@article {2506,
	title = {A new P-Lingua toolkit for agile development in membrane computing},
	journal = {Information Sciences},
	volume = {587},
	year = {2022},
	pages = {1-22},
	doi = {10.1016/j.ins.2021.12.003},
	url = {https://doi.org/10.1016/j.ins.2021.12.003},
	author = {Ignacio P{\'e}rez-Hurtado and David Orellana-Mart{\'\i}n and Miguel {\'A}. Mart{\'\i}nez-del-Amor and Luis Valencia-Cabrera and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {2472,
	title = {Dendrite P Systems toolbox: representation, algorithms and simulators},
	journal = {International Journal of Neural Systems},
	volume = {31},
	year = {2021},
	pages = {2050071},
	doi = {10.1142/S0129065720500719},
	author = {David Orellana-Mart{\'\i}n and Miguel A. Mart{\'\i}nez-del-Amor and Luis Valencia-Cabrera and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2486,
	title = {A membrane computing framework for social navigation in robotics},
	journal = {Computers and Electrical Engineering},
	volume = {95},
	year = {2021},
	pages = {107408},
	doi = {10.1016/j.compeleceng.2021.107408},
	url = {https://doi.org/10.1016/j.compeleceng.2021.107408},
	author = {Ignacio P{\'e}rez-Hurtado and David Orellana-Mart{\'\i}n and Miguel A. Mart{\'\i}nez-del-Amor and Luis Valencia-Cabrera}
}
@article {2479,
	title = {Simulation of Spiking Neural P Systems with Sparse Matrix-Vector Operations},
	journal = {Processes},
	volume = {9},
	year = {2021},
	abstract = {To date, parallel simulation algorithms for spiking neural P (SNP) systems are based on a matrix representation. This way, the simulation is implemented with linear algebra operations, which can be easily parallelized on high performance computing platforms such as GPUs. Although it has been convenient for the first generation of GPU-based simulators, such as CuSNP, there are some bottlenecks to sort out. For example, the proposed matrix representations of SNP systems lead to very sparse matrices, where the majority of values are zero. It is known that sparse matrices can compromise the performance of algorithms since they involve a waste of memory and time. This problem has been extensively studied in the literature of parallel computing. In this paper, we analyze some of these ideas and apply them to represent some variants of SNP systems. We also provide a new simulation algorithm based on a novel compressed representation for sparse matrices. We also conclude which SNP system variant better suits our new compressed matrix representation.},
	issn = {2227-9717},
	doi = {10.3390/pr9040690},
	url = {https://doi.org/10.3390/pr9040690},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and David Orellana-Mart{\'\i}n and Ignacio P{\'e}rez-Hurtado and Francis G. C. Cabarle and Henry N. Adorna}
}
@article {10.1145/3431234,
	title = {A Survey of Nature-Inspired Computing: Membrane Computing},
	journal = {ACM Computing Surveys},
	volume = {54},
	number = {1},
	year = {2021},
	pages = {Article no 22},
	publisher = {Association for Computing Machinery},
	address = {New York, NY, USA},
	abstract = {Nature-inspired computing is a type of human-designed computing motivated by nature, which is based on the employ of paradigms, mechanisms, and principles underlying natural systems. In this article, a versatile and vigorous bio-inspired branch of natural computing, named membrane computing is discussed. This computing paradigm is aroused by the internal membrane function and the structure of biological cells. We first introduce some basic concepts and formalisms of membrane computing, and then some basic types or variants of P systems (also named membrane systems) are presented. The state-of-the-art computability theory and a pioneering computational complexity theory are presented with P system frameworks and numerous solutions to hard computational problems (especially NP-complete problems) via P systems with membrane division are reported. Finally, a number of applications and open problems of P systems are briefly described.},
	keywords = {Computational Complexity, distributed systems, Membrane computing, Nature-inspired computing},
	issn = {0360-0300},
	doi = {10.1145/3431234},
	url = {https://doi.org/10.1145/3431234},
	author = {Bosheng Song and Kenli Li and David Orellana-Mart{\'\i}n and Mario J. P{\'e}rez-Jim{\'e}nez and Ignacio P{\'e}rez-Hurtado}
}
@article {2469,
	title = {From NP-Completeness to DP-Completeness: A Membrane Computing Perspective},
	journal = {Complexity},
	volume = {2020},
	year = {2020},
	month = {2020},
	pages = {10},
	publisher = {Hindawi},
	doi = {10.1155/2020/6765097},
	url = {https://www.hindawi.com/journals/complexity/2020/6765097/},
	author = {Luis Valencia-Cabrera and David Orellana-Mart{\'\i}n and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2481,
	title = {Simulating Population Dynamics P systems with extra parallelism},
	journal = {International Conference on Membrane Computing (ICMC2020)},
	year = {2020},
	month = {09/2020},
	url = {http://2020.e-icmc.org/content/4/$\#$Full\%20Program},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Andr{\'e}s Doncel-Ram{\'\i}rez and David Orellana-Mart{\'\i}n and Ignacio P{\'e}rez-Hurtado}
}
@article {MARTINEZDELAMOR2020,
	title = {Adaptative parallel simulators for bioinspired computing models},
	journal = {Future Generation Computer Systems},
	volume = {107},
	year = {2020},
	pages = {469-484},
	abstract = {In the Membrane Computing area, P systems are unconventional devices of computation inspired by the structure and processes taking place in living cells. Main successful P system applications lie in computability and computational complexity theories, as well as in biological modelling. Given that models become too complex to deal with, simulators for P systems are essential tools and their efficiency is critical. In order to handle the diverse situations that may arise during the computation, these simulators have to take into account that worst-case scenarios can happen, even though they rarely occur. As a result, there is a significant loss of performance. In this paper, the concept of adaptative simulation for P systems is introduced to palliate this problem. This is achieved by passing high-level information provided directly by P system model designers to the simulator, helping it to better adapt to the target model. For this purpose, an existing simulator for an ecosystem modelling framework, named Population Dynamics P systems, is extended to include the information of modules, that are usually employed to define ecosystem models. Moreover, the standard description language for P systems, P-Lingua, has been re-engineered in its version 5. It now includes a new syntactical item, called feature, to express this kind of high-level semantic information. Experiments show that this simple adaptative simulator supporting modules as features doubles the performance when running on GPUs and on multicore processors.},
	keywords = {bio-inspired computing, GPU Computing, P systems, P-Lingua, parallel computing, Parallel simulators},
	issn = {0167-739X},
	doi = {https://doi.org/10.1016/j.future.2020.02.012},
	url = {http://www.sciencedirect.com/science/article/pii/S0167739X19308817},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and David Orellana-Mart{\'\i}n and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2482,
	title = {Extracting Parallelism in Simulation Algorithms for PDP systems},
	journal = {18th Brainstorming Week on Membrane Computing (BWMC2020)},
	year = {2020},
	pages = {79-90},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla},
	url = {http://www.gcn.us.es/files/18bwmc/079_mdcba.pdf},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Andr{\'e}s Doncel-Ram{\'\i}rez and David Orellana-Mart{\'\i}n and Ignacio P{\'e}rez-Hurtado}
}
@article {2363,
	title = {A membrane parallel rapidly-exploring random tree algorithm for robotic motion planning},
	journal = {Integrated Computer-Aided Engineering},
	volume = {27},
	year = {2020},
	pages = {121-138},
	abstract = {In recent years, incremental sampling-based motion planning algorithms have been widely used to solve robot motion planning problems in high-dimensional configuration spaces. In particular, the Rapidly-exploring Random Tree (RRT) algorithm and its asymptotically-optimal counterpart called RRT* are popular algorithms used in real-life applications due to its desirable properties. Such algorithms are inherently iterative, but certain modules such as the collision-checking procedure can be parallelized providing significant speedup with respect to sequential implementations. In this paper, the RRT and RRT* algorithms have been adapted to a bioinspired computational framework called Membrane Computing whose models of computation, a.k.a. P systems, run in a non-deterministic and massively parallel way. A large number of robotic applications are currently using a variant of P systems called Enzymatic Numerical P systems (ENPS) for reactive controlling, but there is a lack of solutions for motion planning in the framework. The novel models in this work have been designed using the ENPS framework. In order to test and validate the ENPS models for RRT and RRT*, we present two ad-hoc implementations able to emulate the computation of the models using OpenMP and CUDA. Finally, we show the speedup of our solutions with respect to sequential baseline implementations. The results show a speedup up to 6x using OpenMP with 8 cores against the sequential implementation and up to 24x using CUDA against the best multi-threading configuration.},
	keywords = {CUDA, Membrane computing, OpenMP, Optimal Motion Planning, Rapidly-exploring Random Tree},
	issn = {1069-2509},
	doi = {10.3233/ICA-190616},
	url = {https://doi.org/10.3233/ICA-190616},
	author = {Ignacio P{\'e}rez-Hurtado and Miguel A. Mart{\'\i}nez-del-Amor and G. Zhang and F. Neri and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2478,
	title = {Simulation challenges in membrane computing},
	journal = {Journal of Membrane Computing},
	volume = {2},
	year = {2020},
	pages = {392{\textendash}402},
	doi = {10.1007/s41965-020-00056-w},
	url = {https://link.springer.com/article/10.1007\%2Fs41965-020-00056-w},
	author = {Luis Valencia-Cabrera and Ignacio P{\'e}rez-Hurtado and Miguel A. Mart{\'\i}nez-del-Amor}
}
@article {PENG2020105064,
	title = {Spiking neural P systems with inhibitory rules},
	journal = {Knowledge-Based Systems},
	volume = {188},
	year = {2020},
	pages = {105064},
	abstract = {Motivated by the mechanism of inhibitory synapses, a new kind of spiking neural P (SNP) system rules, called inhibitory rules, is introduced in this paper. Based on this, a new variant of SNP systems is proposed, called spiking neural P systems with inhibitory rules (SNP-IR systems). Different from the usual firing rules in SNP systems, the firing condition of an inhibitory rule not only depends on the state of the neuron associated with the rule but also is related to the states of other neurons. Moreover, from the perspective of topological structure, the new variant is shown as a directed graph with inhibitory arcs, and therefore seems to have more powerful control. The computational completeness of SNP-IR systems is discussed. In particular, it is proved that SNP-IR systems are Turing universal number accepting/generating devices. Moreover, we obtain a small universal function-computing device for SNP-IR systems consisting of 100 neurons.},
	keywords = {Inhibitory synapse, Membrane computing, spiking neural P systems, Spiking neural P systems with inhibitory rules},
