From Solvable to Executable Models of Biological Systems

Classical modeling approaches for biology are mainly grounded in mathematics, and specifically on ordinary differential equations (ODE). Process calculi-based conceptual and computational tools are an alternative and emergent approach. Here we focus our analysis on BlenX (a beta-binders inspired programming language) showing how it is possible to easily re-use ODE models within this framework. An example will show then the advantages of moving into a stochastic approach. This is the preliminary version of a paper that was published in Proceedings of Pacific Symposium on Biocomputing (PSB 2009), January, 2009. The original publication is available at http://psb.stanford.edu/psb-online/proceedings/psb09/