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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Integrative Mathematical Models

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Shared models need shared data …

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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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Data Explorer

Process Tracking

Metadata-based Query

OMICS Data File Repository Metadata Database

Data Annotation, Content Characterization & Tracking

Data Upload Results Capture

a HUB data support framework

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