Download here. - CBIL

Computational Bioinformatics & Bioimaging Laboratory
caBIG-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
VISDA Overview
VISDA (VIsual Statistical Data Analyzer) is a caBIG-TM
analytical tool for cluster modeling, visualization, and
discovery
• 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 topdown “soft” clustering (hierarchical yet exploratory)
Computational Bioinformatics & Bioimaging Laboratory
VISDA-caBIGTM 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
–
–
–
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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
VISDA-caBIGTM Key Features
•
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.
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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
Computational Bioinformatics & Bioimaging Laboratory
Installation
http://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 GUI
Computational Bioinformatics & Bioimaging Laboratory
VISDA GUI
Computational Bioinformatics & Bioimaging Laboratory
VISDA GUI
Computational Bioinformatics & Bioimaging Laboratory
VISDA 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 caArray
Computational Bioinformatics & Bioimaging Laboratory
Retrieve Data from caArray
Computational Bioinformatics & Bioimaging Laboratory
VISDA API Document
Computational Bioinformatics & Bioimaging Laboratory
VISDA UML Use Case Diagram
ud Use Case Model
Array Clustering
Data in caArray
caArray
«include»
Sav e Outputs
Locally
Import Data
Biological Researcher
«include»
Gene Clustering
Local Files/MAGEML/Tab-Delimited
Computational Bioinformatics & Bioimaging Laboratory
VISDA UML Class Diagram
oedu.vt.cbil.visda
Computational Bioinformatics & Bioimaging Laboratory
VISDA UML Class Diagram
oedu.vt.cbil.visda.data
Computational Bioinformatics & Bioimaging Laboratory
VISDA UML Class Diagram
oedu.vt.cbil.visda.comp
Computational Bioinformatics & Bioimaging Laboratory
VISDA UML Class Diagram
oedu.vt.cbil.visda.view