Miscellaneous Cytoscape plugin development

This page was made as a quick reference on the status of the work I'm doing on Cytoscape plugin development.

Cytoscape is an open source software platform for complex network analysis.

You can contact me if needed. See the home page for details.

Brief history

2012-06-25: Fibonacci Heap version 0.2: explicitly handle null parameter in meldWith; some rearrangement of code.

2012-06-15: First upload of Fibonacci Heap and modifications to NetworkAnalyzer.

Fibonacci Heap

As I couldn't find a Java implementation of a Fibonacci Heap under LGPL license, and it is not clear to me what different licenses are compatible and can be linked together with a Cytoscape core plugin, I decided to write my own implementation and release it under the LGPL v3 or later (same license as Cytoscape).

Status

Version 0.2, feature complete, currently being tested. No real documentation yet except for code comments.

Downloads

Betweenness Centrality in NetworkAnalyzer

The NetworkAnalyzer core plugin does not support weighted networks. Since I needed to calculate Betweenness Centrality indexes on weighted networks, I enhanced the core plugin in Cytoscape 2.8 to meet my needs. This code uses my implementation of the Fibonacci Heap (see above), but it can be adapted to use a different implementation. The FibonacciHeap class must be added to the Cytoscape project in the cytoscape.util.intr package.

Status

This version was coded using SVN rev 29112 of Cytoscape 2.8 trunk as a starting point.

• computes Betweenness Centrality index (on nodes and edges) and Stress Centrality on weighted networks, under the assumption that weights are strictly positive
• currently being tested, might need tweaking (e.g. does the unweighted divide BC by 2 for undirected networks?)
• UI is temporary, currently evaluating possibilities for something more usable. Quick UI supports toggling weighted network analysis, interpreting weights as costs or link strength, and choosing any Double edge attribute as weight
• existing installations of Cytoscape must backup NetworkAnalyzer.xml in the user settings and remove the file, letting NetworkAnalyzer install a new version; otherwise the plugin will exit with an exception on weighted networks

Downloads

The "Files" archive includes FibonacciHeap.java. The "Patch" release does not. Please download it from above. Also, instructions to use the patch file are not provided at this time.