	issn = {0950-7051},
	doi = {https://doi.org/10.1016/j.knosys.2019.105064},
	url = {http://www.sciencedirect.com/science/article/pii/S0950705119304514},
	author = {Hong Peng and Bo Li and Jun Wang and Xiaoxiao Song and Tao Wang and Luis Valencia-Cabrera and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2188,
	title = {When object production tunes the efficiency of membrane systems},
	journal = {Theoretical Computer Science},
	volume = {805},
	year = {2020},
	pages = {218-231},
	doi = {https://doi.org/10.1016/j.tcs.2018.04.013},
	author = {David Orellana-Mart{\'\i}n and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Luis Valencia-Cabrera and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {P{\'e}rez-Hurtado2019,
	title = {P-Lingua in two steps: flexibility and efficiency},
	journal = {Journal of Membrane Computing},
	volume = {1},
	number = {2},
	year = {2019},
	month = {Jun},
	pages = {93{\textendash}102},
	issn = {2523-8914},
	doi = {10.1007/s41965-019-00014-1},
	url = {https://doi.org/10.1007/s41965-019-00014-1},
	author = {Ignacio P{\'e}rez-Hurtado and David Orellana-Mart{\'\i}n and Gexiang Zhang and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2350,
	title = {11 years of P-Lingua: A backward glance},
	journal = {20th International Conference on Membrane Computing, CMC20},
	year = {2019},
	pages = {451-462},
	publisher = {Editura BIBLIOSTAR},
	isbn = {978-606-8493-76-3},
	url = {http://www.cs.us.es/~marper/investigacion/P-Lingua.pdf},
	author = {Ignacio P{\'e}rez-Hurtado and David Orellana-Mart{\'\i}n and Miguel A. Mart{\'\i}nez-del-Amor and Luis Valencia-Cabrera and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2351,
	title = {Dependency Graph Technique Revisited},
	journal = {20th International Conference on Membrane Computing, CMC20},
	year = {2019},
	pages = {513-522},
	publisher = {Editura BIBLIOSTAR},
	isbn = {978-606-8493-76-3},
	url = {http://www.cs.us.es/~marper/investigacion/dependency-graph.pdf},
	author = {Luis Valencia-Cabrera and David Orellana-Mart{\'\i}n and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {10.1007/978-3-030-12797-8_14,
	title = {Design of Specific P Systems Simulators on GPUs},
	journal = {Membrane Computing},
	volume = {11399},
	year = {2019},
	pages = {202{\textendash}207},
	publisher = {Springer International Publishing},
	address = {Cham},
	abstract = {In order to validate P system models and to assist on their formal verification, simulators are indispensable. Moreover, having efficient simulation tools is crucial, and for this purpose, parallel platforms should be employed. So far, several parallel simulators for P systems have been developed, specifically targeting GPUs (Graphics Processing Units). Although being a hot topic within Membrane Computing, mapping P system parallelism on GPUs is still not a mature area. In the past, we have successfully accelerated the simulation of two specific families of P systems solving SAT with GPUs, and learned in the process some semantics ingredients that fit well on these parallel devices. We are extending this exploration by designing an specific simulator of a P system model for the FACTORIZATION problem. In this paper, we analyse the two main approaches for simulators, and depict some design decisions required for this case study.},
	isbn = {978-3-030-12797-8},
	doi = {10.1007/978-3-030-12797-8_14},
	url = {https://doi.org/10.1007/978-3-030-12797-8_14},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and David Orellana-Mart{\'\i}n and Ignacio P{\'e}rez-Hurtado and Luis Valencia-Cabrera and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez},
	editor = {Thomas Hinze and Grzegorz Rozenberg and Arto Salomaa and Claudio Zandron}
}
@article {2356,
	title = {New applications for an old tool},
	journal = {Seventeenth Brainstorming Week on Membrane Computing},
	year = {2019},
	pages = {165-170},
	url = {http://www.cs.us.es/~marper/investigacion/new-applications.pdf},
	author = {Luis Valencia-Cabrera and David Orellana-Mart{\'\i}n and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2459,
	title = {Solving the feasibility problem in robotic motion planning by means of Enzymatic Numerical P systems},
	journal = {The 8th Asian Conference on Membrane Computing (ACMC2019)},
	year = {2019},
	address = {Xiamen (China)},
	author = {Ignacio P{\'e}rez-Hurtado and Miguel A. Mart{\'\i}nez-del-Amor and G. Zhang and F. Neri and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {PENG2019105064,
	title = {Spiking neural P systems with inhibitory rules},
	journal = {Knowledge-Based Systems},
	year = {2019},
	pages = {105064},
	abstract = {Motivated by the mechanism of inhibitory synapses, a new kind of spiking neural P (SNP) system rules, called inhibitory rules, is introduced in this paper. Based on this, a new variant of SNP systems is proposed, called spiking neural P systems with inhibitory rules (SNP-IR systems). Different from the usual firing rules in SNP systems, the firing condition of an inhibitory rule not only depends on the state of the neuron associated with the rule but also is related to the states of other neurons. Moreover, from the perspective of topological structure, the new variant is shown as a directed graph with inhibitory arcs, and therefore seems to have more powerful control. The computational completeness of SNP-IR systems is discussed. In particular, it is proved that SNP-IR systems are Turing universal number accepting/generating devices. Moreover, we obtain a small universal function-computing device for SNP-IR systems consisting of 100 neurons.},
	keywords = {Inhibitory synapse, Membrane computing, spiking neural P systems, Spiking neural P systems with inhibitory rules},
	issn = {0950-7051},
	doi = {https://doi.org/10.1016/j.knosys.2019.105064},
	url = {http://www.sciencedirect.com/science/article/pii/S0950705119304514},
	author = {Hong Peng and Bo Li and Jun Wang and Xiaoxiao Song and Tao Wang and Luis Valencia-Cabrera and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2355,
	title = {A syntax for semantics in P-Lingua},
	journal = {Seventeenth Brainstorming Week on Membrane Computing},
	year = {2019},
	pages = {139-150},
	url = {http://www.cs.us.es/~marper/investigacion/semantics-P-Lingua.pdf},
	author = {Ignacio P{\'e}rez-Hurtado and David Orellana-Mart{\'\i}n and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2475,
	title = {A Decade of Ecological Membrane Computing Applications},
	journal = {Bulletin of the International Membrane Computing Society},
	volume = {6},
	year = {2018},
	month = {12/2018},
	pages = {39-50},
	url = {http://membranecomputing.net/IMCSBulletin/pdf/BulletinDec2018.pdf},
	author = {Luis Valencia-Cabrera and Carmen Graciani and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {2212,
	title = {A Simulation Workflow for Membrane Computing: From MeCoSim to PMCGPU Through P-Lingua},
	journal = {Enjoying Natural Computing: Essays Dedicated to Mario de Jes{\'u}s P{\'e}rez-Jim{\'e}nez on the Occasion of His 70th Birthday},
	year = {2018},
	month = {11/2018},
	pages = {291-303},
	publisher = {Springer International Publishing},
	doi = {https://doi.org/10.1007/978-3-030-00265-7_23},
	author = {Luis Valencia-Cabrera and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado},
	editor = {Carmen Graciani and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Gheorghe P{\u a}un and Gregorz Rozenberg and Arto Salomaa}
}
@proceedings {2186,
	title = {Robot path planning using rapidly-exploring random trees: A membrane computing approach},
	journal = {7th International Conference on Computers Communications and Control (ICCCC2018)},
	year = {2018},
	month = {06/2018},
	publisher = {IEEE},
	isbn = {978-1-5386-1934-6},
	doi = {https://doi.org/10.1109/ICCCC.2018.8390434},
	url = {https://ieeexplore.ieee.org/document/8390434/},
	author = {Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Gexiang Zhang and David Orellana-Mart{\'\i}n}
}
@article {2196,
	title = {Simulation of Computing P Systems: A GPU Design for the Factorization Problem},
	journal = {19th International Conference on Membrane Computing},
	year = {2018},
	pages = {239-242},
	address = {Dresden, Germany},
	isbn = {978-3-96409-030-0},
	url = {http://www.book-on-demand.de/shop/15551},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and David Orellana-Mart{\'\i}n and Ignacio P{\'e}rez-Hurtado and Luis Valencia-Cabrera and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2108,
	title = {Cooperative P Systems and the P versus NP Problem},
	journal = {Bulletin of the International Membrane Computing Society},
	volume = {4},
	year = {2017},
	month = {12/2017},
	pages = {39-64},
	url = {http://membranecomputing.net/IMCSBulletin/pdf/BullDec2017.pdf},
	author = {Luis Valencia-Cabrera and Miguel A. Mart{\'\i}nez-del-Amor and David Orellana-Mart{\'\i}n and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@proceedings {2174,
	title = {Generation of rapidly-exploring random tree by using a new class of membrane systems},
	journal = {Asian Conference on Membrane Computing (ACMC 2017)},
	year = {2017},
	month = {09/2017},
	pages = {534-546},
	author = {Ignacio P{\'e}rez-Hurtado}
}
@inbook {995,
	title = {Membrane System-Based Models for Specifying Dynamical Population Systems},
	booktitle = {Applications of Membrane Computing in Systems and Synthetic Biology},
	series = {Emergence, Complexity and Computation},
	volume = {7},
	year = {2014},
	month = {12/2013},
	pages = {97-132},
	publisher = {Springer Verlag},
	organization = {Springer Verlag},
	chapter = {4},
	address = {Amsterdam, the Netherlands},
	abstract = {Population Dynamics P systems (PDP systems, in short) provide a new
formal bio-inspired modelling framework, which has been successfully used for
modelling population dynamics on real ecosystems. The semantics of these systems
is captured by the Direct distribution based on Consistent Blocks Algorithm (DCBA),
which has been engineered into software simulation tools. In particular,MeCoSim
(Membrane Computing Simulator) is a GUI developed in the framework ofP-Lingua
that can be used as a simulation environment for running virtual experiments. The
parameters of each scenario to be simulated can be easily adjusted in a visual way,
as well as the settings for the desired output format, thus facilitating the validation},
	url = {http://www.springer.com/engineering/computational+intelligence+and+complexity/book/978-3-319-03190-3},
	author = {M. Angels Colomer and Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Luis Valencia-Cabrera}
}
@article {1774,
	title = {A P-Lingua based Simulator for Tissue P Systems with Cell Separation},
	journal = {Romanian Journal of Information Science and Technology},
	volume = {17},
	year = {2014},
	pages = {89-102},
	publisher = {EDITURA ACADEMIEI ROM{\^A}NE},
	address = {Bucure{\c s}ti, Rom{\^a}nia},
	issn = {1453-8245},
	author = {Ignacio P{\'e}rez-Hurtado and Luis Valencia-Cabrera and Jos{\'e} M. Chac{\'o}n and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {945,
	title = {DCBA: Simulating population dynamics P systems with proportional objects distribution},
	journal = {Lecture Notes in Computer Science},
	year = {2013},
	pages = {257-276},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	abstract = {Population Dynamics P systems provide a formal framework for ecological modelling having a probabilistic (while keeping the maximal parallelism). Several simulation algorithms have been developed always trying to reach higher reliability in the way they reproduce the behaviour of the ecosystems being modelled.
