Cytoscape and OPENGL2   Leave a comment

In earlier posts I talked about using Processing to create Cytoscape plugins, and also about the new OpenGL rendering engine for Processing, OPENGL2. This engine introduces several improvements over the original OPENGL renderer, and it is already available in the latest pre-release of Processing, 0194. A few days ago, I put together a simple template project for Eclipse that attempts to make writing Processing-based plugins for Cytoscape a little easier. Now I updated this template to use the OPENGL2 engine as the renderer for the plugin. Download here.

As a first prototype plugin, I wrote a very simple network visualization using force-directed layout where each connected pair of nodes are attached to each other by springs. The nodes and edges are loaded into the plugin from the currently selected data in the Cytoscape session. I used the traer.physics library to generate the particle system with the spring forces between the nodes:

Fig18

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