Bodei C, Bracciali A, Chiarugi D & Gori R (2010) A Taxonomy of Causality-Based Biological Properties. Merelli E (Editor) & Quaglia P (Editor) 3rd Workshop "From Biology To Concurrency and back", FBTC 2010, a satellite event of the Joint European Conference on Theory and Practice of Software, ETAPS 2010, Paphos, Cyprus, 27.03.2010-27.03.2010. Electronic Proceedings in Theoretical Computer Science, 19, pp. 116-133. http://arxiv.org/pdf/1002.4067v1.pdf; https://doi.org/10.4204/EPTCS.19.8
Abstract We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the implication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the characterization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form  calculus. We illustrate an application of this framework to a portion of a real metabolic pathway.
Journal Electronic Proceedings in Theoretical Computer Science: Volume 19