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Discrete event multi-level models for systems biology

Lecture Notes in computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2005年 3380 LNBI卷 66-89页

作者： Uhrmacher, Adelinde M. Degenring, Daniela Zeigler, Bernard Institute for Computer Science University of Rostock Albert-Einstein-Str. 21 D-18059 Rostock Germany Arizona Center of Integrative Modeling and Simulation University of Arizona Tucson AZ 85721 United States

ISBN: (纸本)3540254226

Diverse modeling and simulation methods are being applied in the area of Systems Biology. Most models in Systems Biology can easily be located within the space that is spanned by three dimensions of modeling: continuous and discrete;quantitative and qualitative;stochastic and deterministic. These dimensions are not entirely independent nor are they exclusive. Many modeling approaches are hybrid as they combine continuous and discrete, quantitative and qualitative, stochastic and deterministic aspects. Another important aspect for the distinction of modeling approaches is at which level a model describes a system: is it at the "macro" level, at the "micro" level, or at multiple levels of organization. Although multi-level models can be located anywhere in the space spanned by the three dimensions of modeling and simulation, clustering tendencies can be observed whose implications are discussed and illustrated by moving from a continuous, deterministic quantitative macro model to a stochastic discrete-event semi-quantitative multi-level model. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Data structures

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Hybrid discrete event simulation with model predictive control for semiconductor supply-chain manufacturing

Hybrid discrete event simulation with model predictive contr...

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simulation Winter Conference

作者： H.S. Sarjoughian Dongping Huang G.W. Godding Wenlin Wang D.E. Rivera K.G. Kempf H.D. Mittelmann Arizona Center for Integrative Modeling & Simulation Computer Science & Engineering Department Arizona State University Tempe AZ USA Control Systems Engineering Laboratory Chemical & Materials Engineering Department Arizona State University Tempe AZ USA Decision Technologies Intel Corporation Chandler AZ USA Mathematics & Statistic Dept. Arizona State University Tempe AZ USA

simulation modeling combined with decision control can offer important benefits for analysis, design, and operation of semiconductor supply-chain network systems. Detailed simulation of physical processes provides information for its controller to account for (expected) stochasticity present in the manufacturing processes. In turn, the controller can provide (near) optimal decisions for the operation of the processes and thus handle uncertainty in customer demands. In this paper, we describe an environment that synthesizes discrete-event system specification (DEVS) with model predictive control (MPC) paradigms using a knowledge interchange broker (KIB). This environment uses the KIB to compose discrete event simulation and model predictive control models. This approach to composability affords flexibility for studying semiconductor supply-chain manufacturing at varying levels of detail. We describe a hybrid DEVS/MPC environments via a knowledge interchange broker. We conclude with a comparison of this work with another that employs the Simulink/MATLAB environment.

关键词： Discrete event simulation Predictive models Predictive control Virtual manufacturing Semiconductor device manufacture Mathematical model Analytical models Manufacturing processes Optimal control Uncertainty

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Multi-formalism modeling approach for semiconductor supply/demand networks 04

Multi-formalism modeling approach for semiconductor supply/d...

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simulation Winter Conference

作者： G.W. Godding H.S. Sarjoughian K.G. Kempf Component Automation Systems Intel Corporation Chandler AZ USA Arizona Center for Integrative Modeling & Simulation Computer Science & Engineering Department Arizona State University Tempe AZ USA Decision Technologies Intel Corporation Chandler AZ USA

ISBN: (纸本)9780780387867

Building computational models of real world systems usually requires the interaction of decision modules and simulation modules. Given different models and algorithms, the major hurdles in building a principled and robust system are model composibility and algorithm interoperability. We describe an approach to the composibility problem including initial results. This exposition is given in the context of linear programming as the decision technique and discrete event simulation as the simulation technique, both applied to the design and operation of semiconductor supply/demand networks.

关键词： Computational modeling Decision making Semiconductor materials Robustness Discrete event simulation Context modeling Engines Production facilities Buildings Linear programming

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A unified view of time and causality and its application to distributed simulation

A unified view of time and causality and its application to ...

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2003 Summer computer simulation Conference, SCSC 2003

作者： Nutaro, James J. Sarjoughian, Hessam S. Arizona Center for Integrative Modeling and Simulation Electrical and Computer Engineering Department University of Arizona TucsonAZ85721-0104 United States Arizona Center for Integrative Modeling and Simulation Computer Science and Engineering Department Arizona State University TempeAZ85287-5406 United States

ISBN: (纸本)1565552687

This paper presents a framework for distributed simulation that is based on system-theoretic and logical-process concepts. The framework describes a three-part world-view for developing simulation models. These are modeling formalisms, abstract simulators, and computational environments. A unified view of time and causality allows for the application of system-theoretic notions of causality within a distributed simulation environment. Within this framework, we introduce a unified notion of causality. Further we describe an approach for developing distributed simulation models which evolve from modeling constructs to simulation algorithms and their implementations. The framework is exemplified using the Discrete EVent System Specification (DEVS) modeling formalism, its abstract simulator, and a parallel algorithm that implements the abstract simulator.

关键词： Specifications

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Predictive quantization-based filtering in distributed traffic simulation

Predictive quantization-based filtering in distributed traff...

