I had been wanting for some time to write a CytoScape Plugin, however I decided to modify an existing plugin, CentiScaPe, adding additional features. CentiScaPe calculates certain centrality measures for a network. After a considerable search I found the source code here at https://bitbucket.org/giovanniscardoni/centiscapepublic. I discovered a bug in the eigenvector centrality calculation -- the dominant eigenvector wasn't being chosen. I fixed that and added a transposed version with the transpose of the adjacency matrix, added PageRank and PageRank transpose, two methods of calculation -- the power method and eigenvalue decomposition plus normalize to 1.0 or 100%.
I've added 30 some random number distributions to create edge and or node attributes from the cern.jet.random library (found an issue with Distributions.nextWeibull and Zipf was just the Zeta Distribution) however I have not yet added input screens for selecting among the distributions or to input parameters.
I'm planning to add features to calculate maximum flows and minimum cost transportation in networks, and maybe neural network and markov process modeling and maybe a few other things. Current state of my mods are here in my google drive.
I've moved up to writing java with Eclipse and Maven -- woohoo! I was using jedit and the command prompt. And then I was wondering if Prism Model Checker could be integrated with Cytoscape.