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The mass and complexity of biological information requires computer-aided simulation and analysis to help scientists achieve understanding and guide experimentation. Although living organisms are composed of cells, actual genomic and proteomic data have not yet led to a satisfactory model of working cell in silico. We have set out to devise a user-friendly generic platform, GemCell, for Generic Executable Modeling of Cells, based on whole, functioning cells. Starting with the cell simplifies life, because all cells expresses essentially five generic types of behavior: replication, death, movement (including change of shape and adherence), export (secretion, signaling, etc.) and import (receiving signals, metabolites, phagocytosis, etc.). The details of these behaviors are specified in GemCell for particular kinds of cells as part of a database of biological specifics (the DBS), which specifies the cell properties and functions that depend on the cell’s history, state, environment, etc. The DBS is designed in an intuitive fashion, so users are able to easily insert their data of interest. The generic part of GemCell, built using Statecharts, is a fully dynamic model of a cell, its interactions with the environment and its resulting behavior, individually and collectively. Model specificity emerges from the DBS, so that model execution is carried out by the statecharts executing with the aid of specific data extracted from the DBS dynamically. Our long term goal is for GemCell to serve as a broadly applicable platform for biological modeling and analysis, supporting user-friendly in silico experimentation, animation, discovery of emergent properties, and hypothesis testing, for a wide variety of biological systems. 相似文献
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In this paper we present an approach to the specification and verification of reactive systems. The approach uses Timed Statecharts and Real Time Logic for the specification of temporal behaviour, and theorem proving techniques for the verification of safety and utility properties. Formal verification is achieved through the automation of semi-formal (rigorous) proofs using a theorem prover (Proofpower HOL). To illustrate the approach, we use the Railroad Crossing Problem, which has been proposed, along with a set of criteria for assessment, as a benchmark for the comparison of real-time formalisms. We conclude with our assessment of the approach against the proposed criteria. 相似文献
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This paper addresses the problem of fault detection and isolation for a particular class of discrete event dynamical systems
called hierarchical finite state machines (HFSMs). A new version of the property of diagnosability for discrete event systems
tailored to HFSMs is introduced. This notion, called L1-diagnosability, captures the possibility of detecting an unobservable fault event using only high level observations of the
behavior of an HFSM. Algorithms for testing L1-diagnosability are presented. In addition, new methodologies are presented for studying the diagnosability properties of
HFSMs that are not L1-diagnosable. These methodologies avoid the complete expansion of an HFSM into its corresponding flat automaton by focusing
the expansion on problematic indeterminate cycles only in the associated extended diagnoser.
Andrea Paoli received the master degree in Computer Science Engineering and the Ph.D. in Automatic Control and Operational Research from the University of Bologna in 2000 and 2003 respectively. He currently holds a Post Doc position at the Department of Electronics, Computer Science and Systems (DEIS) at the University of Bologna, Italy. He is a member of the Center for Research on Complex Automated Systems (CASY) Giuseppe Evangelisti. From August to January 2002, and in March 2005 he held visiting positions at the Department of Electrical Engineering and Computer Science at The University of Michigan, Ann Arbor. In July 2005 he won the prize IFAC Outstanding AUTOMATICA application paper award for years 2002-2005 for the article by Claudio Bonivento, Alberto Isidori, Lorenzo Marconi, Andrea Paoli titled