Cytoscape Retreat 2008 & Automatic Label Plugin Progress

17 07 2008

This year’s Cytoscape Retreat is being held on campus (University of Toronto – Terrence Donnelly Centre for Cellular and Biomolecular Research Buildling). It’s been a good chance to meet others that are also working on Cytoscape. And it is also a good place to practice giving demos.. :)

For the past week or so, I’ve been reading more source code! But this time they were graph drawing classes that others have already implemented in Cytoscape. My mentors have suggested that I check if I can use an existing graph drawing algorithm if they’re suitable, instead of writing my own if it already exists. So I’ve been reading the Spring-Embedded JGraph layout code that Cytoscape currently offers through JGraph. I was planning to copy the source code over and make slight modifications to them in order to implement my own plugin. However, the current Spring-Embedded algorithm relies heavily on other JGraph classes within their layout packages. This has become a problem in the development of my plugin, because my plugin will be a Cytsocape plugin and it will not be offered under JGraph. So in order to make this all work, I can either:

  1. Take whatever classes that the Spring-Embedded algorithm relies on, and include them in my label plugin’s jar file.
  2. Write my label plugin based on the Cytoscape plugin template, and copy pieces of the implementation in the Spring-Embedded layout algorithm over to my label plugin, wherever they are relevant.

The first approach does not work out very well. Like as I mentioned above, the Spring-Embedded layout has been implemented in such a way that it relies heavily on its fellow JGraph classes. Hence, if I were to copy over the necessary classes needed in order to make the Spring-Embedded layout run as a simple Cytoscape plugin, I will have to copy over a lot of classes due to the complex dependencies involved. So I’m most likely going to give the second approach a shot, unless I can find a third approach that will be even better. Taking the second approach should not be too difficult since the Spring-Embedded algorithm is quite simple.

I will continue to speak to other Cytoscape developers at the retreat, and see what others think about this problem. I’m sure I will get some interesting feedback on this issue, and maybe even some interesting solutions!




One response

17 07 2008
The Third Bit » Blog Archive » Up On Stage

[…] Having spent most of the last week and a half reading source code, she got up a few minutes ago and gave a quick talk about her Google Summer of Code project at the Cytoscape retreat. I was impressed once again with […]

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