Utilization of hpc in cancer research 2008 ricPresentation Transcript
Utilization of HPCin Cancer ResearchDave Billiter, PMPDirector-Research Informatics CoreThe Research Institute at NationwideChildren’s Hospital, Columbus, OH
Presentation Overview Introduction Research Informatics and Imaging Core Infrastructure Image Analysis Hypothesis Microsoft HPC Conclusion
The Research Institute at NationwideChildren’s Hospital
Research Informatics Core MissionThe Research Informatics Core of TheResearch Institute at Nationwide Children’sHospital, under the vision of Dr. Stephen J.Qualman and direction of Dr. Nilsa Ramirez,is an informatics application developmentteam dedicated to increasing cure rates anddecreasing side effects in therapy throughinnovation of information technology.http://informatics.nchresearch.org/
Informatics Core Team 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
Informatics Core Technology 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” Center for ChildhoodCancer Investigators Children’s OncologyGroup (COG) Gynecologic OncologyGroup (GOG) Cooperative HumanTissue Network (CHTN) Childhood CancerSurvival Studies (CCSS) Cancer TherapyEvaluation Program(CTEP) Center for Innovation inPediatric Practice Biobehavioral Health Nationwide Children’sHospital NCI Group BankingCommittee (GBC) NCI Cancer GenomeAtlas Project Biopathology Center(BPC) The Lance ArmstrongFoundation
Imaging Core Multidisciplinary team Imaging services to enhance biomedical research formultiple national cooperative groups and otherresearchers 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-HardwareOhio Supercomputer Center (OSC) IBM x3455 1U server featuring 1 dual-coreAMD 2.4GHz Opteron processor, with 2GB ofmain memory, and a pair of 70 GB mirroredSATA drives for system software and swapspace. Motherboard has a total of 4 processorsockets, and is capable of being populatedwith quad-core processors in each socket, fora total of 16 cores. Linked to a DDN 8500 SAN (25 TBs), providesstorage for application executables and data.
Infrastructure - Software The operating system is Microsoft HPC Server2008, based on Windows Server 2008 64-bitEdition Built to scale to thousands of cores Features cluster management tools, supportfor third-party clustered file systems, advancedfailover capabilities, service-orientedarchitecture (SOA) job scheduler.
Infrastructure - Software Also includes remote direct memory accessinterface, and cluster interoperability throughstandards such as High PerformanceComputing Basic Profile specificationproduced by the Open Grid Forum. Combines the operating system with amessage passing interface and a jobscheduler into a single package.
HPC Cancer Research-ImagingImage Analysis Anaplasia Mitotic Index Necrosis Impact of Chemotherapy in RadiologyModalities
Whole-Slide Image Tissue Microarray Several patient’s materials on one glassslide Easily compare staining characteristicsof several tumors
Image Analysis Whole-Slide (Image) Search
Image Analysis Whole-Slide Image Processing
Image Analysis Pattern of pixels for Nuclei and ability to locateabnormal clustering.
Image Analysis Algorithms applied to both solid and liquiddiseases.
HPC Cancer Research Hypothesis The association and utilization of a highperformance computing environmentwithin cancer research will enhancedetection and optimize the pathologyreview process thus allowing for rapidand specific patient therapy.
Why Microsoft HPC?INTEGRATION Current Windows based vendorapplications. Familiarity with Informatics developmentenvironment. Windows access to image files stored inLinux-based storage share. Performance.
Microsoft HPC ChallengesLocal 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 allsecurity features enforced – including DEP! Error messages from application services thatrefused to start/stay running did not relate toDEP; implication of DEP had to be deduced.
Accomplished Successful installation and execution ofAperio apps (DSC, Spectrum,ImageScope, ImageServer). Successful installation and execution ofApache web server, configuration ofApache to co-exist with IIS. Configuring path to image storageshares.
In Process and Future Activities Installation of Aperio DataServer, configurationof DataServer and ImageServer. Will need to modify algorithms to write analysisresults to Aperio database & relate to otherimage metadata. Modify Aperio database to accept additionalalgorithm 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’sHospital