Computational Bioinformatics & Bioimaging Laboratory

caBIG-ICR - VISDAcaBIG-ICR - VISDA

VT –GU Developer Team:Huai Li, Jiajing Wang, Yue Wang,

Jianhua Xuan, Robert Clarke

UPenn – The Wistar Institute Adopter Team:Louise Showe, Michael Showe,

Malik Yousef, Hsiuan-Lin Wu, and Michael Nebozhyn

Computational Bioinformatics & Bioimaging Laboratory

• Model clustered data structure via hierarchical mixture of Gaussian kernels (adaptive with cluster validation)

• Visualize data clusters via discriminative projections incorporating human gift for pattern recognition

• Discover and display hidden data clusters via top-down “soft” clustering (hierarchical yet exploratory)

VISDA (VIsual Statistical Data Analyzer)(VIsual Statistical Data Analyzer) is a caBIGis a caBIG-TM-TM analytical tool for cluster modeling, visualization, and analytical tool for cluster modeling, visualization, and discoverydiscovery

VISDA OverviewVISDA Overview

Computational Bioinformatics & Bioimaging Laboratory

VISDA-caBIGVISDA-caBIGTMTM Key Features Key Features

• Supported Data File

– Support data retrieving from caArray – Support local MAGE-ML file format – Support tab-delimited data file with multiple gene annotations as well as

multiple sample annotations

• Analytical Algorithms

– Support sample clustering and gene clustering– Has supervised/unsupervised feature selection– Has PCA and PPM projections– Has hierarchical statistical modeling and parameter estimation by EM

algorithm– Has advanced options for DCA projection and MDL cluster validation

Computational Bioinformatics & Bioimaging Laboratory

• GUI

– Main frame has a history tracking panel as well as a working view panel. Analysis node and Dataset node can be created and deleted from the tree.

– Input file can also have multiple rows for different sample annotation. User has the option to choose one of the rows as label information for analysis.

– Tables of the selected genes for phenotype clustering and their performances can be viewed, and saved.

– Has the three types of 2D-projection visualization.

– Figures can be viewed, zoomed, and saved as PNG or EPS format.

– Support sample/gene annotation view.

– Support cluster visualization by hierarchical display

– History log can be viewed and saved

VISDA-caBIGVISDA-caBIGTMTM Key Features Key Features

Computational Bioinformatics & Bioimaging Laboratory

InstallationInstallationhttp://gforge.nci.nih.gov/frs/download.php/320/visda-Deploy-V1.0.rar

http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/visda/VISDA-Developer/Month-12-yr1/visda-SourceCode-V1.0.rar

Computational Bioinformatics & Bioimaging Laboratory

VISDA GUIVISDA GUI

Computational Bioinformatics & Bioimaging Laboratory

VISDA GUIVISDA GUI

Computational Bioinformatics & Bioimaging Laboratory

VISDA GUIVISDA GUI

Computational Bioinformatics & Bioimaging Laboratory

VISDA Silver CompatibilityVISDA Silver Compatibility

• VISDA can retrieve data from caArray (can be considered as one caGrid node) by utilizing MAGE-OM APIs.

• MAGE-OM CDEs (registered in caDSR) used in VISDA are documented.

• Analysis results got from VISDA are the selected feature set, the "soft-clustering" probabilities of the samples/genes in each cluster and the hierarchical "tree of phenotype" or "tree of gene module" plots which are retained locally.

• Well documented VISDA APIs.

• UML documentation of all VISDA components using Enterprise Architect (EA).

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Retrieve Data from caArrayRetrieve Data from caArray

Computational Bioinformatics & Bioimaging Laboratory

Retrieve Data from caArrayRetrieve Data from caArray

Computational Bioinformatics & Bioimaging Laboratory

VISDA API DocumentVISDA API Document

Computational Bioinformatics & Bioimaging Laboratory

VISDA UML Use Case DiagramVISDA UML Use Case Diagram

ud Use Case Model

Biological Researcher

Array Clustering

Gene Clustering

Import Data

Data in caArray

Local Files/MAGE-ML/Tab-Delimited

caArray

Save Outputs Locally

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Computational Bioinformatics & Bioimaging Laboratory

VISDA UML Class DiagramVISDA UML Class Diagram

oedu.vt.cbil.visda

Computational Bioinformatics & Bioimaging Laboratory

VISDA UML Class DiagramVISDA UML Class Diagram

oedu.vt.cbil.visda.data

Computational Bioinformatics & Bioimaging Laboratory

VISDA UML Class DiagramVISDA UML Class Diagram

oedu.vt.cbil.visda.comp

Computational Bioinformatics & Bioimaging Laboratory

VISDA UML Class DiagramVISDA UML Class Diagram

oedu.vt.cbil.visda.view