Title :

Complex Functional Rates in Rule-Based Languages for Biochemistry

Author(s) :

Versari, Cristian [Auteur correspondant]
Programming Languages for Biological Modeling and Simulation [BioComputing]
Zavattaro, Gianluigi [Auteur]
Foundations of Component-based Ubiquitous Systems [FOCUS]
Department of Computer Science and Engineering [Bologna] [DISI]

Journal title :

Transactions on Computational Systems Biology

Pages :

123-150

Publisher :

Springer

Publication date :

2012

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
Informatique [cs]/Langage de programmation [cs.PL]
Informatique [cs]/Logique en informatique [cs.LO]
Sciences du Vivant [q-bio]

English abstract : [en]

Rule-based languages (like, for example, Kappa, BioNetGen, and BioCham) have emerged as successful models for the representation, analysis, and simulation of bio-chemical systems. In particular Kappa, although based on ...
Show more >Rule-based languages (like, for example, Kappa, BioNetGen, and BioCham) have emerged as successful models for the representation, analysis, and simulation of bio-chemical systems. In particular Kappa, although based on reactions, differs from traditional chemistry as it allows for a graph-like representation of complexes. It follows the "don't care, don't write" approach: a rule contains the description of only those parts of the complexes that are actually involved in a reaction. Hence, given any possible combination of complexes that contain the reactants, such complexes can give rise to the reaction. In this paper we address the problem of extending the "don't care, don't write" approach to cases in which the actual structure of the complexes involved in the reaction could affect it (for instance, the mass of the complexes could influence the rate). The solutions that we propose is κ F , an extension of the Kappa-calculus in which rates are defined as functions of the actually involved complexes.Show less >

Language :

Anglais

Popular science :

Non

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL