Mon, Oct 1, 2012
Sun, Jul 1, 2012
Petri-nets are a simple formalism for modeling concurrent computation. Recently, they have emerged as a powerful tool for the modeling and analysis of biochemical reaction networks, bridging the gap between purely qualitative and quantitative models. These networks can be large and complex, which makes their study difficult and computationally challenging […]
Tue, May 1, 2012
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
Wed, Dec 1, 2010
Wed, Dec 1, 2010
Mon, Nov 1, 2010
Motivation: In Systems Biology, an increasing collection of models of various biological processes is currently developed and made available in publicly accessible repositories, such as biomodels.net for instance, through common exchange formats such as SBML. To date, however, there is no general method to relate different models to each other by abstraction or reduction relationships, and this task is left to the modeler for re-using and coupling models. In mathematical biology, model reduction techniques have been studied for a long time, mainly in the case where a model exhibits different time scales, or different spatial phases, which can be analyzed separately […]
Wed, Sep 1, 2010
In systems biology, the number of 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 show how the validation of a coupled model and the optimization of its parameters with respect to biological properties formalized in temporal logics, can be done automatically by model-checking. More specifically, we illustrate this approach with the coupling of existing models of the mammalian cell cycle, the p53-based DNA-damage repair network, and irinotecan metabolism, with respect to the biological properties of this anticancer drug […]
Tue, Dec 1, 2009
The existence of links between the cell division cycle and the circadian clock has been recently discovered. In this research report, we perform a small in silico analysis of how mutations on the clock genes composing the mammalian circadian clock affect the phenotype of the cell cycle. For this purpose, we use a coupled model of the mammalian circadian clock and the mammalian cell cycle where the latter one is entrained by the former one via a common protein kinase WEE1 […]
Tue, Dec 1, 2009
Tue, Dec 1, 2009
Sat, Aug 1, 2009
Mon, Jun 1, 2009
Sun, Feb 1, 2009
Systems biologists build models of bio-molecular processes from knowledge acquired both at the gene and protein levels, and at the phenotype level through experiments done in wildlife and mutated organisms. In this chapter, we present qualitative and quantitative logic learning tools, and illustrate how they can be useful to the modeler. We focus on biochemical reaction models written in the Systems Biology Markup Language SBML, and interpreted in the Biochemical Abstract Machine BIOCHAM […]
Mon, Dec 1, 2008
Wed, Oct 1, 2008
Abstract interpretation is a theory of abstraction that has been introduced for the analysis of programs. In particular, it has proved useful for organizing the multiple semantics of a given programming language in a hierarchy corresponding to different detail levels, and for defining type systems for programming languages and program analyzers in software engineering. In this paper, we investigate the application of these concepts to systems biology formalisms […]
Fri, Aug 1, 2008
Sun, Jun 1, 2008
Fri, Feb 1, 2008