CceHUB omicsknowledgebase Ann Christine Catlin 3 rd Annual Cancer Care Engineering Retreat June 20, 2008 An Environment for CCE Research.

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Presentation transcript:

cceHUB omicsknowledgebase Ann Christine Catlin 3 rd Annual Cancer Care Engineering Retreat June 20, 2008 An Environment for CCE Research

1. Patient and Control Blood Community-based oncology clinics IUSCC 2. Data Acquisition - OMICS, Prevention, & HSR Data IUSCC - OMICS Labs Regenstrief Institute OMICS Labs, Purdue University 3. Data Storage/Query Center Purdue University 4. Integrative Mathematical Modeling Statistics Dept., Purdue University 5. Real-time Visual Analytics PURVAC, Purdue University 6. Immediate Analysis & Feedback to Clinics the CCE Team 7. Discovery Research Driven by Model Predictions IUSCC Purdue University Identify Molecular Signatures for Cancer the cancercareengineering model A systems approach to the prevention and treatment of cancer

OMICs Laboratory Visual Analytics intensity image viewing Evaluation of potential bio-markers Mass spectra navigation Noise Removal PCA analysis Mathematical Modeling metabolomics data LECO GCGCMS PEG CDF CSV TXT Bio-marker region selection Comparison analysis Population-based Modeling web-based user interface new viewpoints for input & output parameter sweep testing accessibility and usage educational resources for community-shared learning papers, online lectures, videos, presentations Statistical analysis How do CCE researchers collaborate?

cceHUB supports CCE research store and backup all OMICS data contribute data from the labs … attach tracking and search keywords to all datasets explore lab datasets store and backup all modeling tools contribute modeling tools... shared development run modeling tools in web browser store model results … attach tracking and search keywords to all results integrate visualization at every step

the cceHUB omicsknowledgebase immediate & constant availability for ALL OMICS DATA ALL MODELING TOOLS ALL VISUALIZATION TOOLS promoting the discovery of relationships immediate & constant availability for ALL OMICS DATA ALL MODELING TOOLS ALL VISUALIZATION TOOLS promoting the discovery of relationships

sample acquisition omics laboratory analysis Upload data Store data Attach metadata Explore data Prepare input Track model execution Store model results Attach metadata Upload data Store data Attach metadata data linkage visual analytics statistical modeling predictive models visual knowledge discovery integrated OMICS analysis feedback end-to-end support for the cceModel cceHUB omicsknowledgebase

What’s at the cceHUB … Right now … Community-shared Educational resources Modeling tools Data storage & backup User groups, data privacy, modeling tools privacy Help with contributing data and tools Much, much more... By September 2008 … Lab Data Uploader, Lab Data Tracking By September 2009 … Data Explorer, Model Tracking

Metadata Database omics datasetsdatabase omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset omics dataset DATA UPLOADER DATA EXPLORER SHARED DATA REPOSITORY : + store & backupprocess & store locate data of interest Data… storage, tracking, exploration

Supporting more than OMICS … other CCE Knowledge Bases OMICS Knowledge Base Health Services Knowledge Base

OMICS Knowledge Base Dabao Zhang, Min Zhang Statistics Department, Purdue University David Ebert, Wei Chen, Philip Livengood PURVAC, Purdue University OMICS Knowledge Base Contribute Data & Tools Store & Backup Data Explore Data Run Tools Track Data & Tools Eric Sherer e-Enterprise Center, VA CoE, IU HSR CCE research support

Acknowledgements CCE Leadership Team Marietta Harrison, Joe Pekny, Julie Nagel HUB Development Team Mike McLennan, Nick Kisseberg, Swaroop Shivarajapura, George Howlett, John Rosheck, Derrick Kearney, Rick Kennel, Shawn Rice other members of the OMICS Knowledge Base Group Seza Orcun, Mourad Ouzzani, Brandi Marshall Modeling Groups Eric Sherer, Dabao Zhang, Min Zhang Visual Analytics Group Dave Ebert, Wei Chen, Philip Livengood

Backup Slides

create a data support framework The cceHUB is built on the HUB cyberinfrastructure, leveraging its modeling and visualization tools support framework and its community resource-sharing components Data framework: managing end-to-end analysis: data storage, data tracking, data exploration. Data Explorer Process Tracking Metadata-based Query Retrieval OMICS Data File Repository Metadata Database Data Characterization and Tracking Data Upload Results Capture What we need to build …