Methodology for automated Petri Net model generation to support Reliability Modelling

As the complexity of engineering systems and processes increases, determining their optimal performance also becomes increasingly complex. There are various reliability methods available to model performance but generating the models can become a significant task that is cumbersome, error-prone and tedious. Hence, over the years, work has been undertaken into automatically generating reliability models in order to detect the most critical components and design errors at an early stage, supporting alternative designs. Earlier work lacks full automation resulting in semi-automated methods since they require user intervention to import system information to the algorithm, focus on specific domains and cannot accurately model systems or processes with control loops and dynamic features. This thesis develops a novel method that can generate reliability models for complex systems and processes, based on Petri Net models. The process has been fully automated with software developed that extracts the information required for the model from a topology diagram that describes the system or process considered and generates the corresponding mathematical and graphical representations of the Petri Net model. Such topology diagrams are used in industrial sectors, ranging from aerospace and automotive engineering to finance, defence, government, entertainment and telecommunications. Complex real-life scenarios are studied to demonstrate the application of the proposed method, followed by the verification, validation and simulation of the developed Petri Net models. Thus, the proposed method is seen to be a powerful tool to automatically obtain the PN modelling formalism from a topology diagram, commonly used in industry, by: - Handling and efficiently modelling systems and processes with a large number of components and activities respectively, dependent events and control loops. - Providing generic domain applicability. - Providing software independence by generating models readily understandable by the user without requiring further manipulation by any industrial software. Finally, the method documented in this thesis enables engineers to conduct reliability and performance analysis in a timely manner that ensures the results feed into the design process

Patterns In System Modeling Theory

Tez (Yüksek Lisans) -- İstanbul Teknik Üniversitesi, Fen Bilimleri Enstitüsü, 2008Thesis (M.Sc.) -- İstanbul Technical University, Institute of Science and Technology, 2008Günümüzde, İşletmeler sürekli değişen dış ortam ile karşı karşıyadırlar. Uygun yönetim için daha iyi iş akışı ve değişime uyum sağlayacak işletme modelleri gereklidir. İş akışı modellemenin hedefi, iş akışı sisteminini anlamak, performans değerlendirmesini üstünleştirmek, karar vermeyi desteklemek ve sürekli iyileştirme için değiştirme cesareti vermektir. Bu hedefe ulaşmak için, etkili enformasyon teknolojisi gerkelidir. Bu nedenle, İşletme içersinde bilgiye ulaşımı destekleyecek etkili enformasyon teknolojisi gereklidir. Organizasyon yönetimine destek amacı ile model entegrasyonuna destek için bu proje referans mimarisi ve modellemesi çercevesinde pattern modellerin geliştirilmesi üzerine odaklanmıştır. Dahası, Referans mimarisini belirleyen ve Üretim proseslere rehberlik eden pattern modelleri, ilgisi olamayan komponentler arasındaki ilişkiyi kurup prosesin ana elemanlarını tanımlar. Bu çalışmamda içeriği sağlamak için elektronik ticaret konusunda uluslararası camia tarafından Kabul gören Renkli Petri ağları ve UML dili şeçilmiştir.Enterprises today are faced with a rapidly changing environment. There is a need for better process management and increased integration, and enterprise modeling is necessary for proper management. The goal of process modeling is to improve understanding of what happens in the process system, enhance performance evaluation of some parts of the process, support decision-making activities and encourage changes for continuous improvement. Therefore, efficient information technology is required to support the availability of information in the enterprise. In an effort to achieve the integration of models aimed at supporting various facets of organizational management, this project focused on the development of pattern modeling in the context of reference architectures and methodologies. Furthermore the Pattern models, that underlie various reference architectures and the guidelines on modeling manufacturing processes, specifies the main elements of an process and provides a relation between its interrelated components. To provide the context that this work was performed in, Colored Petri Nets and UML which were selected because they result from and are promoted by the major international coalition in the area of e-commerce.Yüksek LisansM.Sc

Hybrid modeling and optimization of biological processes

Proß S. Hybrid modeling and optimization of biological processes. Bielefeld: Bielefeld University; 2013

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

Foundations of Multi-Paradigm Modelling for Cyber-Physical Systems

This open access book coherently gathers well-founded information on the fundamentals of and formalisms for modelling cyber-physical systems (CPS). Highlighting the cross-disciplinary nature of CPS modelling, it also serves as a bridge for anyone entering CPS from related areas of computer science or engineering. Truly complex, engineered systems—known as cyber-physical systems—that integrate physical, software, and network aspects are now on the rise. However, there is no unifying theory nor systematic design methods, techniques or tools for these systems. Individual (mechanical, electrical, network or software) engineering disciplines only offer partial solutions. A technique known as Multi-Paradigm Modelling has recently emerged suggesting to model every part and aspect of a system explicitly, at the most appropriate level(s) of abstraction, using the most appropriate modelling formalism(s), and then weaving the results together to form a representation of the system. If properly applied, it enables, among other global aspects, performance analysis, exhaustive simulation, and verification. This book is the first systematic attempt to bring together these formalisms for anyone starting in the field of CPS who seeks solid modelling foundations and a comprehensive introduction to the distinct existing techniques that are multi-paradigmatic. Though chiefly intended for master and post-graduate level students in computer science and engineering, it can also be used as a reference text for practitioners

Computerised Modelling for Developmental Biology

Many studies in developmental biology rely on the construction and analysis of models. This research presents a broad view of modelling approaches for developmental biology, with a focus on computational methods. An overview of modelling techniques is given, followed by several case studies. Using 3D reconstructions, the heart development of the turtle is examined, with special attention to heart looping and the development of the outflow tract. Subsequently, an ontology system is presented in which anatomical, developmental and physiological information on the vertebrate heart is modelled. Finally, two Petri net models are discussed, which model the developmental process of gradient formation, both in a qualitative and quantitative manner.LEI Universiteit LeidenImagin

Failure modes and criticality analysis of the preliminary design phase of the Mars Desert Research Station considering human factors

This work presents an extension to the traditional FMECA (Failure Modes, Effects and Criticality Analysis) method to include the effects of human factors concerning accessibility/repairability, probability of contact and degree of contact. The authors refer to this extension to the traditional FMECA as the Human Design Approach (HDA). All data used in this study was collected during the stay of two of the authors at the Mars Desert Research Station (MDRS) in the Utah desert, USA. The MDRS is a laboratory for carrying out research in order to understand and investigate the difficulties of how to live and work on another planet. The results show that following the HDA can enhance the safety and reliability of the MDRS. There is still a significant amount of research required concerning reliability analysis of the space habitat in terms of the selection of optimum designs, the modification of systems, as well as access, inspection and maintenance strategies, human factors and environmental impacts. This preliminary study will assist the design engineers with the selection of an optimum configuration for space habitats and can be extended to any case where humans can influence function of an environment

A diversity-aware computational framework for systems biology

L'abstract è presente nell'allegato / the abstract is in the attachmen