It is natural for those algorithms to classify the rules into blocks, comprising rules that share identical left-hand side. Previous algorithms, such as the Binomial Block Based (BBB) or the Direct Non Deterministic distribution with Probabilities (DNDP), do not define a deterministic behaviour for blocks of rules competing for the same resources. In this paper we introduce the Direct distribution based on Consistent Blocks Algorithm (DCBA), a simulation algorithm which addresses that inherent non-determinism of the model by distributing proportionally the resources.},
	issn = {0302-9743},
	doi = {10.1007/978-3-642-36751-9_18},
	url = {http://link.springer.com/chapter/10.1007/978-3-642-36751-9_18},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Luis Valencia-Cabrera and {\'A}lvaro Romero-Jim{\'e}nez and Carmen Graciani-D{\'\i}az and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and M. Angels Colomer and Mario J. P{\'e}rez-Jim{\'e}nez},
	editor = {Erzsebet Csuhaj-Varj{\'u} and Marian Gheorghe and Grzegorz Rozenberg and Arto Salomaa and Gy{\"o}rgy Vaszil}
}
@article {944,
	title = {A formalization of membrane systems with dynamically evolving structures},
	journal = {International Journal of Computer Mathematics},
	volume = {90},
	year = {2013},
	pages = {801-815},
	publisher = {Taylor and Francis},
	address = {London, UK},
	abstract = {This article introduces a general formalism/framework flexible enough to cover descriptions of different variants of P systems having a dynamic membrane structure. Our framework can be useful for the precise definition of new variants of P systems with a dynamic structure and for the comparison of existing definitions as well as for their extension. We give a detailed definition of the formalism and we present some examples of how to translate several existing variants of P systems with a dynamic structure.},
	keywords = {dynamic structure, formal definition, P systems},
	issn = {0020-7160},
	doi = {10.1080/00207160.2012.748899},
	url = {http://www.tandfonline.com/doi/abs/10.1080/00207160.2012.748899},
	author = {Rudolf Freund and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Sergey Verlan}
}
@article {989,
	title = {A P-Lingua based simulator for tissue P systems with cell separation},
	journal = {Second Asian Conference on Membrane Computing},
	year = {2013},
	pages = {208-220},
	author = {Ignacio P{\'e}rez-Hurtado and Luis Valencia-Cabrera and Jos{\'e} M. Chac{\'o}n and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez},
	editor = {Gexiang Zhang and Y. Wang and J. Cheng and T. Wang}
}
@article {979,
	title = {A Rete-based Algorithm for Rule Selection in P Systems},
	journal = {International Journal of Unconventional Computing},
	volume = {9},
	year = {2013},
	pages = {367-384},
	publisher = {Old City Publishing Inc.},
	address = {Philadelphia, USA},
	issn = {1548-7199},
	url = {http://www.oldcitypublishing.com/IJUC/IJUCcontents/IJUCv9n5-6contents.html},
	author = {Carmen Graciani-D{\'\i}az and Miguel A. Guti{\'e}rrez-Naranjo and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and {\'A}lvaro Romero-Jim{\'e}nez}
}
@proceedings {870,
	title = {Proceedings of the Tenth Brainstorming Week on Membrane Computing},
	journal = {Tenth Brainstorming Week on Membrane Computing},
	volume = {I},
	year = {2012},
	month = {30/01/2012},
	pages = {xiv+318},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	url = {http://www.gcn.us.es/10BWMC/10BWMCvolI/bravol2012I.pdf},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Gheorghe Paun and Ignacio P{\'e}rez-Hurtado and Francisco J. Romero-Campero}
}
@article {884,
	title = {DCBA: Simulating population dynamics P systems with proportional object distribution},
	journal = {13th International Conference on Membrane Computing (CMC13)},
	year = {2012},
	month = {08/2012},
	pages = {291-310},
	address = {Budapest, Hungary},
	abstract = {Population Dynamics P systems (PDP systems, in short)
refer to a formal framework for ecological modelling. The semantics
of the model associates probabilities with rules, but inasmuch as
the model is based on P systems, the rules are also applied in a
maximally parallel way. Following the success of the first model using
this framework, initially called multienvironment probabilistic P systems,
several simulation algorithms have been developed in order to better
reproduce the behaviour of the ecosystems being modelled.
It is natural for those algorithms to classify the rules from the model
into blocks, comprising rules that share identical left-hand side. Previous
algorithms, such as the Binomial Block Based (BBB) or the Direct Non
Deterministic distribution with Probabilities (DNDP), do not define
a deterministic behaviour for blocks of rules competing for the same
resources. In this paper we introduce the Direct distribution based on
Consistent Blocks Algorithm (DCBA), a simulation algorithm which
address that inherent non-determinism of the model by distributing
proportionally the resources.
},
	keywords = {DCBA, Membrane computing, P-Lingua, pLinguaCore, Population Dynamics P systems, Probabilistic P systems, Simulation Algorithm},
	isbn = {978-963-311-372-1 },
	url = {http://www.sztaki.hu/tcs/proba/cmc13/CMC13-proceedings.pdf},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Luis Valencia-Cabrera and {\'A}lvaro Romero-Jim{\'e}nez and Carmen Graciani-D{\'\i}az and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and M. Angels Colomer and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {884,
	title = {A formal framework for P systems with dynamic structure},
	journal = {13th International Conference on Membrane Computing (CMC13)},
	year = {2012},
	month = {08/2012},
	pages = {199-210},
	address = {Budapest, Hungary},
	isbn = {978-963-311-372-1},
	url = {http://www.sztaki.hu/tcs/proba/cmc13/CMC13-proceedings.pdf},
	author = {Rudolf Freund and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Sergey Verlan}
}
@article {872,
	title = {DCBA: Simulating Population Dynamics P Systems with Proportional Object Distribution},
	journal = {Tenth Brainstorming Week on Membrane Computing},
	volume = {II},
	year = {2012},
	month = {02/2012},
	pages = {27-56},
	publisher = {F{\'e}nix Editora},
	address = {Seville, Spain},
	abstract = {Population Dynamics P systems refer to a formal framework for ecological
modelling. The semantics of the model associates probabilities to rules, but at the
same time, the model is based on P systems, so the rules are applied in a maximally
parallel way. Since the success of the rst model using this framework [5], initially
called multienvironment probabilistic P systems, several simulation algorithms have been
dened in order to better reproduce the behaviour of the ecosystems with the models.
