Presentations and Reports

2022

Public Seminars

    • Bernard Pope, Jeff Christiansen. Lessons learnt (so far) in building a human genomics data commons, Enabling Openness in Australian Stem Cell Research (EOAR) seminar, Melbourne, 25 April 2022
    • Bernard Pope, Marie Wong-Erasmus, Kamile Taouk, Oliver Hofmann. Establishing Gen3 to enable better human genome data sharing in Australia, Australian BioCommons webinar, Melbourne, 17 February 2022

Conference Presentations

    • Andrew Lonie, Jeff Christiansen, Tiff Nelson, Johan Gustafsson, Nigel Ward, Steven Manos, Bernard Pope, Christina Hall. Australian BioCommons, Bioplatforms Australia 2022 All Hands Meeting, Sydney, 19 October 2022
    • Kylie Davies, Jessica Holliday, Bernard Pope. Importance of requirements elicitation and analysis for successful projects: a case study from the Human Genomes Platform Project, eResearch Australasia 2022 Conference, Brisbane, 19 October 2022
    • Bernard Pope, Chris Hovens, Anis Hamid, Niall Corcoran. Harmonised PPCG Clinical Data, Pan Prostate Cancer Group Annual Meeting, Italy, 11 October 2022
    • Bernard Pope, Gahee Park, Edmund Lau, Chris Hovens, Niall Corcoran, Charlie Massie. Detecting circulating tumour DNA in localised prostate cancer, Pan Prostate Cancer Group Annual Meeting, Italy, 11 October 2022

Poster Presentations

    • Marion Shadbolt, Tiffany Boughtwood, Jeff Christiansen, Joe Copty, Mark Cowley, Kylie Davies, Matthew Downton, Kelsey Druken, Ben Evans, Clara Gaff, Andrew Gilbert, Christina Hall, Matthew Hobbs, Oliver Hofmann, Jessica Holliday, Warren Kaplan, Ross Koufariotis, Sarah Kummerfeld, Conrad Leonard, Angela Lin, Andrew Lonie, Heath Marks, Siobhann McCafferty, David Monro, Andrew Patterson, John Pearson, Bernard Pope, Shyamsundar Ravishankar, Florian Reisinger, Andrew Robinson, Victor San Kho Lin, John Scullen, Mustafa Syed, Kamile Taouk, Andrew Treloar, Jingbo Wang, Marie Wong-Erasmus, Scott Wood. Enhancing Australia’s capability for secure and responsible sharing of human genomics research data, The Australian Bioinformatics and Computational Biology Society (ABACBS) 2022 National Conference, Melbourne, 30 November 2022
    • Marion Shadbolt, Tiffany Boughtwood, Jeff Christiansen, Joe Copty, Mark Cowley, Kylie Davies, Matthew Downton, Kelsey Druken, Ben Evans, Clara Gaff, Andrew Gilbert, Christina Hall, Oliver Hofmann, Jessica Holliday, Warren Kaplan, Ross Koufariotis, Sarah Kummerfeld, Conrad Leonard, Angela Lin, Andrew Lonie, Heath Marks, Siobhann McCafferty, David Monro, Andrew Patterson, John Pearson, Bernard Pope, Shyamsundar Ravishankar, Florian Reisinger, Andrew Robinson, Victor San Kho Lin, John Scullen, Mustafa Syed, Kamile Taouk, Andrew Treloar, Jingbo Wang, Marie Wong-Erasmus, Scott Wood. Enhancing Australia’s capability for secure and responsible sharing of human genome research data: The Human Genomes Platform Project, eResearch Australasia 2022 Conference, Brisbane, 19 October 2022. Winner of best poster award.
    • Marion Shadbolt, Tiffany Boughtwood, Jeff Christiansen, Joe Copty, Mark Cowley, Kylie Davies, Matthew Downton, Kelsey Druken, Ben Evans, Clara Gaff, Andrew Gilbert, Christina Hall, Oliver Hofmann, Jessica Holliday, Warren Kaplan, Ross Koufariotis, Sarah Kummerfeld, Conrad Leonard, Angela Lin, Andrew Lonie, Heath Marks, Siobhann McCafferty, David Monro, Andrew Patterson, John Pearson, Bernard Pope, Shyamsundar Ravishankar, Florian Reisinger, Andrew Robinson, Victor San Kho Lin, John Scullen, Mustafa Syed, Kamile Taouk, Andrew Treloar, Jingbo Wang, Marie Wong-Erasmus, Scott Wood. National and international collaboration to facilitate human genomics data sharing in Australia: The Human Genomes Platform Project, ELIXIR All Hands 2022, Netherlands, 8 June 2022

