1 peter sloot: computational science, university of amsterdam. interactive biomedical problem...
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1Peter Sloot: Computational Science, University of Amsterdam.
Interactive Biomedical Problem Solving on the Grid:
Peter Sloot
Computational Science
http://www.science.uva.nl/research/scs
University of Amsterdam, The Netherlands
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2Peter Sloot: Computational Science, University of Amsterdam.
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3Peter Sloot: Computational Science, University of Amsterdam.
A prototypical killer application
The Grid is not about Science… it is about Engineering…
The science is in the application… -lots on High Energy Physics etc… but…
-let’s forget the ‘Rocket Science’ for a while
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4Peter Sloot: Computational Science, University of Amsterdam.
Changing the Paradigm
In Vivo
In Vitro
In Silico
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5Peter Sloot: Computational Science, University of Amsterdam.
Changing the Paradigm
In Vivo
In Vitro
In Silico
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6Peter Sloot: Computational Science, University of Amsterdam.
Changing the Paradigm
In Vivo
In Vitro
In Silico
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7Peter Sloot: Computational Science, University of Amsterdam.
From Molecule to Man…
DNA Proteins Cellular Pharma-ceutical Treatment
Genomics Proteomics Immunology Medical
Mutations ProteaseReverse Transcriptase
CD-4 Experssion# RNA particles
Vivo-Vitro- ExperimentationSilico-
Molecule
Time
Space10-14 sec
10-10 m
Years
10-1 m
Man
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8Peter Sloot: Computational Science, University of Amsterdam.
•First Principle Modeling
•Genetic Regulatory Networks
•Metabolic Networks
•Immunological Networks
•… Silicon Cell
•Hierarchical data Modeling
•G-P-M & Patient Dbases
AnalyticMolecular DynamicsMonte CarloMesoscopic
AI – GA’s, NN’s, Fuzzy L.
From Molecule to Man…Cont
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9Peter Sloot: Computational Science, University of Amsterdam.
From Molecule to Man…PSE/G
• Mesoscopic Simulation High Performance Computing • Parameter Space Exploration High Throughput Computing
• Data Disclosure Dbase Federation and Integration
• Data Fusion Hierarchical Parameter Transfer
• Access Visualization/VR && Roaming &&PDA
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10Peter Sloot: Computational Science, University of Amsterdam.
Two Projects
AbdominalAorticAneurysm
HIV Expert System
Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I, in series Lecture Notes in Computer Science, vol. 2657, pp. 125-135. Springer Verlag, June 2003. ISBN 3-540-40194-6.
5th International Conference on Cellular Automata for Research and Industry, ACRI 2002, Geneva, Switzerland, October 9-11, 2002. Proceedings, in series Lecture Notes in Computer Science, vol. 2493, pp. 282-293. October 2002.
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11Peter Sloot: Computational Science, University of Amsterdam.
Ariadne’s red rope
Motivation Experimentalsetup
ArchitectureSimulationVisualizationInteraction
Status: Some ‘hot’ results
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12Peter Sloot: Computational Science, University of Amsterdam.
Ariadne’s red rope
Motivation Experimentalsetup
ArchitectureSimulationVisualizationInteraction
Status: Some ‘hot’ results
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13Peter Sloot: Computational Science, University of Amsterdam.
Current Situation
Observation
Diagnosis & Planning
Treatment
Nature March 2002
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14Peter Sloot: Computational Science, University of Amsterdam.
Salami…
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15Peter Sloot: Computational Science, University of Amsterdam.
Example: Proof is in the pudding...
– Diagnostic Findings
• Occluded right iliac artery
• 75% stenosis in left iliac artery
• Occluded left SFA
• Diffuse disease in right SFA
Computer Assisted Radiology and Surgery (Excerpta Medica, International Congress Series 1230), pp. 938-944. Elsevier Science B.V., Berlin, Germany, June 2001.
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16Peter Sloot: Computational Science, University of Amsterdam.
