cce HUB

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

2. a HUB for Cancer Care Engineering A series of somatic mutations leads to clonal expansion and an adenoma. Mutation of an HUB Click to Next Slide • integrate/synthesize biological OMIC data •  biomarker knowledge • OMIC Analysis Labs • Statistical Modelers • Visual Analytics Support for Community-shared Resources

3. CCE integrated project hierarchy Click to Next Slide 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

4. CCE team: collaboration ! Click to Next Slide 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 …

5. Using HUB Technology I Click to Next Slide • Content Management System for Scientists • Collaboration and Social Networking

6. Integrative Mathematical Models Click to Next Slide

7. Shared models need shared data … Click to Next Slide

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

9. What we need to support that’s new … Click to Next Slide • 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

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

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

12. a HUB data support framework Data Explorer Metadata-based Query Results Capture Data Upload Process Tracking Data Annotation, Content Characterization & Tracking OMICS Data File Repository Metadata Database Click to End