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Transcript of CceHUB A Knowledge Discovery Environment for Cancer Care Engineering Research Ann Christine Catlin...
cceHUB
A Knowledge Discovery Environment for Cancer Care Engineering Research
Ann Christine CatlinHUBzero Workshop
November 7, 2008
a HUB for Cancer Care Engineering
integrate/synthesize biological OMIC data
biomarker knowledge
• OMIC Analysis Labs
• Statistical Modelers
• Visual Analytics
HUBA series of somatic mutations leads to clonal expansion and an adenoma. Mutation of an
Support for Community-shared
Resources Click to Next Slide
CCE integrated project hierarchyThe Cancer Care Engineering (CCE) project is a highly innovative, interdisciplinary, multi-institutional endeavor that holds promise for revolutionizing the current paradigms of cancer prevention, detection, treatment and care delivery by focusing on translating cancer research into clinical practice …
The current challenge is to focus the rapid and extraordinary advances using large scale human OMIC analyses to significantly improve survival rates in community-based oncology clinics and develop community-wide prevention efforts. In fact the tremendous scientific advances and rapidly developing capabilities offer an enormous opportunity to catalyze improvement by focusing on the engineering of cancer care. Our vision addresses this opportunity by applying systems engineering principles and unique data visualization and statistical model building to the broad spectrum of cancer prevention, treatment, and care delivery. CCE focuses on identifying opportunities for improvement by analyzing system behavior against best practices and creating predictive models for the treatment and care of patients. Moreover, cancer care delivery is included as part of the cancer treatment system, where novel statistical models are used to predict both disease behavior (effective treatment decisions) and system response
(efficient cancer care delivery).
CCE White Paper, 2007 Indiana University Simon Cancer Center Purdue Cancer Center Oncological Sciences Center e-Enterprise Center Regenstrief Center for Health Care Engineering Regenstrief Institute Roudebush VA Center for Implementing Evidence-Based Practice IU Center for Health Services and Outcomes ResearchDepartment of Medicine, IU School of MedicineDepartment of Medicinal Chemistry and Pharmacology, Purdue UniversitySchool of Chemical Engineering, Purdue UniversitySchool of Electrical and Computer Engineering, Purdue UniversityDepartment of Statistics, Purdue University
The Cancer Care Engineering (CCE) project is a highly innovative, interdisciplinary, multi-institutional endeavor that holds promise for revolutionizing the current paradigms of cancer prevention, detection, treatment and care delivery by focusing on translating cancer research into clinical practice …
The current challenge is to focus the rapid and extraordinary advances using large scale human OMIC analyses to significantly improve survival rates in community-based oncology clinics and develop community-wide prevention efforts. In fact the tremendous scientific advances and rapidly developing capabilities offer an enormous opportunity to catalyze improvement by focusing on the engineering of cancer care. Our vision addresses this opportunity by applying systems engineering principles and unique data visualization and statistical model building to the broad spectrum of cancer prevention, treatment, and care delivery. CCE focuses on identifying opportunities for improvement by analyzing system behavior against best practices and creating predictive models for the treatment and care of patients. Moreover, cancer care delivery is included as part of the cancer treatment system, where novel statistical models are used to predict both disease behavior (effective treatment decisions) and system response
(efficient cancer care delivery).
CCE White Paper, 2007 Indiana University Simon Cancer Center Purdue Cancer Center Oncological Sciences Center e-Enterprise Center Regenstrief Center for Health Care Engineering Regenstrief Institute Roudebush VA Center for Implementing Evidence-Based Practice IU Center for Health Services and Outcomes ResearchDepartment of Medicine, IU School of MedicineDepartment of Medicinal Chemistry and Pharmacology, Purdue UniversitySchool of Chemical Engineering, Purdue UniversitySchool of Electrical and Computer Engineering, Purdue UniversityDepartment of Statistics, Purdue University
Cancer Care Engineering Projects funded by the Regenstrief Foundation
CCE-1: A Multi-Agent Approach to Modeling of the Indiana CRC Care System
CCE-2: An Indianapolis CRC Quality Improvement Initiative
…
CCE-5: A Fusion Center for Cancer Care System Information – the Cancer Care Situation Room
CCE-6: Information Infrastructure and Raw Data Analysis
CCE-7: Augmenting Physical Sample Collection, Clinical Data Collection, OMIC Laboratory Analysis, Conversion to Digital Data
…
… highly innovative, interdisciplinary, multi-institutional endeavor …
CCE TEAM: more than 70 scientists, clinicians, statisticians, physicians, nurses, engineers, computer scientists, health service researchers, university and hospital staff
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CCE team: collaboration !
Integrated Hierarchy of Projects
CCE-1: A Multi-Agent Approach to Modeling of the Indiana CRC Care System
CCE-2: An Indianapolis CRC Quality Improvement Initiative
…
CCE-5: A Fusion Center for Cancer Care System Information – the Cancer Care Situation Room
CCE-6: Information Infrastructure - OMIC Data Collection and Analysis
CCE-7: Augmenting Physical Sample Collection, Clinical Data Collection, OMIC Laboratory Analysis, Conversion to Digital Data
… Click to Next Slide
Using HUB Technology I
• Content Management System for Scientists
• Collaboration and Social Networking
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Using HUB Technology II• Unique Middleware for Modeling and Simulation
scientist
Rappture
modelingcode
VIOLIN
Maxwell’sDaemon
Middleware
Physical Machine
Virtual Machine
ContentDatabase
tool session cluster
visualization servers
rendering farm
collaborator
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What we need to support that’s new …
OMIC workflow biosamples biological data biomarker knowledge …
“data lifecycle” support
end-to-end user support
Data … the new shared resource data repository & data support infrastructure
metadata … annotate, track, characterize content
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OMIC experiment workflowsclinical database,demographics, diet, diagnosis, treatment
IU SimonCancer CenterSample acquisition processing transfer
BLOOD SAMPLECRC PATIENT/CONTROL
transfer to Purdue
350MBspectrum, list of peaks,
1.2GBretention times, m/z, intensities
Bindley Biosciences LaboratoriesSample preparationInstrument analysisData generation raw instrument data pre-processed data
SAMPLE DATAconverted, reduced, selected, filtered,transformed
LECO GC GC MS
instrument generated
PEG
data converters
CDFCSV
data converters
35MBpeak list
more ...DAT/RAWTXT
RAW DATA
PRE-PROCESSEDDATA
Communication & information exchange
external DB linkage
Interactive GUIannotation
Document library & document tagging
protocols
Metadata processingtracking
Interactive GUIannotation
Document library & document tagging
methods
Data transfer upload
tracking Metadata processing
storage File server & backup
metadatalinkage
Metadata processing
cceHUB
sample
datasets
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OMIC data analysis workflows
data exploration
data tracking
tool tracking
ontology support
data capture
storage
metadata linkage
visualization
modeling
annotation
datasets
Laboratory AnalysisStatistical ModelingVisual AnalyticsProcessing multiple samplesComparisons across samplesModeling across samplesVisualization across samples
sample samplesample
sample sample
sample
ANALYZEDDATA
cceHUB
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