cceHUB A Knowledge Discovery Environment for Cancer Care Engineering Research Ann Christine Catlin HUBzero Workshop November 7, 2008

a HUB for Cancer Care Engineering integrate/synthesize biological OMIC data  biomarker knowledge OMIC Analysis Labs Statistical Modelers Visual Analytics HUB A 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 hierarchy 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 Research Department of Medicine, IU School of Medicine Department of Medicinal Chemistry and Pharmacology, Purdue University School of Chemical Engineering, Purdue University School of Electrical and Computer Engineering, Purdue University Department 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 Research Department of Medicine, IU School of Medicine Department of Medicinal Chemistry and Pharmacology, Purdue University School of Chemical Engineering, Purdue University School of Electrical and Computer Engineering, Purdue University Department 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 Click to Next Slide

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 Click to Next Slide

Integrative Mathematical Models Click to Next Slide

Shared models need shared data … Click to Next Slide

Using HUB Technology II Unique Middleware for Modeling and Simulation scientist Rappture modeling code VIOLIN Maxwell’s Daemon Middleware Physical Machine Virtual Machine Content Database tool session cluster visualization servers rendering farm collaborator Click to Next Slide

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, characterizecontent Click to Next Slide

OMIC experiment workflows clinical database, demographics, diet, diagnosis, treatment IU Simon Cancer Center Sample acquisition processing transfer BLOOD SAMPLE CRC PATIENT/CONTROL transfer to Purdue 350MB spectrum, list of peaks, 1.2GB retention times, m/z, intensities Bindley Biosciences Laboratories Sample preparation Instrument analysis Data generation raw instrument data pre-processed data SAMPLE DATA converted, reduced, selected, filtered, transformed LECO GC GC MS instrument generated PEG data converters CDFCSV data converters 35MB peak list more... DAT/RAW TXT RAW DATA PRE- PROCESSED DATA Communication & information exchange external DB linkage Interactive GUI annotation Document library & document tagging protocols Metadata processing tracking Interactive GUI annotation Document library & document tagging methods Data transfer upload tracking Metadata processing storage File server & backup metadata linkage Metadata processing cceHUB sample datasets Click to Next Slide

OMIC data analysis workflows data exploration data tracking tool tracking ontology support data capture storage metadata linkage visualization modeling annotation datasets Laboratory Analysis Statistical Modeling Visual Analytics Processing multiple samples Comparisons across samples Modeling across samples Visualization across samples sample ANALYZED DATA cceHUB Click to Next Slide

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 Click to End