Wolfgang Reisig - Böcker

The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques.This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification.Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin.This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques.This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification.Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin.This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

This book fills a serious gap by providing a conceptual framework for understanding the digital world. This world contains large, heterogeneous systems that have to manage dynamic behavior as well as static items and data. Obviously, new, digital methods are needed to deal with the challenges of the digital world.This book introduces such a method with Heraklit, an intuitively simple, albeit powerful framework for modeling, communicating, and analyzing computer-integrated systems. It integrates proven methods for composing modules, describing behavior with local cause and effect, and digitally representing real- and imagined-world items, resulting in a comprehensive, expressive, concerted, technically simple, digital modeling method.This book is structured according to three Heraklit pillars, starting in Part I with the central Heraklit concept of modules, in particular their composition and refinement. Part II covers the second pillar of Heraklit, dynamics, focusing on modules that describe aspects of behavior. Part III focuses on static aspects. In particular, real- and imagined-world items and their symbolic representation are carefully distinguished and related. Together, these three pillars are consolidated in Part IV, integrating all concepts into a powerful formal framework. The book concludes in Part V with a more comprehensive case study of a typical retail business, recommendations on how to start modeling with Heraklit, and useful graphical conventions for the graphical representation of Heraklit models.Heraklit covers the range from the first informal structuring ideas for a computer-integrated system, through the specification of (business) processes, the contributions of people, organizations, and mechanical devices, up to the construction of software. The book is therefore written for students in areas related to system modeling, system design, and system engineering, as well as for professionals in these fields.

This book offers an overview of the key ideas of Petri nets, how they were developed, and how they were applied in diverse applications.The chapters in the first part offer individual perspectives on the impact of Petri’s work. The second part of the book contains personal memories from researchers who collaborated with him closely, in particular they recount his unique personality. The chapters in the third part offer more conventional treatments on various aspects of current Petri net research, and the fourth part examines the wide applications of Petri nets, and the relationships with other domains.The editors and authors are the leading researchers in this domain, and this book will be a valuable insight for researchers in computer science, particularly those engaged with concurrency and distributed systems.

1 d Petrinetze sind für den Entwurf und die Analyse nicht-sequentieller (paralleler) Prozesse und Systeme geeignet. Insbesondere im Hardware- und Software-Entwurf und in der Systemspezifikation werden sie erfolgreich angewendet. Das Buch führt in die grundlegenden Begriffe und Methoden des Gebietes ein. In drei Teilen werden Netze aus Bedingungen und Ereignissen, Stellen/Transitionen-Netze und schließlich Netze mit beliebigen (individuellen) Marken behandelt. Bei den Analysemethoden werden Fakten, Synchronieabstände und Invarianten ausführlich besprochen - also Methoden, die nicht auf sequentiellen Realisierungen paralleler Prozesse beruhen. Der dritte Teil behandelt den Fakten- und Invariantenkalkül für Prädikat/Ereignis-Netze. Das Buch gibt eine geschlossene, einheitliche Darstellung der Grundbegriffe und typischen Anwendungen der Netztheorie. Es bereitet den Leser darauf vor, Petrinetze angemessen anzuwenden und die Spezialliteratur zu lesen.

Petri Nets represent a long and sustained effort· to develop concepts, theories and tools to aid in design and analysis of concurrent systems. They are used in many areas of computer science including software engineering, data base and in­ formation systems, computer architecture and operating systems, communication protocols and computer networks, process control, and socio-technical systems such as office communication and man-machine interaction. Quite substantial theory has been developed for Petri Nets. It reflects all major problem areas of concurrent distributed systems and covers many successfully applied principles and analysis techniques for systems organisation. Since the time that C. A. Petri has presented his original ideas, a rich body of knowledge has been developed-a recent bibliography (in Advances in Petri Nets 1981) includes more than 2000 entries. Already in 1979 an Advanced Course on Petri Nets was organized in Hamburg, West Germany, aiming at systematizing the existing knowledge and making it well accessible to a wide audience of computer scientists interested in theory and applications of concurrent systems. This course has turned out to be successful in the sense that it has initiated a lot of new research into applications and theory of Petri Nets. This had led to· another Advanced Course in 1986 in Bad Honnef, West Germany - where during two weeks more than 30 lectures were presented covering the most important current developments in the area of Petri Nets.

