siew-­‐Kee Amanda Low The University of Sydney 09:45 – 10:30 I've got my list of differentially expressed genes, now what? Dr Mirana Ramialison Australian Regenerative Medicine Institute, Monash University, Melbourne 10:30 – 11:00 Morning Tea 11:00 – 12:00 Bioinformatics software testing and quality assurance Dr Joshua W.K. Ho Victor Chang Cardiac Research , Institute Sydney 12:00 – 12:30 Panel discussion Chair: Professor Mark Ragan Institute for Molecular Bioscience, The University of Queensland *** FREE WEDNESDAY AFTERNOON *** SPECIAL ACTIVITIES IN THE AFTERNOON 12:30 – 13:00 IMB tour (1) – Limited to 50 attendees only Meeting point: Auditorium foyer 13:00 – 13:30 IMB tour (2) -­‐ If more requests are received and is also limited to 50 attendees only Meeting point: Auditorium foyer 14:00 – 17:00 Special Wednesday Afternoon Workshop An introduction to Galaxy with the NeCTAR Genomics Virtual Laboratory Dr Igor Makunin Research Computing Centre, The of University Queensland Venue: Multi Media Room (Room 3.141, access through the auditorium foyer) (This workshop is limited to 36 attendees only and is intended for bench scientists, and no previous informatics experience is needed.) What is required before attending the workshop? Remember to download Galaxy Workshop Information Sheet from the 2016 Winter School web site. http://bioinformatics.org.au/ws16/program/ iii THURSDAY 7 JULY 2016 ADVANCED BIO-­‐DATA VISUALISATION 09:00 – 10:30 Data sualisation vi in bioinformatics: exploring the ‘dark’ proteome Dr Seán O’Donoghue CSIRO, Sydney 10:30 – 11:00 Morning Tea 11:00 – 12:00 Experimentation at the interface of art and science: narrative, cognitive embodiment and alternative visual language Dr Kate Patterson , Garvan Institute of Medical Research, Sydney 12:00 – 13:00 Lunch 13:00 – 14:00 Network and data visualisation and analysis in Cytoscape Dr Melissa Davis Walter and Eliza Hall Institute for Medical Research, Melbourne 14:00 – 15:00 Big data visual analytics Professor Seok-­‐Hee Hong University of Sydney 15:00 – 15:30 Afternoon Tea 15:30 – 17:00 Creating data visualisations that won’t be forgotten using the R programming language Dr Chris Brown Australian Rivers Institute, Griffith University, Brisbane 17:00 – 17:15 Resource talk: w hat the COMBINE network does for bioinformatics ECRs in and computational b iology Ms Leah Roberts Vice President, COMBINE (Computational Biology d an Bioinformatics Student Group) School of Chemistry Molecular and Biosciences, The University of Queensland iv FRIDAY 8 JULY 2016 ECOGENOMICS 09:00 – 09:05 Welcome & introduction Professor Gene Tyson Australian Centre for Ecogenomics, The University of Queensland 09:05 – 09:45 The extraordinary evolution of the great ape microbiome Professor Howard Ochman University of Texas, Austin, USA 09:45 – 10:30 Tools and methods for microbial ecological genomics Dr David Wood Australian Centre for Ecogenomics, The University of Queensland 10:30 – 11:00 Morning Tea 11:00 – 11:45 Illuminating microbial dark matter -­‐ via single cell genomics Dr Christian Rinke Australian Centre for Ecogenomics, The University of Queensland 12:00 – 13:00 IMB Friday Noon Seminar in conjunction with Winter School Towards 4 dimensional (eco) systems biology in the sea Professor Edward F. DeLong University of Hawaii, Honolulu, USA 13:00 – 13:45 Lunch 13:45 – 14:30 Genomes from metagenomes: recovery and analysis of population genomes Dr Kate Ormerod Australian Centre for Ecogenomics, The University of Queensland 14:30 – 15:15 Community diversity in metagenomes: one, many and thousands Dr Ben Woodcroft Australian Centre for Ecogenomics, The University of Queensland 15:15 – 16:00 Comparing the variome and pan-­‐genome of bacterial isolates A/Professor Torsten Seemann Victorian Life Sciences Computation , Initiative The University of Melbourne 16:00 Winter School wrap-­‐up and refreshment with IMB/ECRs ~*~*~*~*~ v BIOGRAPHY AND ABSTRACT Dr Ken McGrath Brisbane Node Manager Australian Genome Research Facility Ltd (AGRF) Brisbane Biography: Ken McGrath is the node manager of the Brisbane Lab of the Australian Genome Research Facility, based at the UQ St Lucia campus. Ken has worked with plant and microbial genetics and transcriptomics, completed his PhD in biochemistry and molecular pathology at UQ in 2005. Following this, his postdoctoral research involved examining the transcriptomes of mixed microbial communities in industrial and agricultural settings. In 2009, Ken joined the AGRF, and currently manages a range of lab processes and sequencing projects including next-­‐generation sequencing platforms. Ken is also a founding member of the “eXtreme Microbiome Project” -­‐ an international collaboration studying microbial communities of the extreme environments around our planet. Date: Monday 4 July 2016 Presentation title: Next-­‐generation s equencing o verview (Game of Thrones Edition) Abstract: The “Next-­‐Generation Sequencing” landscape is one of constant change, with new and emerging technologies always competing with established platforms -­‐ much like the different characters and families from the “Game of Thrones” universe. Using this analogy, Ken talks about the sequencing technologies that have had their day on the throne, and looks in detail at the current rulers – and who is best positioned to usurp them. In doing so, Ken will explain how the echnologies sequencing t work and give examples of projects that can be run on them, as well as hint at what’s -­‐ “next” in Next Gen. 1 BIOGRAPHY AND ABSTRACT Dr Felicity Newell Research Fellow in Computational Biology Queensland University of Technology Brisbane Biography: Felicity Newell originally trained in the fields of molecular and cellular
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