Cytoscape MiMI Plugin Update and MiMI RDB

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Cytoscape MiMI Plugin Update and MiMI RDB

• Jing Gao
• May 18 2007

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Plugin Update
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Cytoscape and Cytoscape Plugin for MiMI

• Cytoscape is a well-known software platform for
  visualizing molecular interaction networks and
  integrating these interactions with gene
  expression profiles developed by ISB, UCSD,
  MSKCC, Pasteur and Agilent.
• http//www.cytoscape.org/
• Cytoscape MiMI Plugin retrieves molecular
  interactions from MiMI and allows interaction
  networks from MiMI to be visualized using
  Cytoscape

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Overview

• Visualize and Analyze MiMI Molecule Interaction
  Networks on Cytoscape Platform
• Interactive Extension and Editing of Graphs
• Link Out Interactions to External Web Resource
• Integrate with NCIBI BioNlp

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Overview

• Integrate with EECS SAGA
• Node/Edge Annotation Editor
• Apply Cerebral Layout
• Checkout the Latest Plugin Version

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Feature List And Implementation

• Double Click a Node
• Query MiMI to get the node attributes and
• Expand current network with interactions related
  to the clicked node
• Delete nodes related networks
• Double Click an Edge
• Query MiMI to get edge attributes
• Single Click A Node or An Edge
• Get node or edge attribute without query MiMI

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Feature List And Implementation

• Right Click to Get Node/Edge Pop-up Menu
• Link out to MiMI web site and other external
  resources
• Edit node/edge annotation
• Query BioNlp
• Graph Match with SAGA
• Select multiple nodes and edges and get graph
  match via SAGA against KEGG human pathways
  database
• Check Out Latest Version
• Click Get Latest Version button to download
  the latest plugin version

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Plugin Implementation

• Implemented with Java
• All of cytoscape is written in Java
• Cytoscape provides a plugin interface
• Cytoscape v2.4.0
• Java IDE Eclipse 3.2.0
• JDK and JRE 1.5.0_10

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Install Cytoscape MiMI Plugin

• Install JDK, JRE gt1.5
• Install Cytoscape v2.4.0
• Install Cytoscape MiMI Plugin
• Lateste version

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Startup Plugin

• Local
• YourCytoscapeHomeDir/cytoscape.bat
• Parameters
• -P ltproperty filesgt
• WebStart
• http//mimi.ncibi.org/MiMI/search.jsp?actionlucen
  ekeywordpwp1

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Useful Link for Plugin Development

• Cytoscape Wiki
• Google Group Cytoscape Discuss
• Cytoscape User Manual
• Cytoscape Java Doc
• Cytoscpe Plugin Tutorial

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MiMI RDB
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TIMBER gt RDB

• Why?
• XQuery against XML database is too slow and batch
  search is almost impossible
• How?
• XSLT processor Xalan
• openXML

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Acknowledgement

• Dr. David States
• Alex Ade
• Terry Triplett
• Glenn Tarcea
• Yuanyuan Tian
• Terry Weymouth
• Yongsheng Huang

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