Segmentation Through Wave Propagation
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17Peter Sloot: Computational Science, University of Amsterdam.
Methods - MR Imaging
MR Scan of Abdomen MR Scan of Legs
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18Peter Sloot: Computational Science, University of Amsterdam.
Methods - Geometric Models
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19Peter Sloot: Computational Science, University of Amsterdam.
Alternate Treatments
Angio w/ Fem-Fem &
Fem-Pop
AFB w/ E-S Prox.
Anast.
Angio w/Fem-Fem
AFB w/ E-E Prox.
Anast.
Preop
Courtesy Prof. C. Taylor
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20Peter Sloot: Computational Science, University of Amsterdam.
Ariadne’s red rope
Motivation Experimentalsetup
ArchitectureSimulationVisualizationInteraction
Status: Some ‘hot’ results
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21Peter Sloot: Computational Science, University of Amsterdam.
Experimental set-up
MRI, PET Monolith,Cluster
Cave, Wall,PC,PDA
Advanced Infrastructures for Future Healthcare, pp. 275-282. IOS Press, 2000.
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22Peter Sloot: Computational Science, University of Amsterdam.
Design Considerations
– FACTS: New Scanners 1024 x 1024: 128 slices of 2 byte depth == 256 MByte, 10 images per systole == 1 per second
– High Quality presentation– High Frame rate– Intuitive interaction– Real-time response– Interactive Algorithms– High performance computing and networking...
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23Peter Sloot: Computational Science, University of Amsterdam.
Provoking a bit…
Progress in natural sciences comes from taking things apart ...
Progress in computer science comes from bringing things together...
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24Peter Sloot: Computational Science, University of Amsterdam.
Ariadne’s red rope
Motivation Experimentalsetup
ArchitectureSimulationVisualizationInteraction
Status: Some ‘hot’ results
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25Peter Sloot: Computational Science, University of Amsterdam.
PSE/G Architecture
PDAAccess
&SMS
Service
‘Dynamite/G to support
Checkpointing Parallel HPC
Programs
Concurrency and Computation: Practice and Experience, ((Special Issue on Grid Computing Environments)) vol. 14, pp. 1313-1335. John Wiley and Sons, 2002.
Lecture Notes in Computer Science, vol. 1971, pp. 203-213. Springer-Verlag, December 2000.
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26Peter Sloot: Computational Science, University of Amsterdam.
Building the workflow
Contract:
Capability specification
Experiment specification.
Components in Grids wide
Component Broker
Components Candidates
Design a story for components.
Execute the story.
1.
2.
3.
Software bus
Call for agents.
Proceedings of the Communication Networks and Distributed Systems Modeling and Simulation Conference (CNDS 2002), pp. 3-10. January 2002.
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27Peter Sloot: Computational Science, University of Amsterdam.
Actors setting the scene
Start[,]
InitSim[Ds,]
doStep[,]
ExportData[,Dr]
Stop[,]
(succeed,CdU(Ds)
E_Act(init))
(succeed,_,E_Act(doStep))
(succeed,E_Act(stop))
(succeed,_
E_Act(exportData))
(succeed,_E_Act(doStep))
(succeed, _, do(doStep))
(succeed,E_Act(stop))
Actor Conductor
Story
Software bus: RTI of the HLA/G
Communication Agents:Interfacing to software bus.
Module Agents:Application specific activities = Story + my capability.
Story:Application specific specification.
Actor:Doing real activities.
Implementation of actions.
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28Peter Sloot: Computational Science, University of Amsterdam.
Story = {Scenarios}
Start Story
End Story
Scenario 2
Scenario 1
([a=1
], [])
([a>3
], [])
([a<
=3]
, [a
+=
1])
([a<
=3]
, [a
+=
1])
(simulation, startScenario)
(p1,1, [], [],[])
(p3,0, [],[], [])(p2,0, [sa=1],[sa<100], [sa+=1])
(visualization, visualisedata)(simulation, compute)
(simulation, endScenario)
(p4,0, [ ], []) (p5,0, [],[], [])
(p6,0,[], [], [])Story: scenario transition graph.
