In the the previous post I discussed the integration of OpenCL into Processing by means of its library mechanism. An early version of a new OpenCL-physics library, based on traer.physics, was used to simulate a couple of particle systems in real-time (N-Body and Springs). An interesting application of these new methodologies is to carry out GPU-acceleration of compute operations in Cytoscape. Networks of protein-protein interactions handled in Cytoscape usually involve thousands of nodes and edges. The visualization and analysis of such networks is computationally demanding, and the use of parallel processing on GPUs provides a way to cope with this complexity. So what I did as a new experiment with OpenCL and OpenGL was to use CLPhysics to simulate a force-directed network layout in Cytoscape.
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