ccehub sharing , exploring and analyzing data an environment for collaborative cancer research

cceHUBSharing , Exploring and Analyzing Data

An Environment for Collaborative Cancer Research

clinical data observational & scientific data

decision supportcomputation &visualization

Ann Christine Catlin6th Annual Cancer Care Engineering Retreat

05-27-2011

Great Graduate Students !

Ruchith FernandoLancelot Guoheng ChenSahan GamageSudheera FernandoPuneet GuptaSumudinie FernandoPreeti RaoNabeel Yousef

cceHUB Advances in 2001

Clinical Patient Data & Sample Tracking • More detailed and more complete data collection : diagnosis, treatment, surgery, follow-up

• New type of data : behavior lifestyle

• Customized projects: tissue acquisition

Tissue Acquisition : Clinical Data & Biorepository with Tracking

Data Collection : New Data … More Detailed Data

cceHUB Advances in 2001

Laboratory Data Upload & Tracking• Repository size >1 TB• Security upgrades• Data verification and validation• Metadata collection• Help with lab uploads … e.g., mass spectrometry data

Always looking for ways to make uploads easier, more complete, and more accessible to analysis tools.

Lab #SamplesAnalyzed % Total

Files/Samples

Uploaded

Average File Size

Analysis Toolsat cceHUB

Using cceHUB tools ?

Bindley BiosciencesGlobal Proteomics

193 73% 193 files193 samples

80MB Discovery PipelineResults Visualize/Compare

> 800 runs through discovery pipeline

TeegardenVitamin D

225 85% 4 files225 samples

< 1MB Vitamin D-Blood Draw -Clinical Data merge for SAS

DataView

RafteryMetabolomicsGCGC-MS

230 87% 230 files230 samples

1 GB Peak classification /alignmentGCGC-MS Visual Analytics

RafteryMetabolomicsNMR

230 87 % 2 files230 samples

< 1MB

XuLipidomics

143 54% 1 file143 samples

< 1MB Lipidomics-BloodDraw-Clinical Data merge for SAS

DataView

KlaunigTEAC analysis

259 98% 1 file259 samples

< 1MB TEAC-Blood Draw-Clinical Data merge for SAS

DataView

KlaunigComet Assay

101 38% 1 file101 samples

< 1MB CometAssay-Blood Draw-Clinical Data merge for SAS

DataView

KlaunigGenotyping Assay

-- POCRE, MaCH genotype imputation

(used by stat group on their own data)

Other: Laurie ParkerMedicinal Chemistry and Molecular Pharmacology

-- Maldi Quantifier

Laboratory data at cceHUB: Some Statistics

Laboratory data at cceHUB: Metadata

cceHUB Advances in 2001

Analysis Tools / Analysis Data Collections• Proteome Discovery Pipeline• Analysis Data Viewer• Building models & generating results• Output collections for tools• New tools: MacH, Mach Results Visualization, POCRE, Maldi Quantifier, specialized plotting tools

New Analysis Tools

Analysis Data Viewer

Tool Output Collections for Browsing and Analysis

Collaboration : Sharing Idea for Analysis, Getting Results

Our technology extends to other cancer research workflows

Using the HUB cyber infrastructurewith cceHUB data technology

to further collaborativeCancer Care Engineering Research