@article {2455,
	title = {Modeling Diel Vertical Migration with Membrane Computing},
	journal = {Journal of Membrane Computing},
	volume = {3},
	year = {2021},
	month = {03/2021},
	pages = {35-50},
	publisher = {Springer},
	address = {Amsterdam (The Netherlands)},
	abstract = {Climate change is disrupting ecological systems worldwide, including the alteration of animal migration behavior. Diel Vertical Migration (DVM) is an important ecological phenomenon in which zooplankton migrate vertically to deal with tradeoffs associated with greater food availability in shallow waters and lower predator risk in deep waters due to lower light availability. Because of these tradeoffs, DVM dynamics are particularly sensitive to changes in light intensity at the water surface. We propose a new computational model that captures the effect of the annual proportion of cloudy and sunny days on DVM in Daphnia and we use it to explore the impacts of an increased proportion of cloudy days that are predicted to occur with climate change. Our 2-dimensional, spatially explicit model integrates multiple trophic levels, from abiotic nutrients to Daphnia predators. Our model is parameterized based on data from Lake George, NY, USA. We analyzed the effect that different proportions of cloudy and sunny days throughout the summer, as well as different assumptions on predator avoidance dynamics of Daphnia, have on our model. The model simulations suggest that an increase in sunny days promotes a high phytoplankton concentration near the surface but does not necessarily promote an increased abundance of Daphnia. This is because high ultraviolet radiation levels deter Daphnia from migrating to shallow waters, even though phytoplankton biomass is higher, because the risk of predation is greater. Our model suggests that a higher proportion of cloudy days would increase Daphnia abundance due to a shift in the vertical distribution of Daphnia populations towards superficial waters. Our results highlight that climate changes in multiple regions, such as the frequency and duration of precipitation events, will affect animal migrations leading to altered food web dynamics in freshwater ecosystems. },
	keywords = {Daphnia, Diel vertical migration, Limnology, Mathematical modeling, Population Dynamics, simulation},
	issn = {2523-8906},
	doi = {10.1007/s41965-020-00038-y},
	author = {Manuel Garc{\'\i}a-Quismondo and William D. Hintz and Matthew S. Schuler and Rick A. Relyea}
}
@article {2210,
	title = {Membrane Computing as a Modelling Tool: Looking Back and Forward from Sevilla},
	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 = {114-129},
	publisher = {Springer International Publishing},
	doi = {https://doi.org/10.1007/978-3-030-00265-7_10},
	author = {Manuel Garc{\'\i}a-Quismondo and Carmen Graciani and Agust{\'\i}n Riscos-N{\'u}{\~n}ez},
	editor = {Carmen Graciani and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Gheorghe P{\u a}un and Gregorz Rozenberg and Arto Salomaa}
}
@article {2110,
	title = {Modeling Population Dynamics of Roseate Terns (Sterna dougallii) in the Northwest Atlantic Ocean},
	journal = {Ecological Modelling},
	volume = {368},
	year = {2018},
	month = {01/2018},
	pages = {298-311},
	publisher = {Elsevier},
	address = {Amsterdam (The Netherlands)},
	abstract = {The endangered population of roseate terns (Sterna dougallii) in the Northwestern Atlantic Ocean consists of a network of large and small breeding colonies on islands. This type of fragmented population poses an exceptional opportunity to investigate dispersal, a mechanism that is fundamental in population dynamics and is crucial to understand the spatio-temporal and genetic structure of animal populations. Dispersal is difficult to study because it requires concurrent data compilation at multiple sites. Models of population dynamics in birds that focus on dispersal and include a large number of breeding sites are rare in literature. In this work, we propose a stochastic simulation model that captures the dispersal dynamics of this population of roseate terns. The colonization and decolonization (abandonment) of breeding colonies are modeled as discrete events that follow different dynamics than dispersal. We show that our model reproduces the properties of this population that have been observed in field data. We also analyzed the sensitivity of our model to alterations in different variables, and study the impact of these alterations in the model dynamics. Our results suggest that large colony population size exhibits a threshold sensitivity to adult survival, and that regional persistence is maintained by the larger populations.