Other

    • Patrick Carnuccio, Mark Cowley, Kylie Davies, Kelsey Druken, Jessica Holliday, Sarah Kummerfeld, David Monro, Andrew Patterson, John Pearson, Bernie Pope, John Scullen, Marion Shadbolt, Marie Wong-Erasmus, Scott Wood. Human Genomes Platform Project: DAC Automation Discovery Phase Report, Human Genomes Platform Project, 15 June 2022, https://doi.org/10.5281/zenodo.6644049
    • Patrick Carnuccio, Mark Cowley, Kylie Davies, Matthew Downton, Biljana Dumevska, Jessica Holliday, Sarah Kummerfeld, Angela Lin, David Monro, Andrew Patterson, Bernie Pope, Shyamsunder Ravishankar, Andrew Robinson, John Scullen, Marion Shadbolt, Mustafa Syed, Scott Wood, Marie Wong-Erasmus. Human Genomes Platform Project: Federated Identity and Access Management (IAM) Discovery Phase Report, Human Genomes Platform Project, 15 June 2022, https://doi.org/10.5281/zenodo.6644008
    • Cowley, Mark; Downton, Matthew; Holliday, Jessica; Kummerfeld, Sarah; Leonard, Conrad; Lin, Angela; Pope, Bernard; San Kho Lin, Victor; Ravishankar, Shyamsunder; Shadbolt, Marion; Syed, Mustafa; Taouk, Kamile; Wong-Erasmus, Marie. Human Genomes Platform Project: Virtual Cohort Assembly Discovery Phase Report: National Community Needs & Candidate Solutions, Human Genomes Platform Project, 15 Dec 2022, https://doi.org/10.5281/zenodo.7439885

2021

Invited Speaker Presentations

    • Bernard Pope. Detecting circulating tumour DNA in localized prostate cancer, University of Melbourne Centre for Cancer Research (UMCCR) seminar series, 28 July 2021
    • Bernard Pope and Jessica Holliday. Human Genomes Platform Project: A flagship project within Australian BioCommons’ Human Genome Informatics Initiative. eResearch Australasia, October 2021
    • Bernard Pope. Global technologies and standards for sharing human genomics research data. ARDC Project Exchange. March 2021
    • Bernard Pope. Research Computing Services Usage, Research Computing Services Cultural Working Group, series on researchers who use RCS, The University of Melbourne, 25 June 2021.
    • Jess Holliday. Human Genomes Platform Project. Invited to present the project to the AAF Board, 27 October 2021.