The present volume is the second of two parts which constitute the proceedings of the 1986 Advanced Course on Petri Nets in Bad Honnef. It discusses tools supporting the design of petri nets as well as their modification and analysis, presents a variety of applications, and covers the relationship of petri nets to other concurrency models. These current issues of the "Advances in Petri Nets" present the most significant recent results in the application and theory of petri nets to the broad computer science community. They particularly address those who are: - interested in systems design and would like to learn to use petri nets, - familiar with subareas of the theory or the applications of nets and wish to become acquainted with the whole area, - interested in learning about recent results presented within a unified framework, - going to learn about successfully applying petri nets in - various practical situations, - interested in the relationship of petri nets to other models of concurrent systems.

This volume, "Petri Net Technology for Communication-Based Systems," is a state-of-the-artreportin the seriesAdvances in Petri Nets. It showshowvarious well-established and new Petri net notions and techniques can be used for m- elingcommunication-basedsystems,withspecialfocusonwork?owmanagement and business processes. In the last 6 years this topic has been studied by the DFG Forschergruppe Petri Net Technology in Berlin in close cooperation with the international c- munity. The main results of this cooperation were presented at the 1st and 2nd InternationalColloquiaonPetriNetTechnologiesforModelingCommunication- Based Systems, held in Berlin in 1999 and 2001,respectively. A careful selection of contributions by members of the DFG Forschergruppe and by international experts in this ?eld are presented in this volume. Taking into account the fru- ful discussions during the two colloquia and the cross-refereeing process for the accepted papers, a high degree of common understanding was achieved, leading to a highly comprehensive presentation in this volume. The topics of the papers in this volume can be roughly classi?ed into the following two areas: - Petri net technology and - application to communication-based systems.Since most papers comprise aspects of both areas, we chose an alphabetic order. However, in the following we give a rough overview of the contributions in both areas according to the main focus of the corresponding papers.

This volume contains the proceedings of the 25th International Conference on Application and Theory of Petri Nets (ICATPN 2004). The aim of the Petri net conferences is to create a forum for discussing progress in the application and theory of Petri nets. Typically, the conferenceshave 100-150participants,one third of these c- ing from industry, whereas the others are from universities and research insti- tions. The conferences always take place in the last week of June. The conference and a number of other activities are coordinated by a ste- ing committee with the following members: Wil van der Aalst (The Neth- lands),JonathanBillington(Australia),JrgDesel(Germany),SusannaDonatelli (Italy),SergeHaddad(France),KurtJensen(Denmark),MaciejKoutny(United Kingdom), Sadatoshi Kumagai(Japan), GiorgioDe Michelis (Italy), Tadao- rata (USA), Carl Adam Petri (Germany, Honorary Member), Wolfgang Reisig (Germany),GrzegorzRozenberg(TheNetherlands,Chairman)andManuelSilva (Spain). The 2004 conference was organized by the Department of Computer Science of the University of Bologna, Italy. We would like to thank the organizing c- mittee, chaired by Roberto Gorrieri, for the e?ort invested in making the event successful.We are also grateful to the following sponsoring institutions and - ganizations: Associazione Italiana per l'Informatica ed il Calcolo Automatico (AICA), Microsoft Research, and Network Project & Solutions (NPS Group). We received a total of 62 submissions from 26 di?erent countries. The p- gramcommittee?nallyselected19regularpapersand5toolpresentationpapers. This volume comprises the papers that were accepted for presentation. Invited lectures were given by Gianfranco Ciardo, Roberto Gorrieri, Thomas A. H- zinger, Wojciech Penczek, Lucia Pomello and William H. Sanders. Their papers are also included in this volume.

The very ?rst model of concurrent and distributed systems was introduced by C.A. Petri in his seminal Ph.D. thesis in 1964. Petri nets has remained a central model for concurrentsystemsfor40 years,andthey areoften usedasa yardstick for other models of concurrency. As a matter of fact, many other models have been developed since then, and this research area is ?ourishing today. The goal of the 4th Advanced Course on Petri Nets held in Eichsta ..tt, Germany in September 2003 was to present applications and the theory of Petri Nets in the context of a whole range of other models. We believe that in this way the participants of the course received a broad and in-depth picture of research in concurrent and distributed systems. It is also the goal of this volume to convey this picture. The volume is based on lectures given at the Advanced Course, but in order to provide a balanced p- sentation of the ?eld, some of the lectures are not included, and some material not presented in Eichst. att is covered here. In particular, a series of introductory lectures was not included in this volume, as the material they covered is well - tablishedby now,andwellpresentedelsewhere (e.g.,inW.ReisigandG. Roz- berg, eds., "Lectures on Petri Nets," LNCS 1491, 1492, Springer-Verlag, 1997 - these two volumes are based on the 3rd Advanced Course on Petri Nets).

