THE MICROSCOPE FOR 21ST CENTURY DISCOVERY: MASSIVE & CAVE2 PROFESSOR PAUL BONNINGTON, DIRECTOR OF E-RESEARCH CENTRE, MONASH UNIVERSITY AND DR WOJTEK GOSCINSKI, MANAGER, HIGH PERFORMANCE COMPUTING OF E-RESEARCH CENTRE, MONASH UNIVERSITY DR PAUL MCINTOSH, TECHNICAL LEAD, MASSIVE
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SHARE IMAGING LOCUS T N E M INSIGHT E G Lens A N CAVE2 DIGITAL A IMMERSIVE SCIENTIFIC VISUALISATION DESKTOPS M A T A ANALYSIS D Filters MONASH MASSIVE RESEARCH CLOUD CAPTURE Light Source, Samples MONASH AUSTRALIAN BIOMEDICAL RAMACCIOTTI SYNCH IMAGING CRYOEM 3
Ranked in top 0.5% of universities worldwide
Clayton: imaging precinct Globally unique imaging infrastructure - from an atom to a whole animal ▪ Imaging and Medical Beamline (Synchrotron) ▪ X-ray diffraction beamline (Synchrotron) ▪ Monash Biomedical Imaging ▪ Monash Centre for Electron Microscopy ▪ Monash Micro Imaging ▪ Cryo-Electron Microscope
Monash-NVIDIA An Australian node of the NVIDIA Singapore Technology Centre With a focus on medical imaging, robotic vision and smart cities
SHARE IMAGING LOCUS T N E M INSIGHT E G Lens A N CAVE2 DIGITAL A IMMERSIVE SCIENTIFIC VISUALISATION DESKTOPS M A T A ANALYSIS D Filters MONASH MASSIVE RESEARCH CLOUD CAPTURE Light Source, Samples MONASH AUSTRALIAN BIOMEDICAL RAMACCIOTTI SYNCH IMAGING CRYOEM 7
MASSIVE HPC for Characterisation Specialised Facility for Imaging and Visualisation Partners ¡ HPC ¡ Instrument Integration ¡ Monash University 150 active projects 500+ user accounts Australian Synchrotron Integrating with key Australian 100+ institutions across Australia CSIRO Instrument Facilities. Early numbers from 5 Synchrotron Interactive Vis ¡ Beamlines. ¡ Affiliate Partners ¡ 200+ users ARC Centre of Excellence in 166 merit allocated projects Integrative Brain Function 725 users ARC Centre of Excellence in Advanced Molecular Imaging Large cohort of researchers new to HPC ¡
M1 and M2 M1 at Australian M2 at Monash ‣ 20 nodes with 16 cores per node Synchrotron ¡ University running at 2.66GHz - 128 GB RAM per node (2,560 GB RAM total) 42 nodes (504 CPU-cores total) in 118 nodes (1,720 CPU-cores total) in one configuration: four configurations: 264 GPUs & co-processors ‣ 12 cores per node running at ‣ 76 NVIDIA K20 GPU- ‣ 32 nodes with 12 cores per node 2.66GHz coprocessors ‣ 48 GB RAM per node (2,016 GB running at 2.66GHz ‣ 20 NVIDIA M2070Q’s (Vis) - 48 GB RAM per node (1,536 GB RAM total) ‣ 148 NVIDIA M2070’s GPU- ‣ 2 nVidia M2070 GPUs with 6GB RAM total) coprocessors ‣ 10 nodes with 12 cores per node GDDR5 per node (84 GPUs total) ‣ 20 Intel Phi’s (1200 cores) (visualisation / high memory 153 TB of fast access parallel file configuration) 345 TB of fast access parallel file - 192 GB RAM per node (1,920 GB system system RAM total) ‣ 56 nodes with 16 cores per node 4x QDR Infiniband Interconnect 4x QDR Infiniband Interconnect running at 2.66GHz - 64 GB RAM per node (3,584 GB RAM total)
M3 M3 at Monash University A Computer for Next-Generation Data Science 1,700 Intel Haswell CPU-cores Alan Finkel Australia’s Chief Scientist 48 NVIDIA Tesla K80 GPU coprocessors for data processing and high end visualisation 8 NVIDIA Grid K1 GPUs for medium and low end visualisation that will support up to 16 users concurrently A 1.15 petabyte Lustre parallel file system 100 Gb/s Ethernet Mellanox Spectrum Supplied by Dell, Mellanox and NVIDIA Steve Oberlin, Chief Technology Officer Accelerated Computing, NVIDIA
* Australian*Synchrotron* * * Monash*University* * Infrared' MX' IMBL' Monash' Lab'for' Biomedical' Dynamic' CryoEM' XGray' Imaging' Imaging' ' absorp1on ' PD' SAXS' spectrosc WAXS' opy' Characterisa1on' MASSIVE' Virtual'Laboratory' * * Cloud' HPC' Desktop' Integration Key Australian Instruments Atom' Integrated with MASSIVE Monash'Micro' CT'|'PET'|' MicroCT' Probe' Imaging' MRI''' Australian*Characterisa/on** Council*
Fouras et al 4D rabbit pup lungs imaged at Australian Synchrotron, reconstructed and visualized on MASSIVE
Fouras et al 4D rabbit pup lungs imaged at Australian Synchrotron, reconstructed and visualized on MASSIVE
Fouras et al 4D rabbit pup lungs imaged at Australian Synchrotron, reconstructed and visualized on MASSIVE
BREATHING LIFE INTO PRETERM INFANT RESEARCH
CT Performance NVIDIA K20 CSIRO XTRACT / XLI on MASSIVE 4K - CT Wizard 2K - CT Wizard 35 12 30 10 25 8 Time (minutes) Time (minutes) 20 15 mins 6 15 4 2 mins 10 2 5 0 0 0 12 24 36 48 60 72 84 96 108 120 132 144 24 36 48 60 72 84 96 108 120 132 144 156 168 180 192 204 216 228 240 252 Cores Cores MASSIVE MASSIVE
