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Signal Transduction Pathways as Concurrent Reactive Systems: A Modeling and Simulation Approach Using LSCs and the Play-Engine

Claudia Täubner, Silke Eckstein
2008 Electronical Notes in Theoretical Computer Science  
This aspect is part of a bigger approach, where we provide an extendable system to generate models of signal transduction pathways in different modeling languages and to simulate these models with the  ...  In this paper we present our approach to model these signal transduction pathways as concurrent reactive systems by means of Life Sequence Charts and to simulate them using the Play-Engine tool.  ...  Rio Bartulos for providing us with insights in signal transduction pathways, R. Dalkiran and A. Kolossa for grammatical improvements, our colleagues from the Intergenomics project (especially R.  ... 
doi:10.1016/j.entcs.2007.12.011 fatcat:ny7plmbulzbbdfcipycofbbyku

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems [chapter]

Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
2009 Lecture Notes in Computer Science  
Aware that no formalism can fit all purposes we realize Petri Nets as a suitable model for Metabolic Engineering and take a deeper perspective on the role of this formalism as an integrating framework  ...  Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling.  ...  Based on the criteria defined, petri nets sound the most promising formalism for the goals of our work. They are a graphical and mathematical formalism, therefore intuitive and amenable to analysis.  ... 
doi:10.1007/978-3-642-02481-8_161 fatcat:a4jah5qo5vekpcol3c6fqyn2ua

Modeling and Evaluation of Software Systems with Object Stochastic Activity Networks

Mohammad Azgomi, Ali Movaghar
2006 2006 International Conference on Software Engineering Advances (ICSEA'06)  
The object-orientation of OSANs and the flexibility of having functions for activities, make these models more appropriate than other extensions of Petri nets for modeling and evaluation of software systems  ...  Stochastic activity networks (SANs) are a stochastic generalization of Petri nets. SAN models have been used to evaluate a wide range of systems and are supported by several modeling tools.  ...  SANML is based on the Petri nets markup language (PNML) [Billington03]. 3. Model Compiler: The model compiler translates the model and then generates an executable model.  ... 
doi:10.1109/icsea.2006.261314 dblp:conf/icsea/AzgomiM06a fatcat:rggoufvtlzd2tacdtbb6wicrau

Validation of Reactive Software from Scenario-Based Models

Oscar R. Ribeiro, Joao M. Fernandes
2007 6th International Conference on the Quality of Information and Communications Technology (QUATIC 2007)  
This thesis proposal suggests a model-based approach to obtain, from a set of behavioural scenarios of a given reactive software system, a graphical animation for reproducing that set of scenarios for  ...  We validate our approach based on its application to two examples of reactive systems.  ...  There are also works on the synthesis of Petri nets from scenario-based specification.  ... 
doi:10.1109/quatic.2007.33 fatcat:cfoa454cqbcb7mvp76tsg6qn74

Validation of Reactive Software from Scenario-Based Models

Oscar R. Ribeiro, Joao M. Fernandes
2007 6th International Conference on the Quality of Information and Communications Technology (QUATIC 2007)  
This thesis proposal suggests a model-based approach to obtain, from a set of behavioural scenarios of a given reactive software system, a graphical animation for reproducing that set of scenarios for  ...  We validate our approach based on its application to two examples of reactive systems.  ...  There are also works on the synthesis of Petri nets from scenario-based specification.  ... 
doi:10.1109/quatic.2007.27 dblp:conf/quatic/RibeiroF07 fatcat:uwoommctzfep7gzzzykfusbe5q

Design of user-driven interfaces using Petri nets and objects [chapter]

Philippe A. Palanque, Rémi Bastide, Louis Dourte, Christophe Sibertin-Blanc
1993 Lecture Notes in Computer Science  
This paper presents a survey of three formalisms that are used for modelling the dialogue of user-driven interfaces: state diagrams, events and Petri nets.  ...  Petri nets approaches.  ...  Why do we Need Petri Nets and Objects This part justifies the use of Petri nets for the modelling of reactive systems by comparing this approach with the state-based and event-based approaches, which are  ... 
doi:10.1007/3-540-56777-1_30 fatcat:rm5wht3isneaff4z6yrqwfamoq

A Meta-Model Based Approach for Definition of a Multi-Formalism Modeling Framework

Hamid Mohammad Gholizadeh, Mohammad Abdollahi Azgomi
2009 Journal of clean energy technologies  
In this paper, we propose a meta-modeling approach for definition of a multi-formalism modeling framework for Petri nets and related formal modeling languages.  ...  Many software tools and environments are developed for modeling discrete-event systems. Although, most of the existing tool are proposed for modeling with one or a few modeling languages.  ...  Fig. 4 depicts how Petri net is defined in the framework based on meta-modeling structure.  ... 
doi:10.7763/ijcte.2010.v2.121 fatcat:o47z5lo23zetbfmpavck2pqndm

Modules for Rapid Application Development of Web-Based Information Systems (RADWIS)

