Enhancing Collaborative Research and Development with High Definition Video Conference David Abramson ARC Professorial Fellow Faculty of Information Technology, Monash University AUSTRALIA With special thanks to APAN (JB) and AARnet
Nâng cao kh ả n ă ng h ợ p tác nghiên c ứ u và phát tri ể n s ử d ụ ng h ộ i ngh ị truy ề n hình độ phân gi ả i cao David Abramson ARC Professorial Fellow Faculty of Information Technology, Monash University AUSTRALIA With special thanks to APAN (JB) and AARnet
Outline • A new kind of Science … – In Silico Science • Making the World a Little Bit Smaller – Video conferencing • International Engagement through student internships – PRIME & MURPA • Where to?
What to do if you get bored? traceroute to www.monash.edu.au (130.194.11.149), 64 hops max, 40 byte packets 1 110.35.69.1 (110.35.69.1) 13.303 ms 14.961 ms 7.692 ms 2 119.18.142.150 (119.18.142.150) 7.855 ms 8.872 ms 9.784 ms 3 hk-so-03-v4.bb.tein3.net (202.179.241.65) 42.249 ms 48.667 ms 35.950 ms 4 sg-so-01-v4.bb.tein3.net (202.179.241.58) 58.694 ms 82.945 ms 60.095 ms 5 au-pr-v4.bb.tein3.net (202.179.249.62) 60.431 ms 109.873 ms 59.437 ms 6 so-3-2-0.bb1.a.per.aarnet.net.au (202.158.194.145) 105.864 ms 105.786 ms 116.318 ms 7 so-0-1-0.bb1.a.adl.aarnet.net.au (202.158.194.6) 136.263 ms 136.234 ms 137.182 ms 8 so-0-1-0.bb1.a.mel.aarnet.net.au (202.158.194.18) 148.816 ms 183.012 ms 144.980 ms 9 ge-0-0-0.bb1.b.mel.aarnet.net.au (202.158.194.182) 143.332 ms 142.210 ms 143.043 ms 10 tengigabitethernet2-1.er2.monash.cpe.aarnet.net.au (202.158.200.98) 144.283 ms 150.029 ms * 11 gw1.er2.monash.cpe.aarnet.net.au (202.158.200.150) 175.673 ms 173.473 ms 149.983 ms 12 drc0-gw-v592.net.monash.edu.au (130.194.29.149) 153.726 ms 145.303 ms 143.066 ms 13 drc1-gw-t6-4.net.monash.edu.au (130.194.28.149) 142.982 ms 143.015 ms 142.685 ms
IN SILICO SCIENCE
In Vivo, In Vitro, In Silico • Systems Biology – Human Genome Project, Protein function, Virtual Physiological Human, Blue Brain, … • Engineering – Aerospace, civilian, automotive, domestic, … • Environment – Climate, weather, pollution, …. – Chemistry • Drug design, novel pathways, … • Physics – Particle Physics, Xray treatment, Astrophysics, ….
Cardiac Modelling Sher, Gavaghan, Rodriguez, Oxford Mcculloch, Mihaylova, Kerckhoffs, UCSD • Heart disease still leading cause of death • Understanding the underlying physiological mechanisms is cheaper and faster when experimental studies are performed together with mathematical models & computer simulations • Studying pathologies • Developing & Testing drugs
Looking at heart failure? • Leading Causes of HF Include: Normal Ventricular – High blood pressure Rhythm Fibrillation Heart Cross Section – Myocardial Infarctions – Mitral valve disorders – Conduction disorders • Revelli studied – Left Bundle Branch Block – Effects 25% of all HF patients – Increases risk of sudden death considerably • Dan Stokeley studied *Diagram 2 – Long QT Diagram 2- : http://www.healthsystem.virginia.edu/Internet/afibcenter/whatis_afib.cfm Courtesy Scott Revelli, PRIME student
Cardiac Modeling • Mathematical models – Whole organ simulation – Ion movement in single cells – Cardiac mechanics – Fluid flow Movie: Courtesy Andrew McCulluch, UCSD
Astro-physics Daniel Price, Monash University
MAKING THE WORLD A LITTLE SMALLER
Use of Video conference technology (Turn of the century)
HD Video Seminar Room I’ve participated in numerous video conferences to date but nothing like this. The quality was so high that the experience was almost as if we were all in the same room. The massively increased bandwidth was transformational. Quantity begat quality. Alan Finkel, Chancellor, Monash Univ
Monash Brass Ensemble
INTERNATIONAL ENGAGEMENT THROUGH STUDENT INTERNSHIPS
PRIME @ Monash • Engaged in PRIME since 2004 • Projects range from bio-engineering, theoretical chemistry to computer science • Has underpinned long lasting academic collaborations – Publications – Presentations at conferences • Undergraduate students without research experience!
