Models of biochemical systems presented as a set of formal reaction rules with kinetic expressions can be interpreted with different semantics: as either deterministic Ordinary Differential Equations, stochastic continuous-time Markov Chains, Petri nets or Boolean transition systems. While the formal composition of reaction models can be syntactically defined as the (multiset) union of the reactions, the hybrid composition of models in different formalisms is a largely open issue. In this paper, we show that the combination of reaction rules with conditional events, as the ones already present in SBML, does provide the expressive power of hybrid automata and can be used in a non standard way to give meaning to the hybrid composition of heterogeneous models of biochemical processes […]
Sun, Sep 1, 2013
Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing multi-scale models for instance. While perturbation theory is a standard mathematical tool to analyze the different time scales of a dynamical system, and decompose the system accordingly, tropical methods provide a simple algebraic framework to perform these analyses systematically in polynomial systems. The crux of these tropicalization methods is in the computation of tropical equilibrations […]
Sun, Sep 1, 2013
Mon, Oct 1, 2012
Mon, Oct 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
Wed, Dec 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
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Wed, Oct 1, 2008
Abstract
Tue, Jul 1, 2008
Sun, Jun 1, 2008
Fri, Feb 1, 2008
There are 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. On the other hand, the module constructs may interfere with the programming constructs, and may be redundant with the other scope mechanisms of a specific programming language, such as closures for instance […]
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
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