Implicit fault-tolerant control: application to induction motors appeared on AUTOMATICA issue 30(4). Since 2006 he is a member of the IFAC Technical Committee on Fault Detection, Supervision and Safety of Technical Processes (IFAC SAFEPROCESS TC). His current research interests focus on Fault Tolerant Control and Fault Diagnosis in distributed systems and in discrete event systems and on industrial automation software architectures following an agent based approach. His theoretical background includes also nonlinear control and output regulation using geometric approach. Stéphane Lafortune received the B. Eng degree from Ecole Polytechnique de Montréal in 1980, the M. Eng. degree from McGill University in 1982, and the Ph.D. degree from the University of California at Berkeley in 1986, all in electrical engineering. Since September 1986, he has been with the University of Michigan, Ann Arbor, where he is a Professor of Electrical Engineering and Computer Science. Dr. Lafortune is a Fellow of the IEEE (1999). He received the Presidential Young Investigator Award from the National Science Foundation in 1990 and the George S. Axelby Outstanding Paper Award from the Control Systems Society of the IEEE in 1994 (for a paper co-authored with S. L. Chung and F. Lin) and in 2001 (for a paper co-authored with G. Barrett). At the University of Michigan, he received the EECS Department Research Excellence Award in 1994–1995, the EECS Department Teaching Excellence Award in 1997–1998, and the EECS Outstanding Achievement Award in 2003–2004. Dr. Lafortune is a member of the editorial boards of the Journal of Discrete Event Dynamic Systems: Theory and Applications and of the International Journal of Control. His research interests are in discrete event systems modeling, diagnosis, control, and optimization. He is co-developer of the software packages DESUMA and UMDES. He co-authored, with C. Cassandras, the textbook Introduction to Discrete Event Systems—Second Edition (Springer, 2007). Recent publications and software tools are available at the Web site . 相似文献
| Stéphane LafortuneEmail: |
Andrea Paoli received the master degree in Computer Science Engineering and the Ph.D. in Automatic Control and Operational Research from the University of Bologna in 2000 and 2003 respectively. He currently holds a Post Doc position at the Department of Electronics, Computer Science and Systems (DEIS) at the University of Bologna, Italy. He is a member of the Center for Research on Complex Automated Systems (CASY) Giuseppe Evangelisti. From August to January 2002, and in March 2005 he held visiting positions at the Department of Electrical Engineering and Computer Science at The University of Michigan, Ann Arbor. In July 2005 he won the prize IFAC Outstanding AUTOMATICA application paper award for years 2002-2005 for the article by Claudio Bonivento, Alberto Isidori, Lorenzo Marconi, Andrea Paoli titled Implicit fault-tolerant control: application to induction motors appeared on AUTOMATICA issue 30(4). Since 2006 he is a member of the IFAC Technical Committee on Fault Detection, Supervision and Safety of Technical Processes (IFAC SAFEPROCESS TC). His current research interests focus on Fault Tolerant Control and Fault Diagnosis in distributed systems and in discrete event systems and on industrial automation software architectures following an agent based approach. His theoretical background includes also nonlinear control and output regulation using geometric approach. Stéphane Lafortune received the B. Eng degree from Ecole Polytechnique de Montréal in 1980, the M. Eng. degree from McGill University in 1982, and the Ph.D. degree from the University of California at Berkeley in 1986, all in electrical engineering. Since September 1986, he has been with the University of Michigan, Ann Arbor, where he is a Professor of Electrical Engineering and Computer Science. Dr. Lafortune is a Fellow of the IEEE (1999). He received the Presidential Young Investigator Award from the National Science Foundation in 1990 and the George S. Axelby Outstanding Paper Award from the Control Systems Society of the IEEE in 1994 (for a paper co-authored with S. L. Chung and F. Lin) and in 2001 (for a paper co-authored with