Nicoletta Cocco

Petri nets for modelling metabolic pathways: a survey

In the last 15 years, several research efforts have been directed towards the representation and the analysis of metabolic pathways by using Petri nets. The goal of this paper is twofold. First, we discuss how the knowledge about metabolic pathways can be represented with Petri nets. We point out the main problems that arise in the construction of a Petri net model of a metabolic pathway and we outline some solutions proposed in the literature. Second, we present a comprehensive review of recent research on this topic, in order to assess the maturity of the field and the availability of a methodology for modelling a metabolic pathway by a corresponding Petri net.

Preserving Universal Termination through Unfold/Fold

We study how to preserve universal termination besides computed answer substitutions while transforming definite programs. We consider the unfold operation both alone and combined with the introduction of a new definition and fold operations. We prove that unfold always preserves universal termination. Moreover we define a restricted version of the Tamaki-Satos transformation sequence and show that it preserves universal termination as well.

On modular termination proofs of general logic programs

We propose a modular method for proving termination of general logic programs (i.e. logic programs with negation). It is based on the notion of acceptable programs, but it allows us to prove termination in a truly modular way. We consider programs consisting of a hierarchy of modules and supply a general result for proving termination by dealing with each module separately. For programs which are in a certain sense well-behaved, namely well-moded or well-typed programs, we derive both a simple verification technique and an iterative proof method. Some examples show how our system allows for greatly simplified proofs.

Representing and Comparing Metabolic Pathways as Petri Nets with MPath2PN and CoMeta

We present two tools, MPath2PN and CoMeta, which are part of an ongoing project for representing and comparing metabolic pathways as Petri Nets. MPath2PN is intended to support an automatic translation of metabolic pathways from the major biological databases into corresponding Petri nets expressed in the input formalisms for Petri net tools. CoMeta is devised to compare metabolic pathways of different organisms through their Petri net representation produced by MPath2PN. CoMeta automatically takes the data from the KEGG database and, in the comparison, it considers both homology of reactions and behavioural aspects of the pathways as expressed by the T-invariants of the underlying Petri nets.

Comparing Metabolic Pathways through Reactions and Potential Fluxes

Comparison of metabolic pathways is useful in phylogenetic analysis and for understanding metabolic functions when studying diseases and in drugs engineering. In the literature many techniques have been proposed to compare metabolic pathways. Most of them focus on structural aspects, while behavioural or functional aspects are generally not considered. In this paper we propose a new method for comparing metabolic pathways of different organisms based on a similarity measure which considers both homology of reactions and functional aspects of the pathways. The latter are captured by relying on a Petri net representation of the pathways and comparing the corresponding T-invariant bases, which represent minimal subsets of reactions that can operate at a steady state. A prototype tool, CoMeta, implements this approach and allows us to test and validate our proposal. Some experiments with CoMeta are presented.