Nodes: {scenarios};
Transitions: {([Ee], [Eq])};
[Ee]: expression when entering;
[Eq]: expressions when leaving.
Scenario: P/T net:Places: {(name, token, [Ei], [Ee], [Eq])}
[Ei]: expressions when init the P/T net;[Ee]: expressions when enter a place;[Eq]: expressions when leave a place.
Transitions: {(role, action)}
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29Peter Sloot: Computational Science, University of Amsterdam.
Why HLA:
Simulation modules aggregation and reuse; Large and mature user base; legacy
But:
HLA requires explicit description of data and event objects that will be exchanged before the actual federation starts execution Static bootstrapping process required to enable RTI system communication
Our approach:
GT3 index service and data transfer infrastructure evaluated to assess capabilities and limitations with HLA integration
Performance of GT3 GIS infrastructure for querying and modifying RTIexec endpoint information and RTI bootstrap
Current GT3 GIS performance demonstrates the feasibility of the GT3/HLA based GIS for HLA runtime information query, RTI dynamic modification of HLA Federates, and bootstrapping
Added features to HLA like security, extensibility, scalability, and decentralized maintenance.
Implementation: RTI 1.3 NG V5, Amzi Prolog
Grid Service query performance, secured bindings
Migration approach from HLA to GS
Grid Services and HLA
Grid Services for HLA-based Distributed Simulation Frameworks, in First European Across Grids Conference, Santiago de Compostela, Spain, Springer-Verlag, Heidelberg, February 2003.
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30Peter Sloot: Computational Science, University of Amsterdam.
Ariadne’s red rope
Motivation Experimentalsetup
ArchitectureSimulationVisualizationInteraction
Status: Some ‘hot’ results
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31Peter Sloot: Computational Science, University of Amsterdam.
Flow through complex geometry
– After determining the vascular structure simulate the blood-flow and pressure drop…
– Conventional CFD methods might fail:• Complex geometry• Numerical instability wrt interaction• Inefficient shear-stress calculation
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32Peter Sloot: Computational Science, University of Amsterdam.
Solution to interactive flow simulation
– Use Cellular Automata as a mesoscopic model system:• Simple local interaction• Support for real physics and heuristics• Computational efficient
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33Peter Sloot: Computational Science, University of Amsterdam.
Mesoscopic Fluid Model
– Fluid model with Cellular Automata rules
– Collision: particles reshuffle velocities
– Imposed Constraints• Conservation of mass• Conservation of momentum• Isotropy
Details...
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34Peter Sloot: Computational Science, University of Amsterdam.
...Equivalence with NS– For lattice with enough symmetry: equivalent to the continuous incompressible Navier-Stokes equations:
uuu
u
2 1
0
Pt
u
Implicit parallel and complex geometry support.
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35Peter Sloot: Computational Science, University of Amsterdam.
Efficient Calculation of Shear-Stress
AND the momentum stress tensor that is linearly related to the shear stresses
i
if i
iif cu
i
iiif ccΠ
x
u
x
u
~
Perpendicular momentum transfer:
From LBE scheme:
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36Peter Sloot: Computational Science, University of Amsterdam.
Visualization Courtesy J. Steinman
International Journal of Modern Physics B, vol. 17, nr 1&2 pp. 95-98. World Scientific Publishing Company, January 2003.
International Journal of Modern Physics C, vol. 13, nr 8 pp. 1119-1134. October 2002.
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37Peter Sloot: Computational Science, University of Amsterdam.
T.S. Elliot
‘How much wisdom has been lost in knowledge and how much knowledge has been lost in
information...’
How much Information has been lost in Data!!
Fourth IEEE ACMI'02 International Conference on Multimodal Interfaces, Pittsburgh, Pennsylvania, 14-16 October 2002, pp. 313-318. IEEE Computer Society, Los Alamitos, California, USA, 2002.