BBB and DNDP are previous attempts, which dene blocks of rules having the
same left-hand side, but do not dene a deterministic behaviour when dierent rules are
competing for the same resources. That is, dierent blocks of rules present in their left-
hand side common objects, being applicable at the same time. In this paper, we introduce
a new simulation algorithm, called DCBA, which performs a proportional distribution of
resources.},
	keywords = {DCBA, Membrane computing, P-Lingua, pLinguaCore, Population Dynamics, Probabilistic P systems, Simulation Algorithm},
	url = {http://www.gcn.us.es/10BWMC/10BWMCvolII/papers/dcba.pdf},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Luis Valencia-Cabrera and {\'A}lvaro Romero-Jim{\'e}nez and Carmen Graciani-D{\'\i}az and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and M. Angels Colomer and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {859,
	title = {A Formal Framework for P Systems with Dynamic Structure},
	journal = {Tenth Brainstorming Week on Membrane Computing},
	volume = {I},
	year = {2012},
	month = {02/2012},
	pages = {111-122},
	publisher = {F{\'e}nix Editora},
	address = {Seville, Spain},
	abstract = {This article introduces a formalism/framework able to describe different
variants of P systems having a dynamic structure. This framework can be useful for
the definition of new variants of P systems with dynamic structure, for the comparison
of existing definitions as well as for their extension. We give a precise definition of the
formalism and show how existing variants of P systems with dynamic structure can be
translated to it.},
	url = {http://www.gcn.us.es/10BWMC/10BWMCvolI/papers/AgustinSerghei.pdf},
	author = {Rudolf Freund and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Sergey Verlan}
}
@article {822,
	title = {Formal verification of P systems with active membranes through model checking},
	journal = {Lecture Notes in Computer Science},
	volume = {7184},
	year = {2012},
	pages = {215-225},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	abstract = {Formal verification of P systems using model checking has attracted a significant amount of research in recent years. However, up to now only P systems with static structure have been considered. This paper makes significant advances in this area by considering P systems with active membranes, in particular P systems with division rules. The paper presents a theoretical framework for addressing this problem and reports on a complex case study involving a well-known NP-complete problem solved using P systems with membrane division rules. This is implemented in Promela and non trivial properties are verified using Spin. },
	issn = {0302-9743},
	doi = {10.1007/978-3-642-28024-5_15},
	url = {http://www.springerlink.com/content/86113w5748425306/},
	author = {Florentin Ipate and Raluca Lefticaru and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Cristina Tudose}
}
@article {821,
	title = {A P-Lingua based simulator for Spiking Neural P systems},
	journal = {Lecture Notes in Computer Science},
	volume = {7184},
	year = {2012},
	pages = {257-281},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	abstract = {The research within the field of Spiking Neural P systems (SN P systems, for short) is focusing mainly in the study of the computational completeness (they are equivalent in power to Turing machines) and computational efficiency of this kind of systems. These devices have been shown capable of providing polynomial time solutions to computationally hard problems by making use of an exponential workspace constructed in a natural way. In order to experimentally explore this computational power, it is necessary to develop software that provides simulation tools (simulators) for the existing variety of SN P systems. Such simulators allow us to carry out computations of solutions to NP-complete problems on certain instances. Within this trend, P-Lingua provides a standard language for the definition of P systems. As part of the same project, pLinguaCore library provides particular implementations of parsers and simulators for the models specified in P-Lingua. In this paper, an extension of the P-Lingua language to define SN P systems is presented, along with an upgrade of pLinguaCore including a parser and a new simulator for the variants of these systems included in the language. },
	issn = {0302-9743},
	doi = {10.1007/978-3-642-28024-5_18},
	url = {http://www.springerlink.com/content/jrtrt4273v3086m7/},
	author = {Luis F. Mac{\'\i}as-Ramos and Ignacio P{\'e}rez-Hurtado and Manuel Garc{\'\i}a-Quismondo and Luis Valencia-Cabrera and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {springerlink:10.1007/978-3-642-33636-2_15,
	title = {Population Dynamics P Systems on CUDA},
	journal = {Lecture Notes in Bioinformatics},
	volume = {7605},
	year = {2012},
	note = {10.1007/978-3-642-33636-2_15},
	pages = {247-266},
	publisher = {Springer Berlin / Heidelberg},
	edition = {Computational Methods in Systems Biology},
	abstract = {Population Dynamics P systems (PDP systems, in short) provide a new formal bio-inspired modeling framework, which has been successfully used by ecologists. These models are validated using software tools against actual measurements. The goal is to use P systems simulations to adopt a priori management strategies for real ecosystems. Software for PDP systems is still in an early stage. The simulation of PDP systems is both computationally and data intensive for large models. Therefore, the development of efficient simulators is needed for this field. In this paper, we introduce a novel simulator for PDP systems accelerated by the use of the computational power of GPUs. We discuss the implementation of each part of the simulator, and show how to achieve up to a 7x speedup on a NVIDA Tesla C1060 compared to an optimized multicore version on a Intel 4-core i5 Xeon for large systems. Other results and testing methodologies are also included.},
	keywords = {CUDA, Ecological Modeling, GPU Computing, Membrane computing, Parallel Simulation, Population Dynamics},
	isbn = {978-3-642-33635-5},
	doi = {10.1007/978-3-642-33636-2_15},
	url = {http://dx.doi.org/10.1007/978-3-642-33636-2_15},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Adolfo Gastalver-Rubio and Anne C. Elster and Mario J. P{\'e}rez-Jim{\'e}nez},
	editor = {Gilbert, David and Heiner, Monika}
}
@proceedings {749,
	title = {Proceedings of the Ninth Brainstorming Week on Membrane Computing},
	journal = {Ninth Brainstorming  Week on Membrane Computing},
	year = {2011},
	month = {31/01/2011},
	pages = {xiv+374},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	url = {http://www.gcn.us.es/9bwmc_proceedings},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Gheorghe Paun and Ignacio P{\'e}rez-Hurtado and Francisco J. Romero-Campero and Luis Valencia-Cabrera}
}
@article {788,
	title = {Formal Verication of P Systems with Active Membranes through Model Checking},
	journal = {12th International Conference on Membrane Computing (CMC12)},
	year = {2011},
	month = {08/2011},
	pages = {241-252},
	address = {Fontainebleau, France},
	abstract = {Formal verification of P systems using model checking has
attracted a significant amount of research in recent years. However, up
to now only P systems with static structure have been considered. This
paper makes significant advances in this area by considering P systems
with active membranes, in particular P systems with division rules. The
paper presents a theoretical framework for addressing this problem and
reports on a complex case study involving a well-known NP-complete
problem solved using P systems with membrane division rules. This is
implemented in Promela and non trivial properties are verified using
Spin.},
	url = {http://cmc12.lacl.fr/cmc12proceedings.pdf},
	author = {Florentin Ipate and Raluca Lefticaru and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Cristina Tudose}
}
@article {789,
	title = {A P-Lingua based Simulator for Spiking Neural P Systems},
	journal = {Proceedings of the 12th International Conference on Membrane Computing (CMC12)},
	year = {2011},
	month = {08/2011},
	pages = {323-346},
	address = {Fontainebleau, France},
	abstract = {The research within the field of Spiking Neural P systems
(SN P systems, for short) is focusing mainly in the study of the
computational complexity and efficiency of this kind of systems.
These devices have been shown capable of providing polynomial time
solutions to computationally hard problems. In order to experimentally
explore this computational power, it is necessary to develop software
that provides simulation tools (simulators) for the existing variety of
SN P systems. Such simulators allow us to carry out computations of
solutions to computationally hard problems on certain instances. Within
this trend, P-Lingua provides a standard language for the definition of
P systems. As part of the same project, pLinguaCore library provides
particular implementations of parsers and simulators for the models
specified in P-Lingua. In this paper, an extension of the P-Lingua
language to define SN P systems is presented, along with an upgrade
of pLinguaCore including a parser and a new simulator for the variants
of these systems included in the language.},
	url = {http://cmc12.lacl.fr/cmc12proceedings.pdf},
	author = {Luis F. Mac{\'\i}as-Ramos and Ignacio P{\'e}rez-Hurtado and Manuel Garc{\'\i}a-Quismondo and Luis Valencia-Cabrera and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {726,
	title = {Modeling population growth of Pyrenean Chamois (Rupicapra p. pyrenaica) by using P systems},
	journal = {Lecture Notes in Computer Science},
	volume = {6501},
	year = {2011},
	month = {08/2010},
	pages = {144-159},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	abstract = {P systems provide a high level computational modeling framework which integrates the structural and dynamic aspects of ecosystems in a comprehensive and relevant way. In previous works, several ecosystems modeled by using P systems were presented. The good results obtained encourage us to study new ecosystems such as the one presented in this paper. Pyrenean Chamois (Rupicapra p. pyrenaica) is an ungulate species inhabiting the Catalan Pyrenees. In recent years, several diseases have caused a drastic decrease in the number of individuals. Since they provide significant economic contributions in the area and constitutes an important food resource for obligate and facultative scavengers, it is very interesting to provide a model in order to facilitate the management of their ecosystems},
	isbn = {78-3-86805-721-8},
	issn = {0302-9743},
	url = {http://springerlink.com/content/y87522j29m145434},
	author = {M. Angels Colomer and Santiago Lav{\'\i}n and Ignasi Marco and Antoni Margalida and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Delf{\'\i} Sanuy and Eduardo Serrano and Luis Valencia-Cabrera}
}
@article {801,
	title = {Comparing simulation algorithms for multienvironment probabilistic P system over a standard virtual ecosystem},
	journal = {Natural Computing},
	volume = {11},
	year = {2011},
	pages = {369-379},
	publisher = {Springer Verlag},
	address = {Amsterdam, Netherlands},
	abstract = {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. },
	keywords = {Ecosystem modelling, Membrane computing, Probabilistic simulation algorithms},
	issn = {1567-7818},
	doi = {10.1007/s11047-011-9289-2},
	url = {http://www.springerlink.com/content/x20788w42x138967/},
	author = {M. Angels Colomer and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {2113,
	title = {A computational modeling for real ecosystems based on P systems},
	journal = {Natural Computing},
	volume = {10},
	year = {2011},
	pages = {39-53},
	doi = {10.1007/s11047-010-9191-3},
	author = {M. Cardona and M.A. Colomer and Margalida, A. and Palau, A. and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and D. Sanuy}
}
@article {743,
	title = {Membrane Computing (Tutorial)},
	journal = {Lecture Notes in Computer Science},
	volume = {6714},
	year = {2011},
	pages = {38-39},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	issn = {0302-9743},
	author = {Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Francisco J. Romero-Campero}
}
@article {719,
	title = {On a partial affirmative answer for a Paun{\textquoteright}s conjecture},
	journal = {International Journal of Foundations of Computer Science},
	volume = {22},
	year = {2011},
	pages = {55-64},
	publisher = {World Scientific},
	address = {London, U.K.},
	issn = {0129-0541},
	author = {Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Miguel A. Guti{\'e}rrez-Naranjo and Miquel Rius-Font}
}
@article {720,
	title = {A simulation algorithm for multienvironment probabilistic P systems: A formal verification},
	journal = {International Journal of Foundations of Computer Science},
	volume = {22},
	year = {2011},
	pages = {107-118},
	publisher = {World Scientific},
	address = {London, U.K.},
	issn = {0129-0541},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Fernando Sancho-Caparrini}
}
@article {610,
	title = {Length of rules and tractability in tissue-like P systems},
	journal = {Algebraic Computing, Soft Computing, and Program Verification},
	year = {2010},
	month = {April 2010},
	address = {Castro Urdiales, Spain},
	url = {http://www.gimac.uma.es/hard\&soft2010/Home.html},
	author = {Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Ignacio P{\'e}rez-Hurtado}
}
@article {611,
	title = {P-Lingua: a programming language for membrane computing},
	journal = {Algebraic Computing, Soft Computing, and Program Verification},
	year = {2010},
	month = {April 2010},
	address = {Castro Urdiales, Spain},
	url = {http://www.gimac.uma.es/hard\&soft2010/Home.html},
	author = {Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Ignacio P{\'e}rez-Hurtado}
}
@article {659,
	title = {An Overview of P System Simulation on GPUs},
	journal = {I Jornadas J{\'o}venes Investigadores},
	year = {2010},
	month = {17 April 2010},
	pages = {2-7},
	address = {C{\'a}ceres, Spain},
	abstract = {P systems are inherently non-deterministic and parallel theoretical computing devices defined inside the research field of Membrane Computing. Many P system simulators have been presented in this area, but they are inefficient since they can not handle the parallelism of these devices. Nowadays,
we are witnessing the consolidation of the GPUs as a parallel framework to compute general purpose applications. In [1], GPUs are presented as an alternative parallel architecture to improve the performance in the simulation of P systems. In this paper, we present the state of the art in the simulation of P systems with active membranes, showing the simulator developed so far, and providing some aspects to consider in order to improve the performance.
