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