Finding mathematical models satisfying a specification built from the formalization of biological experiments, is a common task of the modeler that techniques like model-checking help solving, in the qualitative but also in the quantitative case. In this article we go one step further by defining a continuous degree of satisfaction of temporal logic formulae with constraints. We show how such a satisfaction measure can be used as a fitness function with state-of-the-art evolutionary optimization methods in order to find biochemical kinetic parameter values satisfying a set of biological properties formalized in temporal logic […]
Wed, Jun 1, 2011
In systems biology, the number of available models of cellular processes increases rapidly, but re-using models in different contexts or for different questions remains a challenging issue. In this paper, we study the coupling of different models playing a role in the mammalian cell cycle and in cancer therapies. We show how the formalization of experimental observations in temporal logic with numerical constraints can be used to compute the unknown coupling kinetics parameter values agreeing with experimental data […]
Sun, May 1, 2011
Mon, Jun 1, 2009
Wed, Oct 1, 2008