Abstract
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Complex network analysis provided deep insight of emerging properties of real systems in many application fields, the
link between topological and functional role of the nodes (system elements) being the most important task of this kind of studies.
Here we propose a Cytoscape plugin (GIANT) able to perform network analysis according to the Guimera-Amaral cartography, providing a vivid picture of the topological/functional relationship at both nodes and global network level.
Screenshot
Requirements
- For Cytoscape 2.8.3: Java Runtime Environment 5 or upper version Cytoscape 2.8.3 or lower version
- For Cytoscape 3.0.0: Java Runtime Environment 7 or upper version Cytoscape 3.0.0
Notes
- For Cytoscape 2.8.3: For the proper plugin functioning, it's necessary to install GIANT using the "Install Plugin from File" button under the "Plugins" menu in the Cytoscape menu bar.
- For Cytoscape 3.0.0: For the proper plugin functioning, it's necessary to install GIANT using the "Install from File..." button in the App Manager under the "Apps" menu in the Cytoscape menu bar. You have to load a network before using GIANT.
Network, Clusters and Attributes File Standard
- Network File Format: GIANT uses the classic Cytoscape Network Importer to load a network. Please see the Cytoscape documentation for more details.
- Clusters File Format: Internally, the clusters file uses a tab separated value standard. For each line, the first element corresponds to the node and the second element corresponds to the specified cluster.
- Attributes File Format: GIANT is able to take in input a Cytoscape nodes attributes file. First line must be the header and the first element must be "ID". Please download the README-FIRST.txt file for more detailed instructions: README-FIRST.txt
Downloads
- For Cytoscape 2.8.3 or older version: GIANT v1.0 JAR GIANT v1.0 JAVA sources
- For Cytoscape 3.0.0: GIANT v1.0 JAR GIANT v1.0 JAVA sources
- Sample Dataset: Hemoglobin
Video Tutorials
- GIANT installation
- How to load a network
- How to load clusters information
- Using built-in clustering algorithms
- Starting cartographic analysis
- A better network visualization
Publication
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Pending publication approval...