Quick Start Guide

1. Quick Start Guide
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http://www.mongkie.org
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2. CONTENTS
 CONTENTS
• Overview
• Features
• Installation
• Tutorials
• Development
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3. Overview
 MONGKIE
• MONGKIE is an integrated network visualization platform which allows us to analyze inter-
connected biological data in an interactive manner with knowledge integration environment. It
provides Import/Export Network, Expression Overlay, Network Clustering/Grouping, Pathway
Integration/Visualization, Over-Representing Analysis(GO/Pathway) and Analysis Pipelines
consisting of other modules.
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4. Features (1/5)
 Features
• Integration & Analysis
 Import/ Export Gene List & Network
 Network Exploring
 Network Clustering & Ranking
 Expression Overlay
 Over-representation Analysis(GO, Pathway)
 Pathway DB Integration Analysis OR Individual Analysis
 Network Pipeline Analysis consisting of integration and analysis
modules(Commonly used network analysis)
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5. Features (2/5)
 Features
• Visualization
 Supports various types of nodes, edges and arrows (To represent
diverse types of biological entities, interactions and controls)
 Offers automatic graph layouts and graph manipulation techniques
 Customize visual properties through the integrated visual editor UI
 Explore networks in many ways through Expansion, Zooming, Panning,
Highlighting, Dragging, Grouping, Filtering, search Functionalities
 Export as XML, CSV, EPS, SVG and various bitmap images
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6. Features (3/5)
 Features
• Optimized Data
 Integrated Protein-Protein interaction data
 Integrated Pathway data (from KoPath, Integrated Human Pathway
Database)
 Can be easily applied to any biological data which can be modeled as
network structures (ex) gene-drug-disease interaction and association
network)
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7. Features (4/5)
 Features
• Architecture (1/2)
 Java-based application built on top of NetBeans platform that supports
modular(plug-in) architecture
 Platform-independent & easily extendable with additional functionalities
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8. Features (5/5)
 Features
• Architecture (2/2)
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9. Installation
 Requirements
• Java SE Download
 http://www.oracle.com/technetwork/java/javase/downloads/index.html
• Download Mongkie :
 http://mongkie.org/index.php/download
 Installation
• Windows
 mongkie-x.x-alpha-windows.exe file to run. Then, installer wizard runs
• Linux
 #sh mongkie-x.x-alpha-linux.sh
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10. Tutorials
 case 1.
• Import GraphML File
• Network Exploring and Layout Setting
• Clustering & Grouping
• Export to Image
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11. Tutorials
 Create Network
• Import file
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12. Tutorials
 Create Network
• Import file
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13. Tutorials
 Create Network
• Import file
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14. Tutorials
 Create Network
• Imported Network
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15. Tutorials
 Network Exploring
• find UBC (symbol name)
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16. Tutorials
 Setting Layout
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17. Tutorials
 Clutering & Grouping
• Select Clustering Algorithm and run
Select algorithm
Run
Select Group
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18. Tutorials
 Export
• Export to Image(JPEG)
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19.  Export
• Export to Image
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20. Q&A
http://www.mongkie.org
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