Archive for the ‘cytoscape’ Tag

OpenCL in Cytoscape   Leave a comment

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.

Read the rest of this entry »


Posted April 26, 2011 by ac in Programming

Tagged with , , ,

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.

Read the rest of this entry »

Using Processing to create Cytoscape plugins   4 comments

Cytoscape is a cross-platform, open source application for visualization and analysis of networks. It is widely used in the field of Systems Biology to visualize different types of biological networks (like protein-protein interactions). It also has a plugin mechanism for extending its core functionality. Cytoscape is written in Java, so this open the possibility of using Processing to create Cytoscape plugins. I just put together a small template for creating Processing plugins for Cytoscape using Eclipse, keep reading for more details.

Read the rest of this entry »

Posted March 17, 2011 by ac in Programming, Science, Visualization

Tagged with , , , ,