On functional module detection in metabolic networks

Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

A proposal of an architecture for the coordination level of intelligent machines

The issue of obtaining a practical, structured, and detailed description of an architecture for the Coordination Level of Center for Intelligent Robotic Systems for Sapce Exploration (CIRSSE) Testbed Intelligent Controller is addressed. Previous theoretical and implementation works were the departure point for the discussion. The document is organized as follows: after this introductory section, section 2 summarizes the overall view of the Intelligent Machine (IM) as a control system, proposing a performance measure on which to base its design. Section 3 addresses with some detail implementation issues. An hierarchic petri-net with feedback-based learning capabilities is proposed. Finally, section 4 is an attempt to address the feedback problem. Feedback is used for two functions: error recovery and reinforcement learning of the correct translations for the petri-net transitions

Formal and Executable Specification of Random Waypoint Mobility Model Using Timed Coloured Petri Nets for WMN

The wireless mesh network (WMN) is an emerging and cost-effective alternative paradigm for the next generation wireless networks in many diverse applications. In the performance evaluation of routing protocol for the WMN, it is essential that it should be evaluated under realistic conditions. The usefulness of specific mobility protocol can be determined by selection of mobility model. This paper introduces a coloured Petri nets (CP-nets) based formal model for implementation, simulation, and analysis of most widely used random waypoint (RWP) mobility model for WMNs. The formal semantics of hierarchical timed CP-nets allow us to investigate the terminating behavior of the transitions using state space analysis techniques. The proposed implementation improves the RWP mobility model by removing the “border effect” and resolves the “speed decay” problem

Colored Petri Net: Its application to Sucrose Biosynthesis Pathway in Plasmodium falciparum

Sucrose plays major role as macromolecule used in organisms including Plasmodium falciparum (P.f.) to generate glucose for energy production in the glycolysis pathway. A metabolic pathway is a series of chemical reactions, which goes through various intermediate compounds to transform input compounds into a product. In this work, we modelled a metabolic pathway in Plasmodium falciparum using Colored Petri Net Markup Language (CPNML). The model was used to examine the dynamic behavior of the sucrose biosynthesis pathway which shows the interactions between the metabolites and the reactions in the sucrose biosynthesis pathway of Plasmodium falciparum. We further analyzed the model for its structural and quantitative properties using Petri Net theory. Our model gives more insight to the structure of the pathway and helps to improve our understanding of the biological processes within this pathway.Keywords: Sucrose, Colored Petri Net, Plasmodium falciparu

Modelling and Simulation of Queuing Models through the concept of Petri Nets

In recent years Petri Nets has been in demand due to its visual depiction. Petri Nets are used as an effective method for portraying synchronization, a concurrency between different system activities. In queuing models Petri networks are used to represent distributed modeling of the system and thus evaluate their performance. By specifying suitable stochastic Petri Nets models, the authors concentrate on representing multi-class queuing systems of various queuing disciplines. The key idea is to define SPN models that simulate a given queue discipline 's behavior with some acceptable random choice. Authors have find system queuing with both a single server and multiple servers with load-dependent service rate. Petri networks in the queuing model have enhanced scalability by combining queuing and modeling power expressiveness of 'petri networks.' Examples of application of SPN models to performance evaluation of multiprocessor systems demonstrate the utility and effectiveness of this modeling method. In this paper, authors have made use of Stochastic Petri nets in queuing models to evaluate the performance of the system