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
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
In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning to ols for querying the temporal properties of the system under all its possible behavi ors […]
Wed, Dec 1, 2004
Recent progress in high-throughput data-production technologies pushes research towardsystems biology, focusing on the global interaction between the components ofbiomolecular processes. In this article we present a formal modelling environment fornetwork biology, called the Biochemical Abstract Machine (BIOCHAM). Biochamdelivers precise semantics to biomolecular interaction maps […]
Fri, Oct 1, 2004