VLSCI is funded by the Victorian Government and contributing institutions and is hosted by the University of Melbourne. This petascale facility delivers expertise and systems for life sciences computing. From 2010-2014 the first ever IBM Research Collaboratory for Life Sciences was co-located at VLSCI. CONTENTS EXECUTIVE REPORTS 06. AustrALIAN HPC AT SupercoMPUTING Steering Committee Chair’s Report ................. 6 2014 ................................................................... 52 Scientific Advisory Committee Chair’s Report 8 Director’s Report ................................................. 9 07. INTERActioNS ................................................ 54 In the news ........................................................ 58 01. VLSCI NOW ....................................................... 12 Industry Engagement....................................... 60 About the VLSCI................................................ 13 Our People ........................................................ 14 08. CAREER DevelopMENT FOR COMPUTATIONAL BioloGists .................... 62 02. 2014 SNAPSHots ........................................... 16 PhD Top-Ups, Summer Internships, UROP .... 64 Research Impact ............................................... 17 Internships 2013-2014 ..................................... 68 Collaborations ................................................... 20 Skills Development ........................................... 69 Martin Krzywinski Melbourne Tour ................. 22 MSc (Bioinformatics) Graduates ..................... 70 Evaluating Return On Investment ................... 25 VLSCI Staff Contributions to University Case Study 1: Seeking out social networks ... 26 Teaching ............................................................ 70 Case Study 2: Finding the missing links in Invited Seminars and Presentations ............... 72 Australia’s plant and fungi records ................. 28 Training Workshops .......................................... 74 Case Study 3: Modelling the vascular system Conference and Travel Grants ........................ 76 to discover patterns that lead to cardiac Sponsorships of Meetings & Conferences .... 77 disease and stroke ............................................ 30 09. Active PROJects IN 2014 ........................... 78 03. SupercoMPUTER SYsteMS ......................... 32 User Satisfaction Survey Data ......................... 35 System Usage .................................................... 38 10. GoverNANCE ................................................. 92 04. LIFE SCIENCES COMPUTATION CENTRE .... 40 11. FINANCIALS ....................................................100 LSCC Highlights ................................................ 42 Grant Account Statement ..............................103 LSCC Subscriptions .......................................... 44 University Contribution Account Statement 104 LSCC Capacity Building Projects .................... 45 GLOSSARY ......................................................105 PUBLISHING INFORMATION .......................106 05. IBM RESEARCH COLLABORAtorY FOR LIFE SCIENCES - MELBOURNE .............................. 48 grateful for the sustained involvement of Prof. Liz Sonenberg very strong endorsement from Dr Ajay Royyuru, IBM, for the establishment of the NeCTAR-funded Genomics Virtual who provided a host of valuable links and helpful feedback scope and scale of VLSCI activities to date, as documented Laboratory and the positive reception from EMBL Australia STEERING COMMITTEE from the host institution, the University of Melbourne. in the 2013 Annual Report. Dr Royyuru confirmed IBM’s of VLSCI’s expression of interest in hosting the next phase unequivocal support for the VLSCI enterprise and its future of Bioinformatics Resource Australia – EMBL. At the end Chair’s REPORT To fulfil its responsibility for reviewing all aspects of the potential within an international context. His comments of the year, this was in the final stage of negotiations and operation of the VLSCI and for providing recommendations were agreed to and endorsed by the Committee. the Committee was hopeful for a positive outcome. On behalf of the former Steering Committee (the Committee) and strategic advice to the host institution, through the of the Victorian Life Sciences Computation Initiative (VLSCI), Deputy Vice Chancellor (Research), Prof. James McCluskey, The Committee wishes to acknowledge the important At the time of writing, Prof. Taylor has resigned as VLSCI which provided advice to the University of Melbourne during the Committee met four times in 2014, in February, July, advocacy activities undertaken by several Committee Director, and returned to Europe to fulfil family and the first