CceHUB Sharing, Exploring and Analyzing Data An Environment for Collaborative Cancer Research clinical dataobservational & scientific data decision supportcomputation.

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Presentation transcript:

cceHUB Sharing, Exploring and Analyzing Data An Environment for Collaborative Cancer Research clinical dataobservational & scientific data decision supportcomputation & visualization Ann Christine Catlin 6 th Annual Cancer Care Engineering Retreat

Great Graduate Students ! Ruchith Fernando Lancelot Guoheng Chen Sahan Gamage Sudheera Fernando Puneet Gupta Sumudinie Fernando Preeti Rao Nabeel 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 #Samples Analyzed % Total Files/ Samples Uploaded Average File Size Analysis Tools at cceHUB Using cceHUB tools ? Bindley Biosciences Global Proteomics %193 files 193 samples 80MBDiscovery Pipeline Results Visualize/Compare > 800 runs through discovery pipeline Teegarden Vitamin D %4 files 225 samples < 1MBVitamin D-Blood Draw - Clinical Data merge for SAS DataView Raftery Metabolomics GCGC-MS %230 files 230 samples 1 GBPeak classification /alignment GCGC-MS Visual Analytics Raftery Metabolomics NMR %2 files 230 samples < 1MB Xu Lipidomics %1 file 143 samples < 1MBLipidomics-BloodDraw- Clinical Data merge for SAS DataView Klaunig TEAC analysis %1 file 259 samples < 1MBTEAC-Blood Draw-Clinical Data merge for SAS DataView Klaunig Comet Assay %1 file 101 samples < 1MBCometAssay-Blood Draw- Clinical Data merge for SAS DataView Klaunig Genotyping Assay --POCRE, MaCH genotype imputation (used by stat group on their own data) Other: Laurie Parker Medicinal 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 infrastructure with cceHUB data technology to further collaborative Cancer Care Engineering Research