John "Scooter" Morris¹
and
Iliana Avila-Campillo², Hood Lab, Institute for Systems Biology, Seattle
¹
Resource for Biocomputing, Visualization, and Informatics
University of California, San Francisco
²
Previously at the Hood Lab, Institute for Systems Biology, Seattle
What are Metanodes?Meta: Something on an abstraction level higher than the current. To go meta means to take a step back and look at the bigger picture.
A metanode is a graph node that represents a subgraph that is at a lower level of abstraction. For example, a metanode can represent a protein complex if it's subgraph is composed of individual nodes and edges representing interacting proteins. A metanode at an even higher level of abstraction can represent a group of protein complexes (metanodes can be recursive). Metanodes simplify complex networks and can be used to represent complex hierarchical systems in two dimensions.
Metanodes PlugInThe Metanodes PlugIn is a Cytoscape PlugIn that provides a dialog (see figure below) that allows users to select a group of nodes in a network and create a metanode that represents them. This metanode can be "collapsed" and "expanded". New metanodes can contain child networks that are composed of metanodes, thus creating a hierarchical structure in the network. The PlugIn transfers node attributes to the new metanode by doing a performing operation on its children nodes.
Installation Instructions
- Download metanodepl.jar
- Copy metanodepl.jar to the plugins folder of your Cytoscape installation
- Restart Cytoscape
- MetaNode commands are now available as node context menus or under the plugins menu
Metanodes LibraryThe Metanodes Library is a Java package for Cytoscape that contains classes and methods to create, collapse, expand, and destroy metanodes. To use the library you can include its jar in your classpath. If you want to load a plugIn into Cytoscape that makes use of it, make sure you include it in your plugIn's jar file.
Download Metanodes Library jar file.
IMPORTANT NOTE: Implementation of MetaNodeUtils class, and other Metanodes classes in the library will change in the future. A complete reimplementation of groups and metanodes is planned for Cytoscape 2.5
Known problems
- Cytoscape Editor and Metanodes PlugIn do not interact well. For example, creating edges between metanodes using the editor, and then expanding/collapsing the metanodes seems to loose the newly created edges.
Laboratory Overview | Research | Outreach & Training | Available Resources | Visitors Center | Search
