Outdated_Cytoscape_3.0/HyperEdges

TableOfContents([2])

About this document

This document considers some of the issues with adding hyperedges to Cytoscape 3. These issues are presented by looking at the feedback and lessons learned in implementing the HyperEdgeEditor plugin.

Introduction and Terminology

A hyperedge is an Edge that connects two or more Nodes. Hyperedges may be useful for representing more complex structures like reactions and protein complexes.

Since this document makes heavy reference to the HyperEdgeAPI, a good familiarity with the existing HyperEdgeEditor plugin is essential. See the References section for informaiton on how to familiarize yourself with this plugin.

The HyperEdgeEditor plugin, adds hyperedge functionality to Cytoscape 2.6 (referred to here as the "plugin model"). The future Cytoscape 3 hyperedge model will be referred to as the "C3 model". There is a skeleton framework for the C3 model in !fastGraphCy3 trunk (http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/mes/fastGraphCy3/src/org/cytoscape/model/).

Status

How to Discuss

To view/add discussion comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Try to keep the discussion as concrete and constructive as possible. Be sure to include today's date and your name for each comment.

Discussion Topic

Source of Issue

Complexities

Use Cases

Possible Solution Strategies

General Notes

References

The HyperEdgeEditor plugin adds an underlying hyperedge model (the HyperEdge API) to Cytoscpe 2.6, along with a very simple editor for creating and editing hyperedges. More information can be obtained on the HyperEdgeEditor plugin from the following sources:

1. See [wiki: HyperEdgeAPI] for more info about the underlying hyperedge model.

2. JavaDocs for the hyperedge model is available at [http://www.cytoscape.org/agilent/build/api-docs/index.html Java HyperEdge API Java Documents].

3. Source code for hyperedge model is available from via SVN from grenache.ucsd.edu/cellar/common/svn/csplugins/trunk/agilent/creech/HyperEdge.

   • See cytoscape.hyperedge.HyperEdge for an overall description of terms and assumptions.

4. Source code for the hyperedge editor is available from via SVN from grenache.ucsd.edu/cellar/common/svn/csplugins/trunk/agilent/creech/HyperEdgeEditor

5. Once the HyperEdgeEditor is loaded, two sample hyperedge networks via File->Import->HyperEdge Sample Networks. This will build two hyperedge networks--Glycolysis Reaction network and a Krebs Cycle network. You can look at the source code that generates these two networks in cytoscape.hyperedge.editor.SampleNetworks.java

Discussion