Agent-Based High-Performance Simulation of Biological Systems on the GPU

Konur, Savas; Kiran, Mariam; Gheorghe, Marian; Burkitt, Mark J.; Ipate, Florentin

doi:10.1109/hpcc-css-icess.2015.253

Cited by 5 publications

(3 citation statements)

References 22 publications

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“…In order to facilitate the specification of system requirements, kPWorkbench features a property language, called kP-Queries, which comprises a list of property patterns written as natural language statements. The properties expressed in kP-Queries are verified using the Spin [13] The simulation component features a native simulator [2,19], which allows the users to simulate kP system models efficiently. In addition, kPWorkbench integrates the Flame simulator [4,23], a general purpose large scale agent based simulation environment, based on a method that allows users to express kP systems as a set of communicating X-machines [11].…”

Section: Kpworkbenchmentioning

confidence: 99%

Modelling and Validating an Engineering Application in Kernel P Systems

et al. 2017

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Abstract. This paper illustrates how kernel P systems (kP systems) can be used for modelling and validating an engineering application, in this case a cruise control system of an electric bike. The validity of the system is demonstrated via formal verification, carried out using the kPWorkbench tool. Furthermore, we show how the kernel P system model can be tested using automata and X-machine based techniques.

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Section: Kpworkbenchmentioning

confidence: 99%

Modelling and Validating an Engineering Application in Kernel P Systems

et al. 2017

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“…The framework features a native simulator [3,23], allowing the simulation of kP system models. In addition, it also integrates the Flame simulator [7], a general purpose large scale agent based simulation environment, based on a method that allows to express kP systems as a set of communicating X-machines [17].…”

Section: Kpworkbenchmentioning

confidence: 99%

An Integrated Model Checking Toolset for Kernel P Systems

et al. 2015

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Abstract. P systems are the computational models introduced in the context of membrane computing, a computational paradigm within the more general area of unconventional computing. Kernel P (kP) systems are defined to unify the specification of different variants of P systems, motivated by challenging theoretical aspects and the need to model different problems. kP systems are supported by a software framework, called kPWorkbench, which integrates a set of related simulation and verification methodologies and tools. In this paper, we present an extension to kPWorkbench with a new model checking framework supporting the formal verification of kP system models. This framework supports both LTL and CTL properties. To make the property specification an easier task, we propose a property language, composed of natural language statements. We demonstrate our proposed methodology with an example.

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“…One such membrane computing model is kernel P systems (kP systems, for short), introduced in [4,5]. kP systems are widely used in various applications, ranging from systems and synthetic biology to engineering applications [6][7][8][9][10][11][12]. It allows models to be simulated and formally verified using third party model checkers using a software framework, called kPWorkbench [13].…”

Section: Introductionmentioning

confidence: 99%

Search-based testing in membrane computing

et al. 2019

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Search-based testing is widely used for generating test sets. It is also applied in the case of model-based testing, especially for (extended) finite state machines. In this paper, we define such an approach for kernel P system models. We consider a specific kernel P system model and a define a search-based testing method. The test set generated consists of input sequences producing a given computation defined by the model. An example illustrates the use of the introduced method.

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Agent-Based High-Performance Simulation of Biological Systems on the GPU

Cited by 5 publications

References 22 publications

Modelling and Validating an Engineering Application in Kernel P Systems

Modelling and Validating an Engineering Application in Kernel P Systems

An Integrated Model Checking Toolset for Kernel P Systems

Search-based testing in membrane computing

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