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Open Discussion of Modeling and Computational Approaches to Cellular Signaling

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Using Simulation Software: What Software Do You Use?

9 August 2006

Nancy R. Gough

In a recent STKE Review, Hlavacek et al. discuss how to use rules based on protein interactions to develop models for studying cell signaling.

Have you developed simulation software or applied any of the existing tools to your system? What kinds of issues have you encountered? How do the existing tools need to evolve? What mark up language are you using for data exchange compatibility? Share your experiences with others people trying to model and simulate cell signaling and biochemical events.

Some rule-based simulation software tools and languages include:

Share your favorite simulation or modeling software!

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Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882