Die Informatik ist eine junge Wissenschaft, die sich durch einen rasanten technischen Fortschritt auszeichnet. Dadurch wird häufig übersehen, dass aktuelle Themen eine teilweise lange Entwicklungsgeschichte durchlaufen haben.Informatikprofessoren der Humboldt-Universität zu Berlin haben zu einigen ihrer aktuellen Arbeitsgebiete die Entwicklungslinien von den Anfängen bis Gegenwart mit einem Ausblick auf die mögliche Zukunft aufgezeichnet. Dieser spannende und lehrreiche Einblick in die Informatik öffnet die Tür zu einem umfassenden und nicht nur technologisch geprägten Verständnis.

This book constitutes the refereed proceedings of the 17th International Conference on Application and Theory of Petri Nets, held in Osaka, Japan, in June 1996.The 26 revised full papers included in the book together with three invited presentations were selected from a total of 78 submissions. The book addresses the current theoretical and applicational aspects of the various types of Petri Nets and competently reflects the state of the art in the area.

Distributed Computing is rapidly becoming the principal computing paradigm in diverse areas of computing, communication, and control. Processor clusters, local and wide area networks, and the information highway evolved a new kind of problems which can be solved with distributed algorithms.In this textbook a variety of distributed algorithms are presented independently of particular programming languages or hardware, using the graphically suggestive technique of Petri nets which is both easy to comprehend intuitively and formally rigorous. By means of temporal logic the author provides surprisingly simple yet powerful correctness proofs for the algorithms.The scope of the book ranges from distributed control and synchronization of two sites up to algorithms on any kind of networks. Numerous examples show that description and analysis of distributed algorithms in this framework are intuitive and technically transparent.

The two-volume set originates from the Advanced Course on Petri Nets held in Dagstuhl, Germany in September 1996; beyond the lectures given there, additional chapters have been commissioned to give a well-balanced presentation of the state of the art in the area. Together with its companion volume "Lectures on Petri Nets II: Applications" this book is the actual reference for the area and addresses professionals, students, lecturers, and researchers who are - interested in systems design and would like to learn to use Petri nets familiar with subareas of the theory or its applications and wish to view the whole area - interested in learning about recent results presented within a unified framework - planning to apply Petri nets in practical situations- interested in the relationship of Petri nets to other models of concurrent systems.

The two-volume set originates from the Advanced Course on Petri Nets held in Dagstuhl, Germany in September 1996; beyond the lectures given there, additional chapters have been commissioned to give a well-balanced presentation of the state of the art in the area. Together with its companion volume "Lectures on Petri Nets I: Basic Models" this book is the actual reference for the area and addresses professionals, students, lecturers, and researchers who are - interested in systems design and would like to learn to use Petri nets familiar with subareas of the theory or its applications and wish to view the whole area - interested in learning about recent results presented within a unified framework - planning to apply Petri nets in practical situations - interested in the relationship of Petri nets to other models of concurrent systems.

Distributed Computing is rapidly becoming the principal computing paradigm in diverse areas of computing, communication, and control. Processor clusters, local and wide area networks, and the information highway evolved a new kind of problems which can be solved with distributed algorithms.In this textbook a variety of distributed algorithms are presented independently of particular programming languages or hardware, using the graphically suggestive technique of Petri nets which is both easy to comprehend intuitively and formally rigorous. By means of temporal logic the author provides surprisingly simple yet powerful correctness proofs for the algorithms.The scope of the book ranges from distributed control and synchronization of two sites up to algorithms on any kind of networks. Numerous examples show that description and analysis of distributed algorithms in this framework are intuitive and technically transparent.