S. Cheresharov, H. Krushkov, S. Stoyanov, I. Popchev
2017 Cybernetics and Information Technologies  
A workflow engine module, based on the Petri Nets theory, allows a graphical and formal mathematical solution for a wide variety of problems.  ...  This paper describes a model of modular system for Rapid Application Development of Web-based Information Systems (RADWIS).  ...  A Petri Net-based model is proposed. One of our modules is based on Petri Nets theory and the mentioned research in [27] gives a possible approach.  ... 
doi:10.1515/cait-2017-0033 fatcat:xakqh2p5obcx7l2ctjyitfpauu

The integration of an automatic reserve switching controller into a railway traffic control system power supply through the use of a Petri net and a graphical programming language

2018 Technical Transactions  
There is a requirement for the use of powerful tools and methods of modelling the function and operation of this system.  ...  The integration of an automatic reserve switching controller into a railway traffic control system power supply through the use of a Petri net and a graphical programming language Integracja sterownika  ...  Based on the developed net and the use of the National Instruments LabView graphical programming language, software applications have been developed.  ... 
doi:10.4467/2353737xct.18.122.8897 fatcat:i2cxanjkzjel5i7imwp2jfpbm4

The Internet of Things Enabled Shop Floor Scheduling and Process Control Method Based on Petri Nets

Xiaoqiang Wu, Songling Tian, Lei Zhang
2019 IEEE Access  
A shop floor scheduling/rescheduling method based on Petri net and ant colony optimization (PN-ACO) is proposed given an abnormal event represented by machine breakdown.  ...  On the basis of the mapping mechanism between the Petri net model and the XML, manufacturing resources become autonomous and interactive distributed intelligent manufacturing resources.  ...  MODELLING AN FJSP WITH TTPNs Modeling methods for the FJSP are often divided into three types based on Petri nets: bottom-up modeling, topdown modeling, and hybrid modeling.  ... 
doi:10.1109/access.2019.2900117 fatcat:oeazjyos5ba7dewbuwgx3i7bie

Petri Net Plans

V. A. Ziparo, L. Iocchi, Pedro U. Lima, D. Nardi, P. F. Palamara
2010 Autonomous Agents and Multi-Agent Systems  
In this paper we present a novel representation framework based on Petri Nets for describing robot and multi-robot behaviors.  ...  The Petri Net Plan (PNP) formalism allows for high level description of complex action interactions that are necessary in programming cognitive robots: non-instantaneous actions, sensing and conditional  ...  The proposed framework, called Petri Net Plans (PNP), is based on Petri nets [Mur89] , a graphical modeling language for dynamic systems.  ... 
doi:10.1007/s10458-010-9146-1 fatcat:wc4psc266zfrhn6niq73bf4n6u

Transformation of UML Models into Analyzable OSAN Models

Ali Kamandi, Mohammad Abdollahi Azgomi, Ali Movaghar
2006 Electronical Notes in Theoretical Computer Science  
The unified modelling language (UML) is a de facto standard for object-oriented modelling.  ...  To solve this problem, Petri net formalism has been used as a complement to UML in several research projects.  ...  Analysis of OSAN Models Generally, methods for the analysis of OSAN models is based on the existing methods for SANs and other high-level extensions of Petri nets.  ... 
doi:10.1016/j.entcs.2005.12.059 fatcat:qgtixwltybf4biigbszi7qcvxa

Distinguishing Environment and System in Coloured Petri Net Models of Reactive Systems

Simon Tjell
2007 2007 International Symposium on Industrial Embedded Systems  
This paper introduces and formally defines the environment-and-system-partitioned property for behavioral models of reactive systems expressed in the formal modeling language Coloured Petri Net.  ...  A prototypical tool has been implemented for performing the structural analysis of Coloured Petri Net models and the principles of this tool is described.  ...  The paper will present a collection of formalized guidelines for models of reactive systems in the formal modeling language Coloured Petri Nets.  ... 
doi:10.1109/sies.2007.4297341 dblp:conf/sies/Tjell07 fatcat:pysumiaiivgchfzqtxql7g4vky

Combining Data-Flows and Petri Nets for Cyber-Physical Systems Specification [chapter]

Fernando Pereira, Luis Gomes
2016 IFIP Advances in Information and Communication Technology  
Petri nets have been traditionally used to model the behavior of reactive systems, whose state evolves depending on the interaction with external events.  ...  This paper proposes a new modeling formalism for the specification of cyber-physical systems, combining the functionality offered by Petri nets and synchronous data flows.  ...  , with advantages over purely Petri net centered based languages.  ... 
doi:10.1007/978-3-319-31165-4_7 fatcat:g7mic6yr65cyrmtiexksykuk74

An Executable System Architecture Approach to Discrete Events System Modeling Using SysML in Conjunction with Colored Petri Net

Renzhong Wang, Cihan H Dagli
2008 2008 2nd Annual IEEE Systems Conference  
The essential step is an asynchronous view of the system and focus on the reactive translating SysAML-based s ecifications into Colored Petri Nets***-translaingSysL-base speciicatinsitoCoorebehavior of  ...  much of the work is still based on the transformation Keywords Discrete-event system, SysMIL, CPN, Modeling, of UML state machines [1].  ...  Extended from UML, SysML is an object-oriented of ordinary Petri Nets with the strength of a high-level modeling language so it shares the same primitives and basic programming language, which provides  ... 
doi:10.1109/systems.2008.4518997 fatcat:nuttunqpprgaxnm3yxbjjbhvz4
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