The Possibilities of Modeling Petri Nets and Their Extensions

This chapter is dedicated to several structure features of Petri nets. There is detailed description of appropriate access in Petri nets and reachable tree mechanism construction. There is an algorithm that describes the minimum sequence of possible transitions. The algorithm developed by us finds the shortest possible sequence for the network promotion state, which transfers the mentioned network state to the coverage state. The corresponding theorem is proven, which states that due to the describing algorithm, the number of transitions in the covering state is minimal. This chapter studies the interrelation of languages of colored Petri nets and traditional formal languages. The Venn diagram, modified by the author, is presented, which shows the relationship between the languages of the colored Petri nets and some traditional languages. As a result, it is shown that the language class of colored Petri nets includes an entire class of context-free languages and some other classes. The results obtained show that it is not possible to model the Patil problem using the well-known semaphores P and V or classical Petri nets, so the mentioned systems have limited properties

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

In-silico-Systemanalyse von Biopathways

Chen M. In silico systems analysis of biopathways. Bielefeld (Germany): Bielefeld University; 2004.In the past decade with the advent of high-throughput technologies, biology has migrated from a descriptive science to a predictive one. A vast amount of information on the metabolism have been produced; a number of specific genetic/metabolic databases and computational systems have been developed, which makes it possible for biologists to perform in silico analysis of metabolism. With experimental data from laboratory, biologists wish to systematically conduct their analysis with an easy-to-use computational system. One major task is to implement molecular information systems that will allow to integrate different molecular database systems, and to design analysis tools (e.g. simulators of complex metabolic reactions). Three key problems are involved: 1) Modeling and simulation of biological processes; 2) Reconstruction of metabolic pathways, leading to predictions about the integrated function of the network; and 3) Comparison of metabolism, providing an important way to reveal the functional relationship between a set of metabolic pathways. This dissertation addresses these problems of in silico systems analysis of biopathways. We developed a software system to integrate the access to different databases, and exploited the Petri net methodology to model and simulate metabolic networks in cells. It develops a computer modeling and simulation technique based on Petri net methodology; investigates metabolic networks at a system level; proposes a markup language for biological data interchange among diverse biological simulators and Petri net tools; establishes a web-based information retrieval system for metabolic pathway prediction; presents an algorithm for metabolic pathway alignment; recommends a nomenclature of cellular signal transduction; and attempts to standardize the representation of biological pathways. Hybrid Petri net methodology is exploited to model metabolic networks. Kinetic modeling strategy and Petri net modeling algorithm are applied to perform the processes of elements functioning and model analysis. The proposed methodology can be used for all other metabolic networks or the virtual cell metabolism. Moreover, perspectives of Petri net modeling and simulation of metabolic networks are outlined. A proposal for the Biology Petri Net Markup Language (BioPNML) is presented. The concepts and terminology of the interchange format, as well as its syntax (which is based on XML) are introduced. BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets. The language makes it possible to exchange biology Petri net diagrams between all supported hardware platforms and versions. It is also designed to associate Petri net models and other known metabolic simulators. A web-based metabolic information retrieval system, PathAligner, is developed in order to predict metabolic pathways from rudimentary elements of pathways. It extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. The system also provides a navigation platform to investigate metabolic related information, and transforms the output data into XML files for further modeling and simulation of the reconstructed pathway. An alignment algorithm to compare the similarity between metabolic pathways is presented. A new definition of the metabolic pathway is proposed. The pathway defined as a linear event sequence is practical for our alignment algorithm. The algorithm is based on strip scoring the similarity of 4-hierarchical EC numbers involved in the pathways. The algorithm described has been implemented and is in current use in the context of the PathAligner system. Furthermore, new methods for the classification and nomenclature of cellular signal transductions are recommended. For each type of characterized signal transduction, a unique ST number is provided. The Signal Transduction Classification Database (STCDB), based on the proposed classification and nomenclature, has been established. By merging the ST numbers with EC numbers, alignments of biopathways are possible. Finally, a detailed model of urea cycle that includes gene regulatory networks, metabolic pathways and signal transduction is demonstrated by using our approaches. A system biological interpretation of the observed behavior of the urea cycle and its related transcriptomics information is proposed to provide new insights for metabolic engineering and medical care

Measurements, Models, Systems and Design

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Understanding the Elements of Executable Architectures Through a Multi-Dimensional Analysis Framework

The objective of this dissertation study is to conduct a holistic investigation into the elements of executable architectures. Current research in the field of Executable Architectures has provided valuable solution-specific demonstrations and has also shown the value derived from such an endeavor. However, a common theory underlying their applications has been missing. This dissertation develops and explores a method for holistically developing an Executable Architecture Specification (EAS), i.e., a meta-model containing both semantic and syntactic information, using a conceptual framework for guiding data coding, analysis, and validation. Utilization of this method resulted in the description of the elements of executable architecture in terms of a set of nine information interrogatives: an executable architecture information ontology. Once the detail-rich EAS was constructed with this ontology, it became possible to define the potential elements of executable architecture through an intermediate level meta-model. The intermediate level meta-model was further refined into an interrogative level meta-model using only the nine information interrogatives, at a very high level of abstraction

Eighth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, October 22-24, 2007

This booklet contains the proceedings of the Eighth Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, October 22-24, 2007. The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop0

Toward Accessible Multilevel Modeling in Systems Biology: A Rule-based Language Concept

Promoted by advanced experimental techniques for obtaining high-quality data and the steadily accumulating knowledge about the complexity of life, modeling biological systems at multiple interrelated levels of organization attracts more and more attention recently. Current approaches for modeling multilevel systems typically lack an accessible formal modeling language or have major limitations with respect to expressiveness. The aim of this thesis is to provide a comprehensive discussion on associated problems and needs and to propose a concrete solution addressing them

The planning coordinator: A design architecture for autonomous error recovery and on-line planning of intelligent tasks

Developing a robust, task level, error recovery and on-line planning architecture is an open research area. There is previously published work on both error recovery and on-line planning; however, none incorporates error recovery and on-line planning into one integrated platform. The integration of these two functionalities requires an architecture that possesses the following characteristics. The architecture must provide for the inclusion of new information without the destruction of existing information. The architecture must provide for the relating of pieces of information, old and new, to one another in a non-trivial rather than trivial manner (e.g., object one is related to object two under the following constraints, versus, yes, they are related; no, they are not related). Finally, the architecture must be not only a stand alone architecture, but also one that can be easily integrated as a supplement to some existing architecture. This thesis proposal addresses architectural development. Its intent is to integrate error recovery and on-line planning onto a single, integrated, multi-processor platform. This intelligent x-autonomous platform, called the Planning Coordinator, will be used initially to supplement existing x-autonomous systems and eventually replace them