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2003 Summer computer simulation Conference, SCSC 2003

作者： Leer, Jongkeun Chit, Sungdo Zeigler, Bernard P. Arizona Center for Integrative Modeling and Simulation Dept. of Electrical and Computer Engineering University of Arizona TucsonAZ85721 United States Intelligent Systems Research Lab. Dept. of Computer Engineering Hangkong University Seoul Korea Republic of

ISBN: (纸本)1565552687

This paper proposed predictive quantization-hased filtering method that uses average speed-based dynamic quantum size to effectively reduce communication overhead that DEVS/HLA-based distributed traffic simulation has. Average speed-based dynamic quantum size monitors dynamically changing road situation at fixed time unit and set vehicles 'average speed to dynamic quantum size. Then it generates individual quantum size offactors such as the distance from the leading vehicle, speed and acceleration that decide traffic models 'behavior by using dynamic quantum size. Therefore, the suggested methodology has an advantage in that it effectively reduces communication overhead among federates of distributed traffic simulation. This paper verified validity of the suggested method by doing distributed modeling the 32km block from East Seoul to Hobup of JOOJ'/GBOO highway in Korea and analyzing the simulation.

关键词： Cost reduction

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Autobiographical retrospectives: The evolution of theory of modeling and simulation

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International Journal of General Systems 2003年第3期32卷 X-236页

作者： Zeigler, Bernard P. Arizona Center for Integrative Modeling and Simulation Department of Electrical and Computer Engineering University of Arizona Tucson AZ 85721 United States

No abstract available

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Semiconductor supply network simulation

Semiconductor supply network simulation

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simulation Winter Conference

作者： Godding Sarjoughian Kempf Component Automation Systems Intel Corporation Chandler AZ USA Arizona Center for Integrative Modeling & Simulation Computer Science & Engineering Department Arizona State University Tempe AZ USA Decision Technologies Intel Corporation Chandler AZ USA

More efficient and effective control of supply networks is conservatively worth billions of dollars to the national and world economy. Developing improved control requires simulation of physical flows of materials involved and decision policies governing these flows. We describe our initial work on modelling each of these flows as well as simulating their integration through the synchronized interchange of data. We show the level of abstraction that is appropriate, formulate and test a representative model, and describe our findings and conclusions.

关键词： Testing Production facilities Computational modeling Raw materials Customer service Costs Material storage Network topology Scalability Automation

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DEVS modeling and simulation: A new layer of middleware 3

DEVS modeling and simulation: A new layer of middleware

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3rd Annual International Workshop on Active Middleware Services, AMS 2001

作者： Zeigler, B.P. Sarjoughian, H.S. Park, Sunwoo Nutaro, J.J. Lee, J.S. Cho, Y.K. Arizona Center for Integrative Modeling and Simulation Electrical and Computer Engineering Department University of Arizona TucsonAZ85721-0104 United States Raytheon Missile Systems TucsonAZ United States

ISBN: (纸本)0769515282

This paper discusses a concept of DEVS middleware that would provide a set of services for constructing discrete event models and executing them in simulation or in real-time. Although generic middleware such as CORBA and MPI supports simulation and simulation-oriented middleware such as High Level Architecture Runtime Infrastructure exists, there are many issues that either not addressed at all or have been inadequately addressed in existing systems. DEVS Middleware would improve modeling and simulations due to the beneficial formal properties of DEVS, enhance interoperability among components adhering to the DEVS protocol, and reduce programming complexity by hiding lower level simulation and execution details. The DEVS Middleware concept includes components for model construction and for mapping models onto simulators or real-time execution engines to support the novel concept of "distributed programming by modeling." This paper discusses several sub-layers that have been identified within the overall DEVS middleware concept, existing work that can be brought to bear on developing these layers and the integration needed to create a widely accepted standard. © 2001 IEEE.

关键词： Middleware

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Design and implementation of distributed real-time DEVS/CORBA

Design and implementation of distributed real-time DEVS/CORB...

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IEEE International Conference on Systems, Man and Cybernetics

作者： Y.K. Cho B.P. Zeigler H.S. Sarjoughian Arizona Center of Integrative Modeling and Simulation Department of Electrical and Computer Engineering University of Arizona Tucson Tucson AZ USA

In this paper the design and implementation of Distributed Real-Time DEVS/CORBA is discussed as an extension of previously developed DEVS-based modeling and simulation frameworks. The major objective in developing Distributed Real-Time DEVS/CORBA is to establish a framework in which the distributed real-time systems can be designed through DEVS-based modeling and simulation studies, and then migrated with minimal additional effort to be executed in the real-time distributed environment. This environment will provide generic support for developing models of distributed embedded software systems, evaluating their performance and timing behavior through simulation and easing the transition from simulation to actual executions In this paper we describe detailed design and implementation aspects of the environment which was implemented over Visibroier CORBA middleware and ACE/TAO real-time CORBA services.

关键词： Real time systems Discrete event simulation Computational modeling Timing computer simulation Embedded software Embedded system Quality of service Discrete event systems Middleware

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DEVS modeling and simulation: a new layer of middleware

DEVS modeling and simulation: a new layer of middleware

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International Workshop on Active Middleware Services

作者： B.P. Zeigler H.S. Sarjoughian Sunwoo Park J.J. Nutaro J.S. Lee Y.K. Cho Arizona Center for Integrative Modeling and Simulation Electrical & Computer Engineering Department University of Arizona Tucson Tucson AZ USA Raytheon Missile Systems Company Tucson AZ USA

ISBN: (纸本)0769515282

关键词： Middleware Application software Discrete event simulation Computational modeling computer simulation Real time systems Protocols Engines Missiles Runtime

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