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    Authors: Paun, Gheorghe; Pérez Jiménez, Mario de Jesús;

    Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC-04200

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    Authors: Colomer, M. Angels; Martínez del Amor, Miguel Ángel; Pérez Hurtado de Mendoza, Ignacio; Pérez Jiménez, Mario de Jesús; +1 Authors

    In this paper, a P systems based general framework for modeling the dynamics of a population biology is presented. Multienvironment probabilistic functional P systems with active membranes provide the syntactical specification, and the semantics is captured by using stochastic or probabilistic strategies implemented through simulation algorithms. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08–TIC-04200

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    Authors: Christinal, Hepzibah A.; Díaz Pernil, Daniel; Gutiérrez Naranjo, Miguel Ángel; Pérez Jiménez, Mario de Jesús;

    Thresholding is the process of splitting a digital image into sets of pixels in order to make it easier to analyze. Pixels are ordered according to a scale of one of their features as brightness or color and the ¯nal image is obtained by comparing the measure of the feature with some thresholds. In this paper we present a family of cell-like P systems which solve the thresholding problem in linear time on the number of pixels. Ministerio de Ciencia e Innovación TIN2008-04487-E Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08–TIC-04200

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    Authors: Ipate, Florentin; Dragomir, Ciprian; Lefticaru, Raluca; Mierla, Laurentiu; +1 Authors

    The newly introduced Kernel P systems offer an unitary and elegant way of integrating established features of existing P system variants with new elements with potential value for formal modelling. This paper presents a case study illustrating the expressive power and efficiency of kernel P systems on the 3-Col problem. The use of model checking (in particular of Spin) for formal verification of kernel P systems is also discussed and illustrated in this case. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08–TIC–04200

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    Authors: García Quismondo, Manuel; Brandusa Pavel, Ana; Pérez Jiménez, Mario de Jesús;

    Enzymatic Numerical P Systems (ENPS), an extension of Numerical P Systems, have been successfully applied to model robot controllers. GPGPU is an innovative technological paradigm which applies the parallel architecture of graphic cards to solve parallel, general{purpose problems. In previous work, a GPU simulator for ENPS was introduced. In this paper, a performance analysis on the simulator is performed in order to experimentally measure the speed-up factors resulting from the simulations. Ministerio de Ciencia e Innovación TIN2009-13192 Junta de Andalucía P08-TIC-04200

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    Authors: Pérez Hurtado de Mendoza, Ignacio; Pérez Jiménez, Mario de Jesús; Riscos Núñez, Agustín; Romero Campero, Francisco José;

    The aim of the tutorial is to give a general overview of the Membrane Computing paradigm [2,5]. Membrane Computing is a quite active research field, initiated by Gh. Păun in 1998 [3]. It is a theoretical machine-oriented model, where the computational devices (known as P systems) are in some sense an abstraction of a living cell. There exist a large number of different definitions of P systems, but most of them share some common features: a membrane structure (defining in a natural way a number of regions or compartments), and an alphabet of objects that are able to evolve and/or move within the membrane structure according to a set of rules (emulating the way substances undergo biochemical reactions in a cell). Ministerio de Ciencia e Innovación TIN2008-04487-E Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC-04200

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    Authors: Cabarle, Francis George C.; Adorna, Henry N.; Martínez del Amor, Miguel Ángel; Pérez Jiménez, Mario de Jesús;

    In this paper we present our results in adapting a Spiking Neural P system (SNP system) simulator to a high performance graphics processing unit (GPU) platform. In particular, we extend our simulations to larger and more complex SNP systems using an NVIDIA Tesla C1060 GPU. The C1060 is manufactured for high performance computing and massively parallel computations, matching the maximally parallel nature of SNP systems. Using our GPU accelerated simulations we present speedups of around 200× for some SNP systems, compared to CPU only simulations. Ministerio de Educación y Ciencia TIN2009–13192 Junta de Andalucía P08–TIC-04200

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    Authors: Niu, Yunyun; Pan, Linqiang; Pérez Jiménez, Mario de Jesús;

