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Simulating P Systems on GPU Device : A Survey

Martínez-del-Amor M. A., García-Quismondo M., Macías-Ramos L. F., Valencia-Cabrera L., Riscos-Núñez A., Pérez-Jiménez M. J.

Fundamenta Informaticae

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2015

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Vol. 136, nr 3

269--284

EN

P systems have been proven to be useful as modeling tools in many fields, such as Systems Biology and Ecological Modeling. For such applications, the acceleration of P system simulation is often desired, given the computational needs derived from these kinds of models. One promising solution is to implement the inherent parallelism of P systems on platforms with parallel architectures. In this respect, GPU computing proved to be an alternative to more classic approaches in Parallel Computing. It provides a low cost, and a manycore platform with a high level of parallelism. The GPU has been already employed to speedup the simulation of P systems. In this paper, we look over the available parallel P systems simulators on the GPU, with special emphasis on those included in the PMCGPU project, and analyze some useful guidelines for future implementations and developments.

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Extending Simulation of Asynchronous Spiking Neural P Systems in P–Lingua

Macías-Ramos L. F., Pérez-Jiménez M. J., Song T., Pan L.

Fundamenta Informaticae

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2015

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Vol. 136, nr 3

253--267

EN

Spiking neural P systems (SN P systems for short) are a class of neural-like computing models in the framework of membrane computing. Inspired by the neurophysiological structure of the brain, SN P systems have been extended in various ways. P–Lingua is a standard language for the definition of P systems, where pLinguaCore library provides particular implementations of parsers and simulators for the models specified in P–Lingua. A support for simulating SN P systems in P–Lingua was introduced recently and soon expanded to cover further features of these systems. In this paper, we present an extension of P–Lingua related to asynchronous SN P systems, in order to incorporate simulation capabilities for limited asynchronous SN P systems and asynchronous SN P systems with local synchronization.

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A P–Lingua Based Simulator for P Systems with Symport/Antiport Rules

Macías-Ramos L. F., Valencia-Cabrera L., Song B., Song T., Pan L., Pérez-Jiménez M. J.

Fundamenta Informaticae

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2015

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Vol. 139, nr 2

211--227

EN

Inspired by mitosis process and membrane fission processes, cell-like P systems with symport/antiport rules and membrane division rules or membrane separation rules have been introduced, respectively. These computation systems have two key features: the ability to have infinite copies of some objects (within an active environment) and to generate an exponential workspace in polynomial time. In this work, we extend the P-Lingua framework for simulating that kind of P systems taking into account these two features. Consequently, a new simulator has been developed and included in pLinguaCore library. The functioning of the simulator has been checked by simulating efficient solutions to SAT problem using a family of cell-like P systems with symport/antiport rules and membrane division rules or membrane separation rules. The corresponding MeCoSim based application is also provided.