ugurdogrusoz
commented
7 years ago Looks like this has already been done with Cytoscape 3.5
Closed maxkfranz closed 7 years ago
ugurdogrusoz
commented
7 years ago Looks like this has already been done with Cytoscape 3.5
Background
Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
Goal
Implement the CoSE layout as a Cytoscape app.
Description
Cytoscape provides compound node support, which means that nodes can be put inside other (i.e. parent) nodes. However, Cytoscape does not yet have a layout that takes into account compound nodes. The CoSE algorithm [1] is already supported by Cytoscape.js with multiple implementations, and there is an implementation of the CoSE algorithm in Java. This project would use the existing CoSE implementation in Java to provide a layout app for Cytoscape.
ChiLay project includes a Java implementation of CoSE: http://www.cs.bilkent.edu.tr/~ivis/chilay.html
The sources are in a Github project (master branch has the latest CoSE): https://github.com/iVis-at-Bilkent/chilay
Section titled “Local Usage” under Chapter 3 of the the Programmer’s Guide has sample code to make use of CoSE in a Java application: http://www.cs.bilkent.edu.tr/~ivis/chilay/ChiLay-2.0-PG.pdf
[1] U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, "A Layout Algorithm For Undirected Compound Graphs", Information Sciences, 179, pp. 980-994, 2009.
Potential Mentors
Ugur Dogrusoz, Christian Lopes, Mike Kucera
Contact
ugurdogrusoz@gmail.com