On deducing causality in metabolic networks

© 2008 Bodei et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution Licens

A Taxonomy of Causality-Based Biological Properties

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

A Formal Approach to Open Multiparty Interactions

We present a process algebra aimed at describing interactions that are multiparty, i.e. that may involve more than two processes and that are open, i.e. the number of the processes they involve is not fixed or known a priori. Here we focus on the theory of a core version of a process calculus, without message passing, called Core Network Algebra (CNA). In CNA communication actions are given not in terms of channels but in terms of chains of links that record the source and the target ends of each hop of interactions. The operational semantics of our calculus mildly extends the one of CCS. The abstract semantics is given in the style of bisimulation but requires some ingenuity. Remarkably, the abstract semantics is a congruence for all operators of CNA and also with respect to substitutions, which is not the case for strong bisimilarity in CCS. As a motivating and running example, we illustrate the model of a simple software defined network infrastructure.Comment: 62 page

Programmazione logica e biochimica: analisi di reflui

L'inquinamento ambientale e' una delle problematiche piu' importanti perche' la vita degli organismi e' in pericolo in presenza di un ambiente contaminato. Il monitoraggio biologico ha lo scopo di tenere sotto controllo il livello di inquinamento studiando le variazioni biologiche che avvengono negli organismi in relazione alla loro esposizioni a sostanze tossiche. Tramite il rilevamento dell'attivita' enzimatica nei reflui e' possibile valutare il livello tossicologico di un refluo per l'ambiente. L'utilizzo della programmazione logica ci ha permesso di descrivere il dominio dei reflui e, partendo dai dati di laboratorio, di indurre la loro composizione individuando le sostanze tossiche responsabili dell'impatto sull'attivita' enzimatica

A static analysis for Brane Calculi providing global occurrence counting information

In this paper we propose a static analysis for Brane Calculi [1], based on Abstract Interpretation [2] techniques. Our analysis statically approximates the dynamic behaviour of Brane systems, by providing a description of the possible hierarchical structure of membranes and of the processes possibly associated to each membrane, together with global occurrence counting information. Our analysis can be computed in polynomial time. We apply it to investigate several biological systems in which occurrence counting information plays a crucial role. In particular, our case study concerns the formation of the haemoglobin polymer in presence of alterations and investigate the influence that such alterations have on the ability of the haemoglobin polymer to bind oxygen molecules