Transcript Utilization of HPC in Cancer Research

Utilization of HPC
in Cancer Research
Dave Billiter, PMP
Director-Research Informatics Core
The Research Institute at Nationwide
Children’s Hospital, Columbus, OH
Presentation Overview
Introduction
 Research Informatics and Imaging Core
 Infrastructure
 Image Analysis
 Hypothesis
 Microsoft HPC
 Conclusion
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The Research Institute at Nationwide
Children’s Hospital
Research Informatics Core Mission
The Research Informatics Core of The
Research Institute at Nationwide Children’s
Hospital, under the vision of Dr. Stephen J.
Qualman and direction of Dr. Nilsa Ramirez,
is an informatics application development
team dedicated to increasing cure rates and
decreasing side effects in therapy through
innovation of information technology.
http://informatics.nchresearch.org/
Informatics Core Team
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Dave Billiter, PMP- Informatics Director
Tom Barr- Imaging Manager
 Bob Neville- Senior Software Developer
 Scott Hargrose- Software Developer/DBA
 Bill Beyer- Software Developer/Business Analyst
 Heather Bao- Software Developer
 Heather Day- Project Manager
 Subha Krishnamachary- Software Developer
 Andy Fox- Software Developer
 Mark Plaskow- Software Architect
 Eric Kramer- Data Architect
 Jason Weis- QA/QC
Informatics Core Capabilities
Custom Application Development
 Informatics Consulting
 Solution Analysis
 Data and Environment Integration
 Project Management
 Systems Architecture
 Web Site Development
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Informatics Core Technology
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Microsoft .NET Framework (.NET Suite)
MS SQL Server 2000/2005/2008 (6.5/7)
 MS Access 97/2000/2003/2007
 MS Team Foundation Server
 MySQL
 Oracle
 ColdFusion
 Java
 Ruby/Ruby On Rails
 Aperio ScanScope and Image Software
 Linux/Apache/PHP/JSP
 Freezerworks
Informatics Core “Clients”
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Center for Childhood
Cancer Investigators
Children’s Oncology
Group (COG)
Gynecologic Oncology
Group (GOG)
Cooperative Human
Tissue Network (CHTN)
Childhood Cancer
Survival Studies (CCSS)
Cancer Therapy
Evaluation Program
(CTEP)
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Center for Innovation in
Pediatric Practice
Biobehavioral Health
Nationwide Children’s
Hospital
NCI Group Banking
Committee (GBC)
NCI Cancer Genome
Atlas Project
Biopathology Center
(BPC)
The Lance Armstrong
Foundation
Imaging Core
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Multidisciplinary team
Imaging services to enhance biomedical research for
multiple national cooperative groups and other
researchers
Currently work with over 30 pathologists
Focus Areas
 Pathology Imaging
 Automated Pathology Review Applications
 Digital Slide Conferencing
 Image Architecture Analysis & Development
 Digitized Pathology Reports
 Online capture of pathology review data
Infrastructure-Hardware
Ohio Supercomputer Center (OSC)
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IBM x3455 1U server featuring 1 dual-core
AMD 2.4GHz Opteron processor, with 2GB of
main memory, and a pair of 70 GB mirrored
SATA drives for system software and swap
space.
 Motherboard has a total of 4 processor
sockets, and is capable of being populated
with quad-core processors in each socket, for
a total of 16 cores.
 Linked to a DDN 8500 SAN (25 TBs), provides
storage for application executables and data.
Infrastructure - Software
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The operating system is Microsoft HPC Server
2008, based on Windows Server 2008 64-bit
Edition
 Built to scale to thousands of cores
 Features cluster management tools, support
for third-party clustered file systems, advanced
failover capabilities, service-oriented
architecture (SOA) job scheduler.
Infrastructure - Software
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Also includes remote direct memory access
interface, and cluster interoperability through
standards such as High Performance
Computing Basic Profile specification
produced by the Open Grid Forum.
 Combines the operating system with a
message passing interface and a job
scheduler into a single package.
HPC Cancer Research-Imaging
Image Analysis
 Anaplasia
 Mitotic Index
 Necrosis
 Impact of Chemotherapy in Radiology
Modalities
Whole-Slide Image
Tissue Microarray
 Several patient’s materials on one glass
slide
 Easily compare staining characteristics
of several tumors
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Image Analysis
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Whole-Slide (Image) Search
Image Analysis
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Whole-Slide Image Processing
Image Analysis
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Pattern of pixels for Nuclei and ability to locate
abnormal clustering.
Image Analysis
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Algorithms applied to both solid and liquid
diseases.
HPC Cancer Research Hypothesis
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The association and utilization of a high
performance computing environment
within cancer research will enhance
detection and optimize the pathology
review process thus allowing for rapid
and specific patient therapy.
Why Microsoft HPC?
INTEGRATION
 Current Windows based vendor
applications.
 Familiarity with Informatics development
environment.
 Windows access to image files stored in
Linux-based storage share.
 Performance.
Microsoft HPC Challenges
Local Microsoft HPC subject matter expertise.
 DEP (Data Execution Prevention)
 MS OS’s like Vista and Server 2008 are very
(overly?) security conscious and install with all
security features enforced – including DEP!
 Error messages from application services that
refused to start/stay running did not relate to
DEP; implication of DEP had to be deduced.
Accomplished
Successful installation and execution of
Aperio apps (DSC, Spectrum,
ImageScope, ImageServer).
 Successful installation and execution of
Apache web server, configuration of
Apache to co-exist with IIS.
 Configuring path to image storage
shares.
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In Process and Future Activities
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Installation of Aperio DataServer, configuration
of DataServer and ImageServer.
 Will need to modify algorithms to write analysis
results to Aperio database & relate to other
image metadata.
 Modify Aperio database to accept additional
algorithm output.
 Modify Spectrum to display analysis metadata,
easily reference annotated images.
Acknowledgements
Brian Hammond- Microsoft HPC
 Kevin Wohlever- OSC
 Lin Li- OSC
 Bill Beyer- RIC
 Mark Plaskow- RIC
 Tom Barr- Biopathology Imaging Core
 Dr. Kathy Nicol- Natiowide Children’s
Hospital
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Conclusion
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Questions & Answers
THANK YOU!!!!