    Common Algorithmic Problem is an optimization problem, which has the nice property that several other NP-complete problems can be reduced to it in linear time. In this work, we deal with its decision version in the framework of tissue P systems. A tissue P system with cell division is a computing model which has two types of rules: communication and division rules. The ability of cell division allows us to obtain an exponential amount of cells in linear time and to design cellular solutions to computationally hard problems in polynomial time. We here present an effective solution to Common Algorithmic Decision Problem by using a family of recognizer tissue P systems with cell division. Furthermore, a formal verification of this solution is given. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC-04200

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    Authors: Juayong, Richelle Ann B.; Cabarle, Francis George C.; Adorna, Henry N.; Martínez del Amor, Miguel Ángel;

    In this report, we present our initial proposal on simulating computations on a restricted variant of Evolution-Communication P system with energy (ECPe system) which will then be implemented in Graphics Processing Units (GPUs). This ECPe sys- tems variant prohibits the use of antiport rules for communication. Several possible levels of parallelizations for simulating ECPe systems computations on GPUs are emphasized. Our work is based on a localized matrix representation for the mentioned variant given in a previous literature. Our proposal employs a methodology for forward computing also discussed in the said literature. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC04200

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    Authors: Colomer, M. Angels; Pérez Hurtado de Mendoza, Ignacio; Pérez Jiménez, Mario de Jesús; Riscos Núñez, Agustín;

    Membrane Computing has recently proved to be a suitable framework for addressing the modelling of dynamical biological systems in general, and ecosystems in particular. Due to the inherent randomness and uncertainty in biological systems, when designing a model the relevant tasks to be addressed are the validation and virtual experimentation processes, rather than the formal verification. It is therefore crucial to rely on software implementations of efficient simulation algorithms. This paper presents a simple (but realistic enough) ecosystem where a carnivore and several herbivorous species interact. The model of this ecosystem has been used to compare experimentally the performance of two different simulation algorithms. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC-04200

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    Authors: Paun, Gheorghe; Pérez Jiménez, Mario de Jesús;

    Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC-04200

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    Authors: Colomer, M. Angels; Martínez del Amor, Miguel Ángel; Pérez Hurtado de Mendoza, Ignacio; Pérez Jiménez, Mario de Jesús; +1 Authors

    In this paper, a P systems based general framework for modeling the dynamics of a population biology is presented. Multienvironment probabilistic functional P systems with active membranes provide the syntactical specification, and the semantics is captured by using stochastic or probabilistic strategies implemented through simulation algorithms. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08–TIC-04200

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    Authors: Christinal, Hepzibah A.; Díaz Pernil, Daniel; Gutiérrez Naranjo, Miguel Ángel; Pérez Jiménez, Mario de Jesús;

    Thresholding is the process of splitting a digital image into sets of pixels in order to make it easier to analyze. Pixels are ordered according to a scale of one of their features as brightness or color and the ¯nal image is obtained by comparing the measure of the feature with some thresholds. In this paper we present a family of cell-like P systems which solve the thresholding problem in linear time on the number of pixels. Ministerio de Ciencia e Innovación TIN2008-04487-E Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08–TIC-04200

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    Authors: Ipate, Florentin; Dragomir, Ciprian; Lefticaru, Raluca; Mierla, Laurentiu; +1 Authors

    The newly introduced Kernel P systems offer an unitary and elegant way of integrating established features of existing P system variants with new elements with potential value for formal modelling. This paper presents a case study illustrating the expressive power and efficiency of kernel P systems on the 3-Col problem. The use of model checking (in particular of Spin) for formal verification of kernel P systems is also discussed and illustrated in this case. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08–TIC–04200

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    Authors: García Quismondo, Manuel; Brandusa Pavel, Ana; Pérez Jiménez, Mario de Jesús;