Conference Presentations

    • Nuwan Goonasekera, Michael D’Silva, Frankie Stevens, Gareth Price. Galaxy CloudStor Integration – linking national resources for secure data transfer between services. Galaxy Community Conference (GCC 2021).
    • Johan Gustafsson, Gareth Price, Nigel Ward. Community engagement and how it influences Galaxy Australia Innovation. Galaxy Community Conference (GCC 2021).
    • Simon Gladman, Gareth Price, Catherine Bromhead, Nicholas Rhodes, Steven Manos, Nigel Ward, Andrew Lonie. Galaxy Australia – the influx state of a national eResearch service. Galaxy Community Conference (GCC 2021).
    • Steve Quenette, Ai Lin Soo, Rhys Francis, Carina Kemp, Adrian Burton, Carmel Walsh, Max Wilkinson. Supporting data life cycles at the macro scale. eResearch Australasia 2021.
    • Melissa Burke, Jeff Christiansen, Christina Hall. Maximising the potential of training materials through FAIRification. eResearch Australasia 2021.
    • Gareth Price, Simon Gladman, Nigel Ward, Steven Manos, Rhys Francis, Andrew Lonie. Galaxy Australia – a strengthened national life science service that engages globally. eResearch Australasia 2021.
    • Tracy Chew, Georgina Samaha, Johan Gustafsson, Sarah Beecroft, Marco De La Pierre, Nigel Ward, Rosemarie Sadsad. Scalable bioinformatics workflows for growing ‘-omics’ datasets on National Collaborative Research Infrastructure Strategy Facilities. eResearch Australasia 2021.
    • Tiff Nelson, Jeff Christiansen, Justin Lee, Gareth Price, Nick Rhodes, Madeline Bassetti, Alejandro Bulgaris, Michael W C Thang, Cameron Hyde, Mark Gray, Melissa Burke, Christina Hall, Brian Davis, Steven Manos, Andrew Lonie, Nigel Ward, Dominique Gorse. The Australian Apollo Service – establishing a national service – the process that got us there. eResearch Australasia 2021.
    • Johan Gustafsson, Jeffrey Christiansen, Tiffanie Nelson, Nigel Ward, Dale Roberts, Brian Davis, Marco De La Pierre, Tracy Chew, Dominique Gorse, Gareth Price, Andrew Lonie. Australian BioCommons ToolFinder: discovery of bioinformatics software in an Australian infrastructure context. eResearch Australasia 2021.
    • Johan Gustafsson, Jeff Christiansen, ACFM (Australian Core MS Facilities Meeting) – an ANZSMS Satellite Meeting.
    • Tiff Nelson, Johan Gustafsson, Julia Voelker, Matt Padula, Hardip Patel. Community: Engagement to Outputs. Australian BioCommons 2021 Showcase.
    • Christina Hall, Melissa Burke, Deanna Deveson, Celia van Gelder. Outreach, collaboration & skills development. Australian BioCommons 2021 Showcase.
    • Andrew Lonie, Corinne Martin, Frederik Coppens, Jen Harrow, Jack DiGiovanna. International linkages in building life science computational infrastructure. Australian BioCommons 2021 Showcase.
    • Sarah Richmond, Joanna Day, Gareth Price, Anna Syme. Assembling reference genomes for Australian species. Australian BioCommons 2021 Showcase.
    • Rhys Francis, Tiff Nelson, Nigel Ward, StevenManos, Gareth Price, Simon Gladman, Anna Syme, Sarah Richmond, Sean Smith. Partnerships. Australian BioCommons 2021 Showcase.
    • Steven Manos, Carmel Walsh, Ryan Fraser, Mark Gray, Sarah Nisbet, Dan Oxnam. Developing a “BioCloud”. Australian BioCommons 2021 Showcase.
    • Rosemarie Sadsad, Tracy Chew, Dale Roberts, Georgina Samah, Johan Gustafsson. Successes and challenges deploying bioinformatics workflows on Australian high performance computers. Australian BioCommons 2021 Showcase.
    • Bernie Pope, Mark Cowley, John Scullen, Peter Meikle. Human genomics data sharing: are we FAIR yet? Australian BioCommons 2021 Showcase.
    • N Goonasekera, A Mahmoud, L Sargent et al. Galaxy Helm Chart v4 – A single stack for dev, testing, and production. Galaxy Community Conference 2021.
    • Chol-hee Jung. Mitochondria Analysis. Pan Prostate Cancer Group Technical meeting September 2021.
    • Khalid Mahmood. Classifying polymerase gene variants by incorporating tumour sequencing data – GECCO Tumor Working Group 2021.
    • Khalid Mahmood. Genetic landscape of early-onset colorectal cancer – Familial Aspects of Cancer 2021.
    • Khalid Mahmood. Germline and somatic landscape of mismatch-repair proficient early-onset colorectal cancer – European Hereditary Tumour Group 2021.

