Tropical geometry can be used to find the order of time scales of variables in chemical reaction networks and search for model reductions [SGF+15]. In this report, we consider the problem of solving tropical equilibration problems in ODE systems of the BioModels model repository. We are interested in the existence of solutions both in R and Z […]
Fri, Apr 1, 2022
Global constraints were introduced two decades ago as a means to model some core aspects of combinatorial problems with one single constraint for which an efficient domain filtering algorithm can be provided, possibly using a complete change of representation. However, global constraints are just constraint schemas on which one would like to apply usual constraint operations such as reification, i.e. checking entailment, disentailment and negating the constraint […]
Mon, Oct 1, 2012
Sun, Jul 1, 2012
Mon, Mar 1, 2010
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
Module systems are an essential feature of programming languages as they facilitate the re-use of existing code and the development of general purpose libraries. There are however two somewhat contradictory ways of looking at modules in a given programming language. On the one hand, module systems are largely independent of the particulars of programming languages, and several examples of module systems have indeed been adapted to different programming languages […]
Fri, Dec 1, 2006
Cancer treatments based on the administration of medicines at different times of the day have been shown to be more efficient against malign cells and less damaging towards healthy ones. These results might be related to the recent discovery of links between the circadian clock, (controlled by the light/dark cycle of a day), and the cell cycle. However, if many models have been developed to describe both of these cycles, to our knowledge none has described a real interaction between them […]
Fri, Dec 1, 2006
Most of the work on temporal representation issues in Machine Learning deals with the problem of learning/mining temporal patterns from a large set of temporal data. In this paper we investigate the somewhat different problem of learning the behavioral rules of a system from its observed temporal properties formalized in temporal logic. Our interest in this problem arose from Systems Biology and the development of machine learning techniques for learning biochemical reaction rules and kinetic parameters in the Biochemical Abstract Machine BIOCHAM […]
Thu, Dec 1, 2005
We present a translation of the asynchronous pi-calculus into linear concurrent constraint languages (LCC), and use that translation and the recent advances in the logical semantics of LCC to give an account of the restriction operator in Intuitionistic Linear Logic. This allows us to express as a Linear Logic theory, a notion of space similar to what has recently been introduced by Gabbay and Pitts in modal logics. It also permits to relate more closely the pi-calculus and CC paradigms that people have wanted to compare for a long time […]
Mon, Dec 1, 2003