- Full text PDF available (41)
This paper investigates a hybrid approach to modeling molecular interactions in biology. P systems, π-calculus, and Petri nets models , and two tools, Daikon, used in software reverse-engineering, and PRISM, a probabilistic model checker, are investigated for their expres-siveness and complementary roles in describing and analyzing biological systems. A… (More)
In this paper we propose a new way to represent recognizer P systems with active membranes based on Production Systems techniques. This representation allows us to express the set of rules and the configurations in each step of the evolution as facts in a knowledge base. We provide a CLIPS program to simulate the evolutions of this variant of P systems.
This paper presents two approaches based on metabolic and stochastic P systems, together with their associated analysis methods, for modelling biological systems and illustrates their use through two case studies.
In this paper we propose an extension of the modelling framework based on P systems which explicitly includes modularity. Modularisation in cellular systems can be produced by chemical specificity and spatial localisation in different compartments. Both these features can be easily specified and analysed in P systems using sets of rewriting rules to… (More)
In this paper we present P systems as a reliable computational modelling tool for Systems Biology that takes into account the discrete character of the quantity of components of biological systems, the inherently randomness in biological phenomena and the key role played by membranes in the function of living cells. We will introduce two different… (More)
Quorum sensing is a cell-density-dependent gene regulation system that allows an entire population of bacterial cells to communicate in order to regulate the expression of certain or specific genes in a coordinated way depending on the size of the population. We present a model of the quorum sensing system in Vibrio fischeri using a variant of membrane… (More)
SUMMARY The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using… (More)
Flowering is a crucial process that demands substantial resources. Carbon metabolism must be coordinated with development through a control mechanism that optimizes fitness for any physiological need and growth stage of the plant. However, how sugar allocation is controlled during the floral transition is unknown. Recently, the role of a CONSTANS (CO)… (More)
We introduce a variant of P systems where rules have associated a real number providing a measure for the " intrinsic reactivity " of the rule and roughly corresponding to the kinetic coefficient which, in biochemistry , is usually associated to each molecular reaction. The behaviour of these P systems is then defined according to a strategy which, in each… (More)