Poster Presentations

    • Sarah Cain, Bernard Pope, Stefano Mangiola, Kate Drummond. Somatic Mutations and Copy Number Alterations in Recurrent Meningioma. Neurological Society of Australasia Annual Scientific Meeting September 2021.
    • Anna Syme, Jeff Christiansen, Nigel Ward, Simon Gladman, Catherine Bromhead, Igor Makunin, Mike Thang, Gareth Price, Andrew Lonie. Driving workforce transition in Australian life science research. Galaxy Community Conference GCC 2021.
    • Nicholas Rhodes, Catherine Bromhead, Gareth Price, Simon Gladman. Galaxy Australia – an ongoing resourcing journey. Galaxy Community Conference GCC 2021.
    • Catherine Bromhead, Thom Cuddihy, Simon Gladman. Galaxy Australia’s automatic tool installation, updates and tests: A public repo. Galaxy Community Conference GCC 2021.
    • Tiffanie M. Nelson, Catherine Bromhead, Melissa Burke, Simon Gladman, Johan Gustafsson, Mark Gray, Dominique Gorse, Christina Hall, Justin Lee, Steven Manos, Igor Makunin, Gareth Price, Audrey Stott, Michael Thang, Nigel Ward, Jeffrey H. Christiansen, Andrew Lonie. Robust public computational services supporting Genome Assembly and Annotation for Australian Researchers. GSA 2021.
    • Gareth Price , Simon Gladman, Tiffanie Nelson, Jeff Christiansen, Nigel Ward, Steven Manos, Rhys Francis, Andrew Lonie. Galaxy Australia – an analytical open-source service for Life Science. 2021 OZSingleCells – Brisbane meeting.

Other

    • Paula Andrea Martinez, Vanessa Crosby, Tom Honeyman, Johan Gustafsson, Stéphane Guillou, Louis Moresi. Report: Data is Only Half the Battle. eResearch Australasia Conference 2021, Australia. Zenodo. https://doi.org/10.5281/zenodo.5637353
2020
    • Jihoon E. Joo, Mark Clendenning, Khalid Mahmood, Christophe Rosty, Ingrid M. Winship, Mark A. Jenkins, Daniel D. Buchanan. Tumor microbiome in subtypes of mismatch repair-deficient colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL.
    • Bernard J. Pope. Somatic variant calling in whole genome sequencing, opportunities, challenges and solutions, Monash Partners Comprehensive Cancer Consortium, Tech Talks series, 20 November 2020.
    • Bernard J. Pope. Best practices for bioinformatics command-line software with Bionitio, Australian Bioinformatics and Computational Biology Society (ABACBS) Conference, 24 November 2020.
    • Bernard J. Pope. Detection of ctDNA in Plasma of Patients with Clinically Localised Prostate Cancer is Associated with Rapid Disease Progression, Victorian Cancer Bionformatics Symposium, 2020, 28 October 2020.
    • Bernard J. Pope. Bionitio: building better bioinformatics tools with batteries included (workshop), Bioinformatics Community Conference 2020 (online, international), 18 June 2020.
    • Bernard J. Pope. Bionitio – building better bioinformatics tools (with batteries included), Australian BioCommons webinar, 20 January 2020.
2019
    • Michael Franklin, Richard Lupat, Jiaan Yu, Evan Thomas, Daniel Park, Bernard Pope, Tony Papenfuss, Jason Li. Janis: A Python framework for Portable Pipelines, Australian Bioinformatics and Computational Biology Society annual conference, Sydney, Australia, December 2019.
    • Richard Lupat, Michael Franklin, Bernard Pope, Daniel Park, Evan Thomas, Mohammad Bhuyan, Tony Papenfuss, Jason Li. Janis: An open source tool to machine generate type-safe CWL and WDL workflows, BOSC COSI: Bioinformatics Open Source Conference, Basel, Switzerland, July 2019.
    •  Chol-Hee Jung, Khalid Mahmood, Bernard J. Pope, Daniel J. Park. Revisiting the frequency of sex-chromosome abnormality using DNA methylation profiles from public datasets, Australasian Genomic Technologies Association Conference, Sunshine Coast, Australia, 2019.
    • Michael Franklin, Richard Lupat, Jiaan Yu, Evan Thomas, Daniel Park, Bernie Pope, Jason Li. Portable variant-calling pipelines for cancer, Victorian Cancer Bioinformatics Symposium, Victorian Comprehensive Cancer Centre, Melbourne, Australia, 2019.