},
	keywords = {Islands, Metapopulation, Population persistence, Roseate terns, Source-sink},
	issn = {0304-3800},
	doi = {10.1016/j.ecolmodel.2017.12.007},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380017304945},
	author = {Manuel Garc{\'\i}a-Quismondo and Nisbet, Ian C T and Mostello, Carolyn S and J. Michael Reed}
}
@article {2081,
	title = {Evolutionary response of a native butterfly to concurrent plant invasions: simulation of population dynamics},
	journal = {Ecological Modelling},
	volume = {360},
	year = {2017},
	month = {09/2017},
	pages = {410-424},
	publisher = {Elsevier},
	address = {Amsterdam (The Netherlands)},
	abstract = {The habitat of the green-veined white butterfly Pieris oleracea in eastern North America has undergone invasions by the exotic plant garlic mustard (Alliaria petiolata), which is replacing native hosts of P. oleracea such as Cardamine diphylla. A. petiolata was originally lethal to most larvae of the native butterfly but during the past 20+ years it has been incorporated successfully into the larval diet, likely through evolutionary change. The region was also invaded by another exotic plant, Cardamine pratensis, on which the native butterfly larvae readily develops, allowing the possibility
of population rescue. Further complicating the butterfly{\textquoteright}s reproductive dynamics, it is multigenerational within a summer, and host plant availability and location change during the summer. Our goal is to model the expected dynamics of the native butterfly population in this evolving, dynamic landscape by using a new bio-inspired paradigm known as Membrane Computing. In this context, a Probabilistic Guarded Scripted P system has been designed to model and explore the conditions under which an allele conferring ability of P. oleracea larvae to develop on A. petiolata might have proliferated. The design describes a population dynamics model whose parameter values are derived from experimental and observational data. Our modeling framework is spatially explicit and our model integrates seasonal as well as annual dynamics. The simulation results from our model qualitatively match our field observations and experimental laboratory results, and agree with the results from a previous model on the genotypic adaptation of this butterfly species. From the simulations we identified the likely trajectories for the spatio-temporal distribution of alleles enabling P. oleracea to use the invasive plant species across this selective and phenological mosaic.},
	keywords = {Invasive species, Membrane computing, Pieris oleracea, Population Dynamics, Probabilistic Guarded Scripted P system},
	issn = {0304-3800},
	doi = {10.1016/j.ecolmodel.2017.06.030},
	author = {Manuel Garc{\'\i}a-Quismondo and J. Michael Reed and Frances S. Chew and Miguel A. Mart{\'\i}nez-del-Amor and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {1952,
	title = {Modeling regenerative processes with Membrane Computing},
	journal = {Information Sciences},
	volume = {381},
	year = {2017},
	month = {03/2017},
	pages = {229{\textendash}249},
	publisher = {Elsevier},
	address = {Amsterdam (The Netherlands)},
	keywords = {bioinformatics, Membrane computing, modeling, P systems, Planarian, Regeneration},
	issn = {0020-0255},
	doi = {10.1016/j.ins.2016.11.017},
	url = {http://www.sciencedirect.com/science/article/pii/S0020025516318187},
	author = {Manuel Garc{\'\i}a-Quismondo and Michael Levin and Daniel Lobo-Fern{\'a}ndez}
}
@article {1813,
	title = {Simulating P Systems on GPU Devices: A Survey},
	journal = {Fundamenta Informaticae},
	volume = {136},
	year = {2015},
	month = {02/2015},
	pages = {269-284},
	publisher = {IOS Press},
	address = {Warsaw, Poland},
	keywords = {CUDA, GPU Computing, Membrane computing, P systems, parallel computing},
	issn = {0169-2968},
	doi = {10.3233/FI-2015-1157},
	url = {http://iospress.metapress.com/content/101684hh3785365u/},
	author = {Miguel A. Mart{\'\i}nez-del-Amor and Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Luis Valencia-Cabrera and Agust{\'\i}n Riscos-N{\'u}{\~n}ez and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@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 {1782,
	title = {Probabilistic Guarded P Systems, A formal Definition},
	journal = {Twelfth Brainstorming Week on Membrane Computing (BWMC2014)},
	year = {2014},
	pages = {183-206},
