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.

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

Version Release date ZIP Archive
0.2 2012-06-25 fibonacci_heap_v0.2.zip
0.1 2012-06-15 fibonacci_heap_v0.1.zip

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.

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.

Version FibonacciHeap Release date ZIP - Files ZIP - Patch
0.1 0.2 2012-06-25 networkanalyzer_mod_v0.1+fh_v0.2.zip --
0.1 0.1 2012-06-15 networkanalyzer_mod_v0.1.zip networkanalyzer_mod_v0.1_patch.zip