G. Barrett). At the University of Michigan, he received the EECS Department Research Excellence Award in 1994–1995, the EECS Department Teaching Excellence Award in 1997–1998, and the EECS Outstanding Achievement Award in 2003–2004. Dr. Lafortune is a member of the editorial boards of the Journal of Discrete Event Dynamic Systems: Theory and Applications and of the International Journal of Control. His research interests are in discrete event systems modeling, diagnosis, control, and optimization. He is co-developer of the software packages DESUMA and UMDES. He co-authored, with C. Cassandras, the textbook Introduction to Discrete Event Systems—Second Edition (Springer, 2007). Recent publications and software tools are available at the Web site . 相似文献
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This paper presents the combined use of meta-modelling and graph grammars for the generation of visual modelling tools for simulation formalisms. In meta-modelling, formalisms are described at a meta-level. This information is used by a meta-model processor to generate modelling tools for the described formalisms. We combine meta-modelling with graph grammars to extend the model manipulation capabilities of the generated modelling tools: edit, simulate, transform into another formalism, optimize and generate code. We store all (meta-)models as graphs, and thus, express model manipulations as graph grammars.We present the design and implementation of these concepts in AToM3 (A_To_ol for M_ulti-formalism, M_eta-M_odelling). AToM3 supports modelling of complex systems using different formalisms, all meta-modelled in their own right. Models in different formalisms may be transformed into a single common formalism for further processing. These transformations are specified by graph grammars. Mosterman and Vangheluwe [18] introduced the term multi-paradigm modelling to denote the combination of multiple formalisms, multiple abstraction levels, and meta-modelling. As an example of multi-paradigm modelling we present a meta-model for the Object-Oriented Continuous Simulation Language OOCSMP, in which we combine ideas from UML class diagrams (to express the OOCSMP model structure), Causal Block Diagrams (CBDs), and Statecharts (to specify the methods of the OOCSMP classes). A graph grammar is able to generate OOCSMP code, and then a compiler for this language (C-OOL) generates Java applets for the simulation execution. 相似文献
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C4ISR系统基于仿真的设计方法需要良好的建模方法的支持,Statecharts是一种支持动态行为建模的建模方法,能够描述系统中的层次性、并发和同步,具有结构清晰、逻辑关系明确的优点.将Statecharts方法应用于C4ISR系统的建模过程中,可以对系统在运行过程中实体的状态以及状态的变化进行较为完整的描述,可以增进建模人员对C4ISR系统的理解,提高系统开发的效率.该文在对Statecharts建模方法进行研究的基础上,着重对Statecharts方法在C4ISR系统分析、建模过程中的应用进行了探讨,为C4ISR系统的建模分析提供了支持. 相似文献
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Nandamudi Lankalapalli Vijaykumar Solon Venancio de Carvalho & Vakulathil Abdurahiman 《International Transactions in Operational Research》2002,9(3):321-336
This paper shows that Statecharts, a high-level specification technique, can be used to represent performance models. This is a powerful technique and is based on state-transition diagrams added with concepts of hierarchy and orthogonality to represent a system behavior. It is shown that Statecharts may conveniently be used to represent models with richness and clarity. Using an analytical approach the technique to determine performance measurements is provided. Three examples are presented and the results show Statecharts' potential for representing systems for performance evaluation. 相似文献
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统一建模语言UML已被广泛应用于软件设计和开发中,而验证UML模型是否满足关键的性质需求成为一个重要问题.由于空间爆炸和语义的复杂性,对Statecharts进行模型检验受到软件规模和设计精化程度的制约.本文在用扩展层次自动机(EHA)结构化的表示UML Statecharts后,通过分析EHA中存在的层次、并发和事件同步等特征定义了一组依赖关系.对于由状态和迁移组成的切片准则,给出对EHA进行切片的算法.该算法能保证切片后的EHA与原来的Statecharts对性质具有相同的可满足性,且删除了与被验证性质无关的层次和并发状态,缓解了空间爆炸问题. 相似文献
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尽管Statecharts在反应式实时系统建模领域获得了广泛应用,基于Statecharts开发的实时软件的测试仍然十分困难.由于引入了时间维,待测系统的行为空间变得非常庞大,使得难以对其进行全面深入测试.本文提出了一种面向性质的实时系统测试方法.首先对UML Statecharts作适当实时扩展,使得扩展后能描述non-trivial时间约束;然后用一种受限实时逻辑描述待测系统的功能特性;在此基础上根据待测性质从系统模型生成有针对性的测试序列.实验表明,在相同测试深度下,面向性质测试比非面向性质测试需要少得多的测试序列. 相似文献