},
	isbn = {978-84-693-1707-5},
	url = {http://www.jovenesinvestigadores.com/},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Jos{\'e} M. Cecilia and Gin{\'e}s D. Guerrero and Ignacio P{\'e}rez-Hurtado}
}
@article {696,
	title = {A new simulation algorithm for multienvironment probabilistic P systems},
	journal = {IEEE Fifth International Conference on Bio-inpired Computing: Theories and Applications (BIC-TA 2010)},
	volume = {1},
	year = {2010},
	month = {09/2010},
	pages = {59-68},
	publisher = {IEEE Press.},
	address = {Changsha, China},
	abstract = {Multienvironment P systems are the base of a
general framework for modeling ecosystems dynamics. On one
hand, this modeling framework represents the structural and
dynamical aspects of real ecosystems in a discrete, modular and
compressive way. On the other hand, the inherent randomness
and uncertainty of biological systems are captured by using
probabilistic strategies. Nowadays, the simulation of these P
systems based models is fundamental for experimentation and
validation. In this paper, we introduce a new simulation algorithm,
called DNDP, which performs object distribution and
maximal consistency in the application of rules, that are crucial
aspects of these systems.
The paper also depicts a parallel implementation of the
algorithm, and a comparison with the existing algorithm in
PLinguaCore is provided. In order to test the performance of the
presented algorithm, several experiments (simulations) have been
carried out over four simple P systems with the same skeleton
and different number of environments.},
	isbn = {978-1-4244-6439-5},
	url = {http://www.cs.us.es/~marper/investigacion/dndp.pdf},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and M. Angels Colomer},
	editor = {K. Li and Z. Tang and R. Li and Atulya Nagar and R. Thamburaj}
}
@article {698,
	title = {Simulating Tritrophic Interactions by Means of P Systems},
	journal = {IEEE Fifth International Conference on Bio-inpired Computing: Theories and Applications (BIC-TA 2010)},
	volume = {2},
	year = {2010},
	month = {09/2010},
	pages = {637-643},
	publisher = {IEEE Press.},
	address = {Liverpool, UK},
	abstract = {P systems provide a high level computational modelling
framework that combines the structural and dynamical
aspects of ecosystems in a compressive and relevant way. The
inherent randomness and uncertainty in biological systems is
captured by using probabilistic strategies. The design of efficient
simulation algorithms in order to reproduce the behavior of these
computational models over conventional computers is fundamental
for the validation and virtual experimentation processes.
In this paper, we describe the modelling framework and two
different simulation algorithms. As a case study, a P system
based model of an ideal ecosystem with three trophic levels is
designed and simulated by both simulation algorithms, providing
comparisons of efficiency between them.},
	isbn = {978-1-4244-6438-8},
	url = {http://www.cs.us.es/~marper/investigacion/tritrophic.pdf},
	author = {M. Angels Colomer and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez},
	editor = {Atulya Nagar and R. Thamburaj and K. Li and Z. Tang and R. Li}
}
@article {697,
	title = {A uniform framework for modeling based on P Systems},
	journal = {IEEE Fifth International Conference on Bio-inpired Computing: Theories and Applications (BIC-TA 2010)},
	volume = {1},
	year = {2010},
	month = {09/2010},
	pages = {616-621},
	publisher = {IEEE Press.},
	address = {Changsha, China},
	abstract = {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.},
	isbn = {978-1-4244-6439-5},
	url = {http://www.cs.us.es/~marper/investigacion/marco-bicta-2010.pdf},
	author = {M. Angels Colomer and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez},
	editor = {K. Li and Z. Tang and R. Li and Atulya Nagar and R. Thamburaj}
}
@article {695,
	title = {Modeling population growth of Pyrenean Chamois (Rupicapra p. pyrenayca) by using P systems},
	journal = {Eleventh International Conference on Membrane Computing (CMC11)},
	year = {2010},
	month = {08/2010},
	pages = {121-135},
	publisher = {Verlag ProBusiness Berlin},
	address = {Jena, Germany},
	abstract = {P systems provide a high level computational modeling framework
which integrates the structural and dynamic aspects of ecosystems
in a comprehensive and relevant way. In previous work [1, 2], there have
been presented several ecosystems modeled by P systems. The good results
obtained suggest studying new ecosystems as the one presented in
this paper. Pyrenean Chamois is a species inhabiting the Catalan Pyrenees.
In recent years it has been hit by diseases that cause a drastic
decrease in the number of individuals. Its presence leads to signicant
economic contributions in the area, so it is very interesting to provide a
model in order to facilitate the management.},
	isbn = {978-3-86805-721-8},
	url = {http://cmc11.uni-jena.de/proceedings/colomer.pdf},
	author = {M. Angels Colomer and Santiago Lav{\'\i}n and Ignasi Marco and Antoni Margalida and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Delf{\'\i} Sanuy and Emmanuel Serrano and Luis Valencia-Cabrera},
	editor = {Marian Gheorghe and Thomas Hinze and Gheorghe Paun}
}
@article {614,
	title = {A P-Lingua based simulator for Tissue Psystems},
	journal = {Journal of Logic and Algebraic Programming},
	volume = {79},
	year = {2010},
	note = {Membrane computing and programming },
	month = {08/2010},
	pages = {374-382},
	publisher = {Elsevier B.V.},
	address = {North Holland},
	abstract = {Investigations within the field of tissue-like P systems are being conducted, on one hand studying their computational efficiency, and on the other hand exploring the possibilities to use them as a computational modelling framework to biological phenomena.