five years of operation of the VLSCI, from 2010 to September and December. With the official end of the initial members and Victorian University Deputy Vice-Chancellors professional commitments. The Committee wishes him well in 2014, I am pleased to commend this 2014 Annual Report. five-year grant period, the December meeting was thus the which contributed to the assurance of funding for 2015- the future and thanks him for all his fine work in building and last formal meeting of the Committee in its original form. 16 operations to sustain VLSCI in the short-term. sustaining VLSCI through its first five highly productive years. Prior to its disbandment at the end of 2014, the Committee included senior nominees from Melbourne, Monash and With a well-managed budget, relatively low levels of The extensive information assembled in support of the At the conclusion of this five years of operation, the La Trobe Universities, the Walter and Eliza Hall Institute of downtime, high levels of user satisfaction, a growing list 2015-16 funding strategy strengthened the Committee’s Committee was satisfied that the first essential stage in 6 7 Medical Research (WEHI), Melbourne Health, the National of Life Sciences Computation Centre (LSCC) subscriptions view that VLSCI is an extremely important component of securing the long-term funding for VLSCI had been reached Computational Infrastructure (NCI) and an active outreach and skills life science research infrastructure in Victoria and that its with the Victorian Government’s commitment to ongoing and IBM, in addition to the Chair development program, the main focus ongoing funding will be essential if Australia is to keep funding for 2015-16. It saw the immediate tasks ahead of the VLSCI Scientific Advisory of the Committee during 2014 was up with the fast-moving international developments in as including the establishment of a revised governance Committee (SAC) Prof. Tony Bacic, on achieving long-term sustainability life sciences computing, emerging developments in structure reflecting the new stakeholder arrangements. who joined as incoming SAC Chair in for VLSCI. The Business Plan 2014 personalised medicine and the opportunities provided early 2014, and the VLSCI Director, identified the tasks involved, with by a rejuvenated biotechnology sector. The Committee I have greatly appreciated the opportunity to be Prof. Peter Taylor. The Committee was an important challenge being urged the University and the VLSCI management team to associated with the rollout of this important piece of pleased, at the start of the year, to achievement of firm commitments continue their high-level discussions with partner institutions Australian research infrastructure and I am sure that welcome the addition of a nominee from existing and potential new and stakeholders in order to progress the formulation all past members of this Committee will be looking from the Victorian Comprehensive stakeholders for cash contributions of an agreed sustainability strategy beyond 2015-16. forward to watching the future success of VLSCI. Cancer Centre, Prof. David Bowtell to VLSCI operations through 2015- of the Peter MacCallum Cancer 16 as the essential foundation for The Committee considered that LSCC activities are Centre. At its July meeting, the development of a long-term funding key to the case for VLSCI funding as part of the long- Committee thanked retiring member, Dr Mark Kosten of strategy, including through demonstration of the key role of term national research infrastructure. It was particularly La Trobe University, and welcomed Prof. Brian Smith as his VLSCI in the overall national research infrastructure strategy. impressed by the example set by successful projects such John W. Zillman AO FAA FTSE replacement at the September meeting. The Committee was At its July meeting, the Committee was pleased to receive as the partnership with the University of Queensland in the VICTORIAN LIFE SCIENCES COMPUTATION INITIATIVE ANNUAL REPORT 2014 VICTORIAN LIFE SCIENCES COMPUTATION INITIATIVE ANNUAL REPORT 2014 of VLSCI in relation to the national policy framework. With the strategic focus for VLSCI being one of ongoing SCIENTIFIC ADVISORY sustainability, the Committee directed its efforts on discussing the future requirements in life sciences computing, noting that Director’s REPORT COMMITTEE all governments will be wanting to address policy problems It is my pleasure to commend to you my fifth VLSCI Annual in agri-food production systems and infectious diseases Chair’s REPORT Report. The growth of the enterprise continues to display arising out of economic, demographic and climate pressures. its success: starting with 62 projects with 241 people Given that all solutions to these issues require some form The SAC