PRIME @ Monash: Nearly always a PRIME number! Melissa DiCiero-Monash
PRIME @ Monash • Projects usually involve application of our software (Nimrod) to an interesting application • Leverage investment in PRAGMA infrastructure
PRIME Projects – Monash 2008 • Analyzing Adverse Effects of the Antidepressant Emsam in Silico, Haley-Hunter Zinck • Binding Energy and Mechanisms of Conjugated Enediynes with a Ruthenium complex, Lynn Tai • Modeling Calcium Ion Transients in the Sarcoplasmic Reticulum, Arielle Yablonovitch • Effects of Tissue Level Parameter Variation on Cardiac Output, Randy Lee • Transmural Heterogeneity of Mechanics in the Normal Heart, M. Amalia Prada Fernandez • Medical Research Data Visualization on Tiled Display Wall, Sirvard Nshanyan • Simulation of Particle Incorporation during Electrocodeposition Process, David Allen Wong
Lead placement for CRT Revelli, Kirchoffs, UCSD • Study left bundle branch block • Determine the optimal pacing sites for CRT • 2 or 3 leads are inserted into the heart • Challenges: – Placing the leads – Scar tissue effects pacing
PRIME embedded in local events
MURPA @ UCSD • A research oriented ‘summer mode’ undergraduate subject that allows students to complete a research project abroad; • Collaborative research between Monash academics and peers overseas; • A video conference based seminar stream that imports real time presentations from leading international researchers;
MURPA 2008-9 • Hoang Nguyen: – Kepler interface to Optiportal – Ilkay Altintas, UCSD • Mr. Peter Serwylo: – Urban image manipulation – Jurgen Schultz, UCSD • Nicholas Barnes: – Parallel computation of biomechanics problems – Roy Kerckhoffs, UCSD • Aimee Li: – Virtual screening for inhibitors against avian flu – Wilfred Li, UCSD
MURPA 2009-10 • Aisa Na’im: – Data quality assurance in scientific workflows – Ilkay Altintas UCSD, Maria Indrawan Monash • Jonathan McClure – Mining for Bullet Clusters in Galaxies – Mike Norman UCSD, Ann Nicholson Monash • Andrew Paterson – Interactively Visualising Density Fields – Jurgen Schulze UCSD, Daniel Price Monash • Ben Morgan – Visualization of tensor data in cardiac models – Roy Kerckhoffs UCSD, David Abramson Monash
Astro-physics in the Star Cave Andrew Paterson, Monash
Applying Video Conference Technology MURPA SEMINAR SERIES
MURPA Lectures 2008 Mark Ellisman Integrating Neuroscience Knowledge: Brain Research in the Digital Age Larry Smarr CAMERA: Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis Ilkay Altintas On Accelerating Scientific Discovery using Scientific Workflows and the Kepler System, Jurgen Schulze Visualization, Wilfred Li Avian Flu Modeling, Andrew McCulloch Cardiac modeling, Kim Baldridge Quantum Chemistry
MURPA Lectures 2009 Peter Arzberger Benefiting Society through Information Technology: Why Changes in Education are Needed Fran Berman Harnessing the Data Deluge Ilkay Altintas On Basics of Using Workflows for Scientific Exploration and the Kepler System Roy Kerckhoffs Multi Scale Modelling of the Cardio System Cindy Zheng Introduction to PRAGMA Grid Wilfed Li Machine Learning Approaches in Avian Flu Drug Discovery Phil Papadopoulos User-defined Clusters - Introduction to the Rocks Cluster Toolkit : Merging Clouds and Clusters Mike Norman Exploring OptIPortals as Petascale Simulation End Stations Larry Smarr Can a Greener Internet Help Us Moderate Climate Change? Jurgen Schulze Immersive Virtual Reality Research at Calit2
MURPA Lectures 2010 Nancy Wilkins-Diehr Science Gateways and their tremendous potential for Science and Engineering Jurgen Schulze Latest Developments in Virtual Reality at Calit2 Ania Sher Mathematical models of cardiac muscle cells: Predicting drug- induced arrhythmias. Robert Konecny Multiscale Modeling of Proteins Phil Papadopolous Extending Rocks Clusters into Amazon EC2 Using Condor Wilfred Li Workflows for Computer Aided Drug Discovery: New Twitter for the Old Problem Philip Bourne New Modes of Scholarly Communication Mike Norman Gordon: A New Kind of Supercomputer for Data-Intensive Applications Larry Smarr Global Climatic Disruption and its Impact on Victoria and California Sameer Tilak Cyberinfrastructure for Large-Scale Environmental Observing Systems
2009 Student Seminars UCSD -> Monash
2010 3 Way HD – AU/UCSD/JAPAN
PRIME seminars Monash -> UCSD
What are we doing next? • Adding new MURPA partners – National Centre for Supercomputing Applications (NCSA) @ UIUC (US) – Warwick University (UK) – Technion (Israel)
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