In both cases it is necessary to develop software that provides simulation tools (simulators) for the existing variety of tissue P systems. Such simulators allow us to carry on computations of solutions to computationally hard problems on certain (small) instances. Moreover, they also provide a way to verify tissue-like models for real biological processes, by means of experimental data.},
	keywords = {Membrane computing, P{\textendash}Lingua, Simulators, Tissue P Systems},
	issn = {1567-8326},
	doi = {dx.doi.org/10.1016/j.jlap.2010.03.009},
	url = { http://dx.doi.org/10.1016/j.jlap.2010.03.009},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {615,
	title = {Simulating a P system based efficient solution to SAT by using GPUs },
	journal = {Journal of Logic and Algebraic Programming},
	volume = {79},
	year = {2010},
	note = {Membrane computing and programming },
	month = {08/2010},
	pages = {317-325},
	publisher = {Elsevier B.V.},
	address = {North Holland},
	abstract = {P systems are inherently parallel and non-deterministic theoretical computing devices defined inside the field of Membrane Computing. Many P system simulators have been presented in this area, but they are inefficient since they cannot handle the parallelism of these devices. Nowadays, we are witnessing the consolidation of the GPUs as a parallel framework to compute general purpose applications. In this paper, we analyse GPUs as an alternative parallel architecture to improve the performance in the simulation of P systems, and we illustrate it by using the case study of a family of P systems that provides an efficient and uniform solution to the SAT problem. Firstly, we develop a simulator that fully simulates the computation of the P system, demonstrating that GPUs are well suited to simulate them. Then, we adapt this simulator to the GPU architecture idiosyncrasies, improving the performance of the previous simulator.},
	keywords = {GPUs, Membrane computing, P systems, SAT},
	issn = {1567-8326},
	doi = {dx.doi.org/10.1016/j.jlap.2010.03.008},
	url = {http://dx.doi.org/10.1016/j.jlap.2010.03.008},
	author = {Jos{\'e} M. Cecilia and Jos{\'e} M. Garc{\'\i}a and Gin{\'e}s D. Guerrero and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {516,
	title = {Simulation of P systems with active membranes on CUDA},
	journal = {Briefings in Bioinformatics},
	volume = {11},
	year = {2010},
	note = {Parallel and Ubiquitous methods and tools in Systems Biology
Impact Factor of 9.283},
	month = {03/2010},
	pages = {313-322},
	publisher = {Oxford University Press},
	abstract = {P systems or Membrane Systems provide a high-level computational modelling framework that combines the structure and dynamic aspects of biological systems in a relevant and understandable way. They are inherently parallel and non-deterministic computing devices. In this article, we discuss the motivation, design principles and key of the implementation of a simulator for the class of recognizer P systems with active membranes running on a (GPU). We compare our parallel simulator for GPUs to the simulator developed for a single central processing unit (CPU), showing that GPUs are better suited than CPUs to simulate P systems due to their highly parallel nature.},
	keywords = {CUDA, GPU, Membrane computing, Natural computing, P systems, parallel computing},
	issn = {1477-4054},
	doi = {10.1093/bib/bbp064},
	url = {http://bib.oxfordjournals.org/cgi/content/abstract/bbp064v1},
	author = {Jos{\'e} M. Cecilia and Jos{\'e} M. Garc{\'\i}a and Gin{\'e}s D. Guerrero and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {511,
	title = {Implementing P systems parallelism by means of GPUs},
	journal = {Lecture Notes in Computer Science},
	volume = {5957},
	year = {2010},
	note = {Membrane Computing, 10th International Workshop, WMC 2009, Curtea de Arges, Romania, August 24-27, 2009, Revised Selected and Invited Papers},
	month = {01/2010},
	pages = {227-241},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	abstract = {Software development for Membrane Computing is growing up yielding new applications. Nowadays, the efficiency of P systems simulators have become a critical point when working with instances of large size. The newest generation of GPUs (Graphics Processing Units) provide a massively parallel framework to compute general purpose computations. We present GPUs as an alternative to obtain better performance in the simulation of P systems and we illustrate it by giving a solution to the N-Queens problem as an example. },
	issn = {0302-9743},
	doi = {10.1007/978-3-642-11467-0_17},
	url = {http://springerlink.com/content/p711691h1p64x7u3/?p=700938793a854ec885f89e0657ea06f4\&pi=16},
	author = {Jos{\'e} M. Cecilia and Jos{\'e} M. Garc{\'\i}a and Gin{\'e}s D. Guerrero and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {510,
	title = {An overview of P-Lingua 2.0},
	journal = {Lecture Notes in Computer Science},
	volume = {5957},
	year = {2010},
	note = {Membrane Computing, 10th International Workshop, WMC 2009, Curtea de Arges, Romania, August 24-27, 2009, Revised Selected and Invited Papers.},
	month = {01/2010},
	pages = {264-288},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	abstract = {P{\textendash}Lingua is a programming language for membrane computing which aims to be a standard to define P systems. In order to implement this idea, a Java library called pLinguaCore has been developed as a software framework for cell{\textendash}like P systems. It is able to handle input files (either in XML or in P{\textendash}Lingua format) defining P systems from a number of different cell{\textendash}like P system models. Moreover, the library includes several built{\textendash}in simulators for each supported model. For the sake of software portability, pLinguaCore can export a P system definition to any convenient output format (currently XML and binary formats are available). This software is not a closed product, but it can be extended to accept new input or output formats and also new models or simulators.
The term P{\textendash}Lingua 2.0 refers to the software package consisting of the above mentioned library together with a user interface called pLinguaPlugin (more details can be found at http://www.p-lingua.org).
Finally, in order to illustrate the software, this paper includes an application using pLinguaCore for describing and simulating ecosystems by means of P systems.
},
	issn = {0302-9743},
	doi = {10.1007/978-3-642-11467-0_20},
	url = {http://springerlink.com/content/9019651332615113/?p=4515b9a3d094496995e253d08e41004d\&pi=19},
	author = {Manuel Garc{\'\i}a-Quismondo and Rosa Guti{\'e}rrez-Escudero and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {512,
	title = {A P system based model of an ecosystem of some scavenger birds},
	journal = {Lecture Notes in Computer Science},
	volume = {5957},
	year = {2010},
	note = {Membrane Computing, 10th International Workshop, WMC 2009, Curtea de Arges, Romania, August 24-27, 2009, Revised Selected and Invited Papers.},
	month = {01/2010},
	pages = {182-195},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	abstract = {In [1], we presented a P system in order to study the evolution of the bearded vulture in the Pyrenees (NE Spain). Here, we present a new model that overcomes some limitations of the previous work incorporating other scavenger species and additional prey species that provide food for the scavenger intraguild and interact with the Bearded Vulture in the ecosystem. After the validation, the new model can be a useful tool for the study of the evolution and management of the ecosystem. P systems provide a high level computational modelling framework which integrates the structural and dynamical aspects of ecosystems in a compressive and relevant way. The inherent randomness and uncertainty in ecosystems is captured by using probabilistic strategies.},
	issn = {0302-9743},
	doi = {10.1007/978-3-642-11467-0_14},
	url = {http://springerlink.com/content/ek1778t6081r040k/?p=4515b9a3d094496995e253d08e41004d\&pi=13},
	author = {M{\'o}nica Cardona and M. Angels Colomer and Antoni Margalida and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Delf{\'\i} Sanuy}
}
@proceedings {645,
	title = {Proceedings of the Eighth Brainstorming Week on Membrane Computing},
	journal = {Eighth Brainstorming Week on Membrane Computing},
	year = {2010},
	month = {01/02/2010},
	pages = {XI+342},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Spain},
	isbn = {978-84-614-2357-6},
	url = {http://www.gcn.us.es/?q=proc8bwmc},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Gheorghe Paun and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {655,
	title = {A computational modeling for real ecosystems based on P systems},
	journal = {Natural Computing},
	volume = {10},
	year = {2010},
	pages = {39-53},
	publisher = {Springer Verlag},
	address = {Amsterdam, Netherlands},
	abstract = {In this paper, a P systems based general framework for modeling ecosystems dynamics is presented. Particularly, ecosystems are specified by means of multienvironment P systems composed of a finite number of environments, each of them having an extended P system with active membranes. The semantics is of a probabilistic type and it is implemented by assigning each rule of the system a probabilistic constant which depends on the environment and the run time. As a case study, two real ecosystems are described: scavenger birds in the Catalan Pyrenees and the zebra mussel (Dreissena Polymorpha) in Ribarroja reservoir (Spain). },
	keywords = {Dynamics, Ecosystem, Mussel, P-System, Probabilistic, Scavenger},
	issn = {1567-7818},
	doi = {10.1007/s11047-010-9191-3},
	url = {http://www.springerlink.com/content/k5346u33465h5u50/},
	author = {M{\'o}nica Cardona and M. Angels Colomer and Antoni Margalida and Antoni Palau and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Delf{\'\i} Sanuy}
}
@article {694,
	title = {MeCoSim: A general purpose software tool for simulating biological phenomena by means of P Systems},
	journal = {IEEE Fifth International Conference on Bio-inpired Computing: Theories and Applications (BIC-TA 2010)},
	volume = {I},
	year = {2010},
	pages = {637-643},
	publisher = {IEEE, Inc.},
	address = {Changsha, China},
	abstract = {In recent years, the increasing importance of the
computational systems biology is leading to an impressive growth
of the knowledge of several real-life phenomena. In this framework,
membrane computing is an emergent branch within natural
computing that has been succesfully used to model biological
phenomena. The study of these phenomena usually requires the
execution of virtual experiments using mechanisms of simulation,
implying the development of ad-hoc tools to simulate. However,
the advance of the research is demanding general solutions
to avoid the necessity of custom software developments for
each matter of study, when there are some common problems
to resolve. MeCoSim (Membrane Computing Simulator) is a
first step in this direction providing the users a customizable
application to generate custom simulators based on membrane
computing by simply writing a configuration file.},
	isbn = {978-1-4244-6439-5},
	url = {http://www.cs.us.es/~marper/investigacion/mecosim.pdf},
	author = {Ignacio P{\'e}rez-Hurtado and Luis Valencia-Cabrera and Mario J. P{\'e}rez-Jim{\'e}nez and M. Angels Colomer and Agust{\'\i}n Riscos-N{\'u}{\~n}ez},
	editor = {K. Li and Z. Tang and R. Li and Atulya Nagar and R. Thamburaj}
}
@article {523,
	title = {Software for P systems},
	journal = {The Oxford Handbook of Membrane Computing},
	year = {2010},
	pages = {437-454},
	publisher = {Oxford University Press},
	chapter = {17},
	address = {Oxford (U.K.)},
	isbn = {9780199556670},
	url = {http://www.us.oup.com/us/catalog/general/subject/Mathematics/ComputerScience/?view=usa\&sf=toc\&ci=9780199556670},
	author = {Daniel D{\'\i}az-Pernil and Carmen Graciani-D{\'\i}az and Miguel A. Guti{\'e}rrez-Naranjo and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez},
	editor = {Gheorghe Paun and Grzegorz Rozenberg and Arto Salomaa}
}
@article {501,
	title = {Analysis of P systems simulation on CUDA},
	journal = {XX Jornadas de Paralelismo},
	year = {2009},
	note = {Webpage of the conference: http://jornadas2009.gac.des.udc.es/},
	month = {September 2009},
	pages = {289-294},
	publisher = {Servizo de Publicaci{\'o}ns, Universidade da Coru{\~n}a},
	address = {A coru{\~n}a, Spain},
	abstract = {GPUs (Graphics Processing Unit) have been con- 
solidated as a massively data-parallel coprocessor to
develop many general purpose computations, and en-
able developers to utilize several levels of parallelism
to obtain better performance of their applications.
