cceHUB omicsknowledgebase

Ann Christine Catlin3rd Annual Cancer Care Engineering Retreat

June 20, 2008

An Environment for CCE Research

1. Patient and Control BloodCommunity-based oncology clinicsIUSCC

2. Data Acquisition - OMICS, Prevention, & HSR DataIUSCC - OMICS LabsRegenstrief InstituteOMICS Labs, Purdue University

3. Data Storage/Query CenterPurdue University

4. Integrative Mathematical ModelingStatistics Dept., Purdue University

5. Real-time Visual AnalyticsPURVAC, Purdue University

6. Immediate Analysis & Feedback to Clinicsthe CCE Team

7. Discovery Research Driven by Model PredictionsIUSCCPurdue 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-markersMass spectra navigationNoise Removal

PCA analysis

Mathematical Modeling

metabolomics dataLECO GCGCMS

PEGCDF

CSV

TXT

Bio-marker region

selection

Comparison analysis

Population-based Modelingweb-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

sampleacquisition

omicslaboratoryanalysis

Upload dataStore dataAttach metadata

Explore data Prepare inputTrack model executionStore model resultsAttach metadata

Upload dataStore dataAttach metadata

data linkage visual

analytics

statisticalmodeling predictive

models

visualknowledgediscovery

integrated OMICS analysis

feedback

feedbackfeedback

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

MetadataDatabase

omics datasets database

omicsdatasetomics

datasetomicsdatasetomics

datasetomicsdatasetomics

dataset

omicsdatasetomics

datasetomicsdatasetomics

datasetomicsdatasetomics

dataset

omicsdatasetomics

datasetomicsdatasetomics

datasetomicsdatasetomics

dataset

DATA UPLOADER

DATA EXPLORER

SHARED DATA REPOSITORY : +

store & backup process & store

locate data of interest

Data… storage, tracking, exploration

Supporting more than OMICS …

other CCEKnowledge

Bases

OMICSKnowledge

Base

Health ServicesKnowledge

Base

OMICS

KnowledgeBase

Dabao Zhang, Min ZhangStatistics Department, Purdue University

David Ebert, Wei Chen, Philip LivengoodPURVAC, Purdue University

OMICS Knowledge Base

Contribute Data & ToolsStore & Backup DataExplore DataRun ToolsTrack Data & Tools

Eric Sherere-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 …