A Taxonomy of Causality-Based Biological Properties

Chiara Bodei
(Dipartimento di Informatica - Università di Pisa)
Andrea Bracciali
(Dipartimento di Informatica - Università di Pisa)
Davide Chiarugi
(Dipartimento di Scienze Matematiche e Informatiche, Università di Siena)
Roberta Gori
(Dipartimento di Informatica - Università di Pisa)

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.

In Emanuela Merelli and Paola Quaglia: Proceedings Third Workshop From Biology To Concurrency and back (FBTC 2010), Paphos, Cyprus, 27th March 2010, Electronic Proceedings in Theoretical Computer Science 19, pp. 116–133.
Published: 26th February 2010.

ArXived at: https://dx.doi.org/10.4204/EPTCS.19.8 bibtex PDF

Comments and questions to: eptcs@eptcs.org
For website issues: webmaster@eptcs.org