The massively parallel nature of certain computa-
tions leads to use GPUs as an underlying architec-
ture, becoming a good alternative to other paral-
lel approaches. P systems or membrane systems
are theoretical devices inspired in the way that liv- 
ing cells work, providing computational models and
a high level computational modeling framework for
biological systems. They are massively parallel dis-
tributed, and non-deterministic systems. In this pa-
per, we evaluate the GPU as the underlying archi-
tecture to simulate the class of recognizer P systems
with active membranes. We analyze the performance
of three simulators implemented on CPU, CPU-GPU 
and GPU respectively. We compare them using a pre-
sented P system as a benchmark, showing that the
GPU is better suited than the CPU to simulate those
P systems due to its massively parallel nature.},
	isbn = {84-9749-346-8},
	url = {http://www.p-lingua.org/~miguel/papers/2009/psystem_jornadas09.pdf},
	author = {Gin{\'e}s D. Guerrero and Jos{\'e} M. Cecilia and Jos{\'e} M. Garc{\'\i}a and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {502,
	title = {Simulation of P Systems with active membranes on CUDA},
	journal = {2009 International Workshop on High Performance Computational Systems Biology},
	year = {2009},
	note = {Webpage of the conference: http://www.cosbi.eu/hibi09/ },
	month = {October 2009},
	pages = {61-71},
	publisher = {IEEE Computer Society},
	address = {Trento, Italy},
	abstract = {P systems or membrane systems provide a high
level computational modeling framework that combines the
structural and dynamic aspects of biological systems in a
relevant and understandable way. P systems are massively
parallel distributed, and non-deterministic systems. In this
paper, we describe the implementation of a simulator for the
class of recognizer P systems with active membranes by using
the GPU (Graphics Processing Unit). We compare the high-
performance parallel simulator for the GPU to the simulator
developed on a single CPU (Central Processing Unit), and we
show that the GPU is better suited than the CPU to simulate
P systems due to its highly parallel nature.
},
	isbn = {978-0-7695-3809-9},
	doi = {10.1109/HiBi.2009.13},
	url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=\&arnumber=5298701\&isnumber=5298664},
	author = {Jos{\'e} M. Cecilia and Gin{\'e}s D. Guerrero and Jos{\'e} M. Garc{\'\i}a and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {500,
	title = {A massively parallel framework using P systems and GPUs},
	journal = {Symposium on Application Accelerators in High Performance Computing},
	year = {2009},
	note = {Poster also available: http://www.p-lingua.org/~miguel/papers/2009/psystem_poster_saahpc09.pdf
Webpage of the conference: http://saahpc.ncsa.illinois.edu/09/agenda.html},
	month = {July 2009},
	address = {Illinois, USA},
	abstract = {Since CUDA programing model appeared on the 
general purpose computations, the developers can extract all 
the power contained in GPUs (Graphics Processing Unit) across        
many computational domains. Among these domains, P systems                                                                     
or membrane systems provide a high level computational mod-                                                                   
eling framework that allows, in theory, to obtain polynomial                                                                    
time solutions to NP-complete problems by trading time for
space, and also to model biological phenomena in the area of         
computational systems biology. P systems are massively parallel     
distributed devices and their computation can be divided in two                                                                  
levels of parallelism: membranes, that can be expressed as blocks                                                                   
in CUDA programming model; and objects, that can be expressed                                                                  
as threads in CUDA programming model. In this paper, we
present our initial ideas of developing a simulator for the class of
recognizer P systems with active membranes by using the CUDA      
programing model to exploit the massively parallel nature of                                                                     
those systems at maximum. Experimental results of a preliminary                                                              
version of our simulator on a Tesla C1060 GPU show a 60X of                                                               
speed-up compared to the sequential code.                                                                     },
	url = {http://www.p-lingua.org/~miguel/papers/2009/psystem_saahpc09.pdf},
	author = {Jos{\'e} M. Cecilia and Gin{\'e}s D. Guerrero and Jos{\'e} M. Garc{\'\i}a and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {475,
	title = {A P system based model of an ecosystem of some scavenger birds},
	journal = {10th Workshop on Membrane Computing},
	year = {2009},
	month = {24-27/8/2009},
	pages = {153-168},
	publisher = {Marpapublicidad},
	abstract = {The Bearded Vulture (Gypaetus Barbatus) is an endangered species in Eu-
rope that feeds almost exclusively on bone remains provided by wild and domestic ungu-
lates. In [1], we presented a P system in order to study the evolution of these species in
the Pyrenees (NE Spain). Here, we present a new model that overcomes some limitations
of the previous work incorporating other scavenger species (predatory) and additional
prey species that provide food for the scavenger intraguild and interact with the Bearded
Vulture in the ecosystem. After the validation, the new model can be a useful tool for
the study of the evolution and management of the ecosystem. P systems provide a high
level computational modelling framework which integrates the structural and dynamical
aspects of ecosystems in a compressive and relevant way. The inherent randomness and
uncertainty in ecosystems is captured by using probabilistic strategies.
},
	url = {http://www.gcn.us.es/?q=procwmc10},
	author = {M{\'o}nica Cardona and M. Angels Colomer and Antoni Margalida and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Delf{\'\i} Sanuy},
	editor = {Gheorghe Paun and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {477,
	title = {A first attempt to model notch signalling by means of P systems},
	journal = {10th Workshop on Membrane Computing},
	year = {2009},
	month = {24-27/08/2009},
	pages = {265-268},
	publisher = {Marpapublicidad},
	address = {Curtea de Arges, Rumania},
	abstract = {During mammalian central nervous system development, an enormous variety
of cell types are generated. This cell diversity is due in part to asymmetrical cell
division. Indeed, in some sense Notch signals link the fate decisions of one cell to those
of its neighbours. This fundamental signalling pathway has not yet been modeled within
membrane computing framework.},
	url = {http://www.gcn.us.es/files/265notch.pdf},
	author = {Manuel Garc{\'\i}a-Quismondo and Beverley M. Henley and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez},
	editor = {Gheorghe Paun and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {476,
	title = {An overview of P-lingua 2.0},
	journal = {10th Workshop on Membrane Computing},
	year = {2009},
	month = {24-27/08/2009},
	pages = {240-264},
	publisher = {Marpapublicidad},
	abstract = {P-Lingua is a programming language for membrane computing which aims
to be a standard to dene P systems. In order to implement this idea, a Java library
called pLinguaCore has been developed as a software framework for cell-like P systems.
It is able to handle input les (either in XML or in P-Lingua format) dening P systems
from a number of dierent cell{like P system models. Moreover, the library includes
several built-in simulators for each supported model. For the sake of software portability,
pLinguaCore can export a P system denition to any convenient output format (currently
XML and binary formats are available). This software is not a closed product, but it can
be extended to accept new input or output formats and also new models or simulators.
The term P-Lingua 2.0 refers to the software package consisting of the above mentioned
library together with a user interface called pLinguaPlugin (more details can be
found at http://www.p-lingua.org).
Finally, in order to illustrate the software, this paper includes an application using
pLinguaCore for describing and simulating ecosystems by means of P systems.},
	url = {http://www.gcn.us.es/?q=procwmc10},
	author = {Manuel Garc{\'\i}a-Quismondo and Rosa Guti{\'e}rrez-Escudero and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {480,
	title = {Simulating active membrane systems using GPUs},
	journal = {10th Workshop on Membrane Computing},
	year = {2009},
	month = {24-27/08/2009},
	pages = {369-384},
	publisher = {Marpapublicidad},
	address = {Curtea de Arges, Rumania},
	abstract = {Software development for cellular computing is growing up yielding new applications.
In this paper, we describe a simulator for the class of recognizer P systems
with active membranes, which exploits the massively parallel nature of P systems computations
by using GPUs (Graphics Processing Units). The newest generation of GPUs
provide a massively parallel framework to compute general purpose computations. We
present GPUs as an alternative to obtain better performance in the simulation of P
systems and we illustrate it by giving a solution to the N-Queens problem as an example.},
	url = {http://www.gcn.us.es/?q=procwmc10},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Jos{\'e} M. Cecilia and Gin{\'e}s D. Guerrero and Jos{\'e} M. Garc{\'\i}a},
	editor = {Gheorghe Paun and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {452,
	title = {P-Lingua 2.0: A software framework for cell-like P systems},
	journal = {International Journal of Computers, Communications and Control},
	volume = {IV},
	year = {2009},
	month = {09/2009},
	pages = {234-243},
	publisher = {Agora University Editing House - CCC Publications},
	address = {Oradea, Romania},
	abstract = {P-Lingua is a programming language for membrane computing. It was first presented in Edinburgh, during the Ninth Workshop on Membrane Computing (WMC9). In this paper, the models, simulators and formats included in P-Lingua in version 2.0 are explained. We focus on the stochastic model, associatedsimulators and updated features. Finally, we present one of the first applications based on P-Lingua: a tool for describing and simulating ecosystems.