Hardware Layer Integration User view Remote Desktop with Australian Synch credentials Systems View
Long tail users and impact User publications accepted or published, Agricultural and Research undertaken Veterinary Sciences 2% as reported in Project Leader Reports using massive Earth Sciences Medical and through beamline 18% 260 MASSIVE underpins a Health Sciences 11% wide range of research 240 access at Australian across the partners and 220 Synchrotron nationally. This graph 218 Number of publications 200 shows the aggregate 180 Physical publications in 2012, Life 160 Sciences Chemical 2013 and 2014 across Biological 160 Sciences Sciences 140 and Eng. Sciences 35% MASSIVE projects, as 17% 120 reported in annual 100 Project Leader Reports. 80 Environmental 74 60 Sciences 6% Physical 40 Sciences 1% 20 Engineering 0 4% Other 6% 2012 2013 2014
SHARE IMAGING LOCUS T N E M INSIGHT E G Lens A N CAVE2 DIGITAL A IMMERSIVE SCIENTIFIC VISUALISATION DESKTOPS M A T A ANALYSIS D Filters MONASH MASSIVE RESEARCH CLOUD CAPTURE Light Source, Samples MONASH AUSTRALIAN BIOMEDICAL RAMACCIOTTI SYNCH IMAGING CRYOEM 19
perforin a drug candidate for improving transplant success
Perforin Data Sources
These data were merged and processed using XDS 31 , POINTLESS and SCALA 32 . Five per cent of the data sets were flagged as a validation set for calculation of the R free with neither a σ nor a low-resolution cut-off applied to the data. Experimental phases (Supplementary Table 1) were obtained by the MIRAS method; a native (Native1) data set and three heavy atom derivatives (ethylmercury phosphate, ammonium hexachloroiridate(iii) and iodine) were used for phasing. Experimental phasing was carried out using autoSHARP 33 ; heavy atom positions were located using SHELXC/SHELXD 34 and refined using SHARP 35 with resulting isomorphous (acentric) and anomalous phasing powers of 0.982 and 0.950, respectively. The initial phases were improved by solvent flipping using SOLOMON 36 and density modification using DM 37 , which dramatically increased the figure of merit (FOM) from 0.34 to 0.86. Such a large increase in FOM is probably due to the very high solvent content of the crystal (70.2%). One molecule was found per asymmetric unit and an initial model was generated using BUCCANEER 38 . Model building was performed using COOT 39 while refinement was performed using PHENIX 40 , REFMAC 41 and … The NAG model was made using the PRODRG server (http://davapc1.bioch.dundee.ac.uk/prodrg/). The final model also contains three glycerols, two chloride ions and four iodide ions. Crystallographic and structural analysis was performed using CCP4 suite 43 , WHATIF 44 and MUSTANG 45 unless otherwise specified. Figs 1, 2, 3, 4 and Supplementary Figs 2, 4, 5, 6 and 11 were generated in part using PYMOL 46 . Structural validation was performed using MolProbity 47 . In the final structure, two residues (L307 and Y486) are in disallowed regions in the Ramachandran plot. The MolProbity score is 1.56, which is in the 100th percentile of structures reported at this resolution. A summary of diffraction and refinement statistics can be found in Supplementary Table 1. The coordinates of perforin, together with the structure factors are deposited in the Protein Data Bank . All diffraction images are deposited in TARDIS (http://tardis.edu.au/) and are freely available.
Scientific Desktops NeCTAR Characterisation Virtual Laboratory Domain-specific Environments for Science Tailored “workspaces” - tools for scientific data processing available on the Australian research cloud to all CryoEM CryoEM ! CT | PET | MRI ! CT | PET | MRI ANU ANU MicroCT MicroCT ! Atom Probe ! Atom Probe Light Micros. Light Micros. ! Australian researchers Daris MyTardis, MyTardis AMMRF DF Underpinning fast & large CCP, Chimera, CAW, Crystallography, EMAN, ImageJ, parallel FS EFFOFF, Fourier 3D Slicer, AFNI / IMAGIC, IMOD, Transform 3D & 4D, MRF, NN, POSminus, SUMA, Diffusion Phenix, Pymol, Pos to Obj Export, Rdf- TK, FSL, MINC Relion, ShelXle, kd, SDM-1D-calculate, Slider, TiltPicker, Tools, MRICRON, Accelerated rendering SDM-2D-calculate, Trackvis VMD, XMIPP Mango XRNG Editor (NVIDIA K20, K80 and K1 UQueensland ANU MonashU USydney GPUs)
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