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).
Computational Bioinformatics & Bioimaging Laboratory
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
«include»
«include»
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