},
	keywords = {Membrane computing, P systems, P-Lingua, Programming languages, software development},
	issn = {1841-9836},
	url = {http://www.journal.univagora.ro/?page=article_details\&id=368},
	author = {Manuel Garc{\'\i}a-Quismondo and Rosa Guti{\'e}rrez-Escudero and Miguel A. Mart{\'\i}nez-del-Amor and Enrique F. Orejuela-Pinedo and Ignacio P{\'e}rez-Hurtado}
}
@article {457,
	title = {P system based model of an ecosystem of the scavenger birds },
	journal = {7th Brainstorming Week on Membrane Computing},
	volume = {I},
	year = {2009},
	month = {02/02/2009},
	pages = {65-80},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	abstract = {The Bearded Vulture (Gypaetus Barbatus) is an endangered species in Eu-
rope that feeds almost exclusively on bone remains provided by wild and domestic ungu-
lates. In [1], we presented a P system in order to study the evolution of these species in
the Pyrenees (NE Spain). Here, we present a new model that overcomes some limitations
of the previous work incorporating other scavenger species (predatory) and additional
prey species that provide food for the scavenger intraguild and interact with the Bearded
Vulture in the ecosystem. After the validation, the new model can be a useful tool for
the study of the evolution and management of the ecosystem. P systems provide a high
level computational modelling framework which integrates the structural and dynamical
aspects of ecosystems in a compressive and relevant way. The inherent stochasticity and
uncertainty in ecosystems is captured by using probabilistic strategies.
},
	isbn = {978-84-613-2837-6},
	url = {http://www.gcn.us.es/?q=node/414},
	author = {M{\'o}nica Cardona and M. Angels Colomer and Antoni Margalida and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Delf{\'\i} Sanuy}
}
@article {460,
	title = {P-Lingua 2.0: New features and first applications},
	journal = {7th Brainstorming Week on Membrane Computing},
	volume = {I},
	year = {2009},
	month = {02/02/2009},
	pages = {141-168},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	abstract = {P-Lingua is a programming language for membrane computing. It was first
presented in Edinburgh, during the Ninth Workshop on Membrane Computing (WMC9).
In this paper, the models, simulators and formats included in P-Lingua in version 2.0 are
explained. We focus on the stochastic model, associated simulators and updated features.
Finally, we present two new applications based on P-Lingua 2.0: a tool for describing and
simulating ecosystems and a framework (currently under development) for P systems
design.
},
	isbn = {978-84-613-2837-6},
	url = {http://www.gcn.us.es/7BWMC/volume/18_plingua_2_0.pdf},
	author = {Manuel Garc{\'\i}a-Quismondo and Rosa Guti{\'e}rrez-Escudero and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@proceedings {453,
	title = {Seventh Brainstorming Week on Membrane Computing. Volumen I},
	journal = {7th Brainstorming Week on Membrane Computing},
	volume = {I},
	year = {2009},
	note = {Rosa Guti{\'e}rrez-Escudero; Miguel {\'A}ngel Guti{\'e}rrez-Naranjo; Gheorghe Paun; Ignacio P{\'e}rez-Hurtado; Agust{\'\i}n Riscos-N{\'u}{\~n}ez (eds)},
	month = {02/02/2009},
	pages = {X+248},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	isbn = {978-84-613-2837-6},
	url = {http://www.gcn.us.es/?q=node/414},
	author = {Rosa Guti{\'e}rrez-Escudero and Miguel A. Guti{\'e}rrez-Naranjo and Gheorghe Paun and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@proceedings {454,
	title = {Seventh Brainstorming Week on Membrane Computing. Volumen II},
	journal = {7th Brainstorming Week on Membrane Computing},
	volume = {II},
	year = {2009},
	note = {Miguel {\'A}ngel Mart{\'\i}nez-del-Amor; Enrique Francisco Orejuela-Pinedo; Gheorghe Paun; Ignacio P{\'e}rez-Hurtado; Agust{\'\i}n Riscos-N{\'u}{\~n}ez (eds.)},
	month = {02/02/2009},
	pages = {X+254},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	isbn = {978-84-613-2839-0},
	url = {http://www.gcn.us.es/?q=node/414},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Enrique F. Orejuela-Pinedo and Gheorghe Paun and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {456,
	title = {Simulation of recognizer P systems by using manycore GPUs },
	journal = {7th Brainstorming Week on Membrane Computing},
	volume = {II},
	year = {2009},
	month = {02/02/2009},
	pages = {45-58},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	abstract = {Software development for cellular computing is growing up yielding new
applications. In this paper, we describe a simulator for the class of recognizer P systems
with active membranes, which exploits the massively parallel nature of the P systems
computations by using a massively parallel computer architecture, such as Compute
Unified Device Architecture (CUDA) from Nvidia, to obtain better performance in the
simulations. We illustrate it by giving a solution to the N-Queens problem as an example.
},
	isbn = {978-84-613-2839-0},
	url = {http://www.gcn.us.es/?q=node/414},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Jos{\'e} M. Cecilia and Gin{\'e}s D. Guerrero and Jos{\'e} M. Garc{\'\i}a}
}
@article {455,
	title = {Solving the N-Queens puzzle with P systems },
	journal = {7th Brainstorming Week on Membrane Computing},
	volume = {I},
	year = {2009},
	month = {02/02/2009},
	pages = {199-210},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	abstract = {The N -queens puzzle consists on placing N queens on an N {\texttimes} N grid in such
way that no two queens are on the same row, column or diagonal line. In this paper we
present a family of P systems with active membranes (one P system for each value of N )
that provides all the possible solutions to the puzzle.
},
	isbn = {978-84-613-2837-6},
	url = {http://www.gcn.us.es/?q=node/414},
	author = {Miguel A. Guti{\'e}rrez-Naranjo and Miguel A. Mart{\'\i}nez-del-Amor and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {447,
	title = {A P-lingua programming environment for Membrane Computing},
	journal = {Lecture Notes in Computer Science},
	volume = {5391},
	year = {2009},
	month = {01/2009},
	pages = {187-203},
	publisher = {Springer Berlin / Heidelberg},
	abstract = {A new programming language for membrane computing, P-Lingua, is developed in this paper. This language is not designed for a specific simulator software. On the contrary, its purpose is to offer a general syntactic framework that could define a unified standard for membrane computing, covering a broad variety of models. At the present stage, P-Lingua can only handle P systems with active membranes, although the authors intend to extend it to other models in the near future.
P-Lingua allows to write programs in a friendly way, as its syntax is very close to standard scientific notation, and parameterized expressions can be used as shorthand for sets of rules. There is a built-in compiler that parses these human-style programs and generates XML documents that can be given as input to simulation tools, while different plugins can be designed to produce specific adequate outputs for existing simulators.
Furthermore, we present in this paper an integrated development environment that plays the role of an interface where P-Lingua programs can be written and compiled. We also present a simulator for the class of recognizer P systems with active membranes, and we illustrate it by following the writing, compiling and simulating processes with a family of P systems solving the SAT problem.},
	isbn = {978-3-540-95884-0},
	doi = {10.1007/978-3-540-95885-7_14},
	url = {http://www.springerlink.com/content/74177526wg3p7j1j/},
	author = {Daniel D{\'\i}az-Pernil and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {347,
	title = {A P-lingua programming environment for Membrane Computing},
	journal = {9th Workshop on Membrane Computing},
	year = {2008},
	month = {July 28-31, 2008},
	pages = {187-203},
	address = {Edinburgh, The U.K.},
	author = {Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Daniel D{\'\i}az-Pernil and Mario J. P{\'e}rez-Jim{\'e}nez and Ignacio P{\'e}rez-Hurtado}
}
@article {368,
	title = {Graphics and P systems: Experiments with JPLANT},
	journal = {Proceedings of the Sixth Brainstorming Week on Membrane Computing},
	year = {2008},
	pages = {241-254},
	publisher = {F{\'e}nix Editora},
	url = {http://www.gcn.us.es/6BWMC/volume/jplant.pdf},
	author = {Elena Rivero-Gil and Miguel A. Guti{\'e}rrez-Naranjo and Mario J. P{\'e}rez-Jim{\'e}nez},
	editor = {Daniel D{\'\i}az-Pernil and Carmen Graciani-D{\'\i}az and Miguel A. Guti{\'e}rrez-Naranjo and Gheorghe Paun and Ignacio P{\'e}rez-Hurtado and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@article {434,
	title = {P-Lingua: A programming language for membrane computing },
	journal = {6th Brainstorming Week on Membrane Computing},
	volume = {6},
	year = {2008},
	pages = {135-155},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Spain},
	abstract = {Software development for cellular computing has already been addressed,
yielding a first generation of applications. In this paper, we develop a new programming
language: P-Lingua. Furthermore, we present a simulator for the class of recognizing P
systems with active membranes. We illustrate it by giving a solution to the SAT problem
as an example.},
	isbn = {978-84-612-44 },
	url = {http://www.gcn.us.es/6BWMC/volume/plingua.pdf},
	author = {Daniel D{\'\i}az-Pernil and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez and Agust{\'\i}n Riscos-N{\'u}{\~n}ez}
}
@proceedings {436,
	title = {Sixth brainstorming week on membrane computing},
	journal = {6th Brainstorming Week on Membrane Computing},
	year = {2008},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Spain},
	isbn = {978-84-612-44 },
	url = {http://www.gcn.us.es/6BWMC/6BWMC_proceedings.htm},
	author = {Miguel A. Guti{\'e}rrez-Naranjo and Daniel D{\'\i}az-Pernil and Carmen Graciani-D{\'\i}az and Gheorghe Paun and Ignacio P{\'e}rez-Hurtado and Mario J. P{\'e}rez-Jim{\'e}nez}
}
