Le développement de langages formels pour modéliser les systèmes biologiques ouvre la voie à la conception de nouveaux outils de raisonnement automatique destinés au biologiste modélisateur. La machine abstraite biochimique BIOCHAM est un environnement logiciel qui offre un langage simple de règles pour modéliser des interactions biomoléculaires, et un lan-gage puissant fondé sur la logique temporelle pour formaliser les propriétés biologiques du sys-tème. En s'appuyant sur ces deux langages formels, il devient possible d'utiliser des techniques d'apprentissage automatique pour inférer de nouvelles règles de réaction, estimer les valeurs des paramètres cinétiques, et corriger ou compléter les modèles semi-automatiquement […]
Sat, Dec 1, 2007
One central issue in systems biology is the definition of formal languages for describing complex biochemical systems and their behavior at different levels. The biochemical abstract machine BIOCHAM is based on two formal languages, one rule-based language used for modeling biochemical networks, at three abstraction levels corresponding to three semantics: boolean, concentration and population; and one temporal logic language used for formalizing the biological properties of the system. In this paper, we show how the temporal logic language can be turned into a specification language […]
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
BIOCHAM (the BIOCHemical Abstract Machine) is a software environment for modeling biochemical systems. It is based on two aspects: (1) the analysis and simulation of boolean, kinetic and stoch-astic models and (2) the formalization of biological properties in temporal logic. BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model […]
Sat, Apr 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
Beyond numerical simulation, the possibility of performing symbolic computation on bio-molecular interaction networks opens the way to the design of new automated reasoning tools for biologists/modelers. The Biochemical Abstract machine BIOCHAM provides a precise semantics to biomolecular interaction maps as concurrent transition systems. Based on this formal semantics, BIOCHAM offers a compositional rule-based language for modeling biochemical systems, and an original query language based on temporal logic for expressing biological queries about reachability, checkpoints, oscillations or stability […]
Thu, Dec 1, 2005
Fri, Jul 1, 2005
With the advent of formal languages for modeling bio-molecu-lar interaction systems, the design of automated reasoning tools to assist the biologist becomes possible. The biochemical abstract machine BIOCHAM software environment offers a rule-based language to model bio-molecular interactions and an original temporal logic based language to formalize the biological properties of the system. Building on these two formal languages, machine learning techniques can be used to infer new molecular interaction rules from temporal properties […]
Fri, Apr 1, 2005