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38Peter Sloot: Computational Science, University of Amsterdam.
Immersive Environments
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39Peter Sloot: Computational Science, University of Amsterdam.
3D Information and Interaction
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40Peter Sloot: Computational Science, University of Amsterdam.
VR-Interaction
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41Peter Sloot: Computational Science, University of Amsterdam.
VR Portal
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42Peter Sloot: Computational Science, University of Amsterdam.
Ariadne’s red rope
Motivation Experimentalsetup
ArchitectureSimulationVisualizationInteraction
Status: Some ‘hot’ results
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43Peter Sloot: Computational Science, University of Amsterdam.
DAS2 SEs Storage Elements (SE) in UvA, NIKHEF, and Leiden EDG 2.0 release candidate with VDT-1.1.8-6, installed and configured manually instead of LCFG, because is
a shared system No R-GMA running, using the MDS interface on port 2135 Distributed ASCI Supercomputer 2 (DAS-2) Myrinet multi-Gigabit wide-area distributed computer of 200 Dual Pentium-III nodes Fast Ethernet used as OS network Each node contains:
Two 1-Ghz Pentium-IIIs At least 1 GB RAM At least 20 GByte local IDE disk A Myrinet and Fast Ethernet interface cards Linux 2.4.7-10
CrossGrid CEs Currently EDG 1.2.2 and 1.2.3 deployed in the production testbed EDG 1.4.3 being tested at several validation sites Production testbed resources:
15 Computing Elements 69 Worker Nodes 115 CPUs 2.7TB Storage Capacity
MD Local repository for remote navigation, data transfer and D-VRE initialization Requirements:
Web Browser Java Plugin 1.4 or newer with JAR cache disabled Firewalls open for 8080 port Pool 13000-17000 and port 2811 open in both directions between local workstation and remote SE
(se.crossgrid.man.poznan.pl) Valid x509 certificate credentials
The Specs
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44Peter Sloot: Computational Science, University of Amsterdam.
Shear stress, velocities,
masses, etc.
ce (CrossGrid)
se2 (D-VRE machine)
MD login and Grid certificates submission
Bypass creation LB mesh generation
Job submission Job monitoring
MR image Segmentation(soon a GS!)
se1 (e.g., Leiden)
Patient at MRI scanner
MR image
Virtual Node Creation
The Scenario
Simulated flow
ce (CrossGrid)
I have no GVK images,
ask Elena
Proceedings of the First European HealthGrid Conference, January, 16th-17th, 2003, pp. 57 - 66.
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45Peter Sloot: Computational Science, University of Amsterdam.
Recorded Session
September 25th 2003
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46Peter Sloot: Computational Science, University of Amsterdam.
A peek in the kitchen…
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47Peter Sloot: Computational Science, University of Amsterdam.
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48Peter Sloot: Computational Science, University of Amsterdam.
Wrapping up– Agent based iPSE (Simulation, Interaction and Visualization)– Vascular Reconstruction– Dynamic task Migration support for HPC on the Grid– Migrating Desktop X# integrated with VRE
– Working on:• Human Machine Interaction (trial in 3 Hospitals)• Stent Placement• Alternative VR: DesktopVR • OGSA and HLA-Grid
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49Peter Sloot: Computational Science, University of Amsterdam.
AcknowledgementsStanford:
Charley Taylor, PhD.
Christopher K. Zarins, PhD. M.D.
UvA:
Denis Shamonin
Roman Shulakov
Alfredo Tirado Ramos
Robert Belleman, PhD
Alfons Hoekstra, PhD
Dick van Albada, PhD
Elena Zudilova, PhD
RUL/AZL:
H. Reiber, PhD.
Bloem, PhD, M.D.
U. Wisconsin
M. Livney, PhD
SARA:
A. de Koning, PhD.
Krakow
Marian Bubak, PhD
Katarzyna Zajac
X#X#
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50Peter Sloot: Computational Science, University of Amsterdam.
http://www.science.uva.nl/research/scs