    Enzymatic Numerical P Systems (ENPS), an extension of Numerical P Systems, have been successfully applied to model robot controllers. GPGPU is an innovative technological paradigm which applies the parallel architecture of graphic cards to solve parallel, general{purpose problems. In previous work, a GPU simulator for ENPS was introduced. In this paper, a performance analysis on the simulator is performed in order to experimentally measure the speed-up factors resulting from the simulations. Ministerio de Ciencia e Innovación TIN2009-13192 Junta de Andalucía P08-TIC-04200

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    Authors: Pérez Hurtado de Mendoza, Ignacio; Pérez Jiménez, Mario de Jesús; Riscos Núñez, Agustín; Romero Campero, Francisco José;

    The aim of the tutorial is to give a general overview of the Membrane Computing paradigm [2,5]. Membrane Computing is a quite active research field, initiated by Gh. Păun in 1998 [3]. It is a theoretical machine-oriented model, where the computational devices (known as P systems) are in some sense an abstraction of a living cell. There exist a large number of different definitions of P systems, but most of them share some common features: a membrane structure (defining in a natural way a number of regions or compartments), and an alphabet of objects that are able to evolve and/or move within the membrane structure according to a set of rules (emulating the way substances undergo biochemical reactions in a cell). Ministerio de Ciencia e Innovación TIN2008-04487-E Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC-04200

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    Authors: Cabarle, Francis George C.; Adorna, Henry N.; Martínez del Amor, Miguel Ángel; Pérez Jiménez, Mario de Jesús;

    In this paper we present our results in adapting a Spiking Neural P system (SNP system) simulator to a high performance graphics processing unit (GPU) platform. In particular, we extend our simulations to larger and more complex SNP systems using an NVIDIA Tesla C1060 GPU. The C1060 is manufactured for high performance computing and massively parallel computations, matching the maximally parallel nature of SNP systems. Using our GPU accelerated simulations we present speedups of around 200× for some SNP systems, compared to CPU only simulations. Ministerio de Educación y Ciencia TIN2009–13192 Junta de Andalucía P08–TIC-04200

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    Authors: Niu, Yunyun; Pan, Linqiang; Pérez Jiménez, Mario de Jesús;

    Common Algorithmic Problem is an optimization problem, which has the nice property that several other NP-complete problems can be reduced to it in linear time. In this work, we deal with its decision version in the framework of tissue P systems. A tissue P system with cell division is a computing model which has two types of rules: communication and division rules. The ability of cell division allows us to obtain an exponential amount of cells in linear time and to design cellular solutions to computationally hard problems in polynomial time. We here present an effective solution to Common Algorithmic Decision Problem by using a family of recognizer tissue P systems with cell division. Furthermore, a formal verification of this solution is given. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC-04200

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    Authors: Juayong, Richelle Ann B.; Cabarle, Francis George C.; Adorna, Henry N.; Martínez del Amor, Miguel Ángel;

    In this report, we present our initial proposal on simulating computations on a restricted variant of Evolution-Communication P system with energy (ECPe system) which will then be implemented in Graphics Processing Units (GPUs). This ECPe sys- tems variant prohibits the use of antiport rules for communication. Several possible levels of parallelizations for simulating ECPe systems computations on GPUs are emphasized. Our work is based on a localized matrix representation for the mentioned variant given in a previous literature. Our proposal employs a methodology for forward computing also discussed in the said literature. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC04200

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    Authors: Colomer, M. Angels; Pérez Hurtado de Mendoza, Ignacio; Pérez Jiménez, Mario de Jesús; Riscos Núñez, Agustín;

    Membrane Computing has recently proved to be a suitable framework for addressing the modelling of dynamical biological systems in general, and ecosystems in particular. Due to the inherent randomness and uncertainty in biological systems, when designing a model the relevant tasks to be addressed are the validation and virtual experimentation processes, rather than the formal verification. It is therefore crucial to rely on software implementations of efficient simulation algorithms. This paper presents a simple (but realistic enough) ecosystem where a carnivore and several herbivorous species interact. The model of this ecosystem has been used to compare experimentally the performance of two different simulation algorithms. Ministerio de Ciencia e Innovación TIN2009–13192 Junta de Andalucía P08-TIC-04200

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