Yuri Gurevich has played a major role in the discovery and development of - plications of mathematical logic to theoretical and practical computer science. His interests have spanned a broad spectrum of subjects, including decision p- cedures, the monadic theory of order, abstract state machines, formal methods, foundations of computer science, security, and much more. In May 2010, Yuri celebrated his 70th birthday. To mark that occasion, on August 22, 2010,a symposium was held in Brno, the Czech Republic, as a sat- lite event of the 35th International Symposium on Mathematical Foundations of Computer Science (MFCS 2010) and of the 19th EACSL Annual Conference on Computer Science Logic (CSL 2010). The meeting received generous support from Microsoft Research. In preparation for this 70th birthday event, we asked Yuri’s colleagues (whether or not they were able to attend the symposium) to contribute to a volume in his honor. This book is the result of that e?ort. The collection of articles herein begins with an academic biography, an annotated list of Yuri’s publications and reports, and a personaltribute by Jan Van den Bussche. These are followed by 28 technical contributions. These articles – though they cover a broad range of topics – represent only a fraction of Yuri’s multiple areas of interest. Each contribution was reviewed by one or two readers. In this regard, the editors wish to thank several anonymous individuals for their assistance.

With their intuitive graphical approach and expressive analysis techniques, Petri nets are suitable for a wide range of applications and teaching scenarios, and they have gained wide acceptance as a modeling technique in areas such as software design and control engineering. The core theoretical principles have been studied for many decades and there is now a comprehensive research literature that complements the extensive implementation experience.In this book the author presents a clear, thorough introduction to the essentials of Petri nets. He explains the core modeling techniques and analysis methods and he illustrates their usefulness with examples and case studies. Part I describes how to use Petri nets for modeling; all concepts are explained with the help of examples, starting with a generic, powerful model which is also intuitive and realistic. Part II covers the essential analysis methods that are specific to Petri nets, introducing techniques used to formulate keyproperties of system nets and algorithms for proving their validity. Part III presents case studies, each introducing new concepts, properties and analysis techniques required for very different modeling tasks. The author offers different paths among the chapters and sections: the elementary strand for readers who wish to study only elementary nets; the modeling strand for those who wish to study the modeling but not the analysis of systems; and finally the elementary models of the modeling strand for those interested in technically simple, but challenging examples and case studies.The author achieves an excellent balance between consistency, comprehensibility and correctness in a book of distinctive design. Among its characteristics, formal arguments are reduced to a minimum in the main text with many of the theoretical formalisms moved to an appendix, the explanations are supported throughout with fully integrated graphical illustrations, and each chapter ends with exercises and recommendations for further reading.The book is suitable for students of computer science and related subjects such as engineering, and for a broad range of researchers and practitioners.

Net theory is a theory of systems organization which had its origins, about 20 years ago, in the dissertation of C. A. Petri [1]. Since this seminal paper, nets have been applied in various areas, at the same time being modified and theoretically investigated. In recent time, computer scientists are taking a broader interest in net theory. The main concern of this book is the presentation of those parts of net theory which can serve as a basis for practical application. It introduces the basic net theoretical concepts and ways of thinking, motivates them by means of examples and derives relations between them. Some extended examples il­ lustrate the method of application of nets. A major emphasis is devoted to those aspect which distinguish nets from other system models. These are for instance, the role of concurrency, an awareness of the finiteness of resources, and the pos­ sibility of using the same representation technique of different levels of ab­ straction. On completing this book the reader should have achieved a system­ atic grounding in the subject allowing him access to the net literature [25]. These objectives determined the subjects treated here. The presentation of the material here is rather more axiomatic than in­ ductive. We start with the basic notions of 'condition' and 'event' and the con­ cept of the change of states by (concurrently) occurring events. By generali­ zation of these notions a part of the theory of nets is presented.

Petri nets provide a formal framework for system modelingand validation which has proven to be very reliable inpractice. This book presents variousnet models appropriatefor designing specific systems, where systems are understoodvery generally as "organizational systems" in whichregulatedflows of objects and information are significant.The models are interrelated in the sense that they havecommon interpretation patterns: together they can beunderstood as a method for specifying any given system orany section of such a system to any given degree ofrefinement. The simple and immediately understandableprinciples of system modelling with nets makes it possibleto provide an illustrated description of this method withoutgoing into the mathematics behind it. The text is based oncourses the author developed for project engineers andproject managers in the area of embedded computer systems.

With their intuitive graphical approach and expressive analysis techniques, Petri nets are suitable for a wide range of applications and teaching scenarios, and they have gained wide acceptance as a modeling technique in areas such as software design and control engineering.