	publisher = {F{\'e}nix Editora},
	isbn = {978-84-940056-4-0},
	url = {http://www.gcn.us.es/12bwmc_proceedings},
	author = {Manuel Garc{\'\i}a-Quismondo and Miguel A. Mart{\'\i}nez-del-Amor and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {1789,
	title = {Probabilistic Guarded P systems, a New Formal Modelling Framework},
	journal = {15th Conference on Membrane Computing, pre-proceedings},
	year = {2014},
	pages = {169-190},
	address = {Opava, Czech Republic},
	isbn = {978-80-7510-036-8},
	url = {http://cmc15.slu.cz/wp-content/uploads/2014/01/cmc15_proceedings.pdf},
	author = {Manuel Garc{\'\i}a-Quismondo and Miguel A. Mart{\'\i}nez-del-Amor and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {1894,
	title = {Probabilistic Guarded P Systems, A New Formal Modelling Framework},
	journal = {Lecture Notes in Computer Science},
	volume = {8961},
	year = {2014},
	pages = {194-214},
	publisher = {Springer},
	address = {Amsterdam, The Netherlands},
	abstract = {Multienvironment P systems constitute a general, formal framework for modelling the dynamics of population biology, which consists of two main approaches: stochastic and probabilistic. The framework has been successfully used to model biologic systems at both micro (e.g. bacteria colony) and macro (e.g. real ecosystems) levels, respectively.
In this paper, we extend the general framework in order to include a new case study related to P. Oleracea species. The extension is made by a new variant within the probabilistic approach, called Probabilistic Guarded P systems (in short, PGP systems). We provide a formal definition, a simulation algorithm to capture the dynamics, and a survey of the associated software.},
	issn = {0302-9743},
	url = {http://link.springer.com/chapter/10.1007\%2F978-3-319-14370-5_12},
	author = {Manuel Garc{\'\i}a-Quismondo and Miguel A. Mart{\'\i}nez-del-Amor and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {893,
	title = {3-COL problem modelling using simple Kernel P systems},
	journal = {International Journal of Computer Mathematics},
	volume = {90},
	year = {2013},
	month = {10/2013},
	pages = {816-830},
	publisher = {Taylor and Francis},
	address = {London, UK},
	abstract = {This paper presents the newly introduced class of (simple) kernel P systems ((s)kP systems) and investigates through a 3-colouring problem case study the expressive power and efficiency of kernel P systems. It describes two skPsystems that model the problem and analyzes them in terms of efficiency and complexity. The skP models prove to be more succinct (in terms of number of rules, objects, number of cells and execution steps) than the corresponding tissue P system, availablein the literature, that solves the same problem, at the expense of a greater length of the rules.},
	keywords = {3-colour problem, Formal Verification, kernel P systems, Membrane computing, Tissue P Systems},
	issn = {0020-7160},
	doi = {10.1080/00207160.2012.743712},
	url = {http://dx.doi.org/10.1080/00207160.2012.743712},
	author = {Marian Gheorghe and Florentin Ipate and Raluca Lefticaru and Mario J. P{\'e}rez-Jim{\'e}nez and Adrian Turcanu and Luis Valencia-Cabrera and Manuel Garc{\'\i}a-Quismondo and Laurentiu Mierla}
}
@article {969,
	title = {Modeling Logic Gene Networks by Means of Probabilistic Dynamic P Systems},
	journal = {International Journal of Unconventional Computing},
	volume = {9},
	number = {5-6},
	year = {2013},
	month = {10/2013},
	pages = {445-464},
	publisher = {Old City Publishing Inc.},
	address = {Philadelphia, USA},
	abstract = {Gene regulatory networks are useful models for biologists to understand the interactions among genes in living organisms. In this work, we consider a special class of gene regulatory networks, called logical networks, where the {\textquotedblleft}links{\textquotedblright} among genes are inferred by logic analysis of phylogenetic profiles. We provide a formalization of logic networks, and introduce a membrane computing model for reconstructing logical networks and reproducing their dynamics. An example logical network is simulated by using software P-Lingua and MeCoSim. The simulation result shows that membrane computing is a versatile framework for modeling different biological scenarios.},
	keywords = {gene, genetic network, logic network, Membrane computing, P system, System biology},
	issn = {1548-7199},
	url = {http://www.oldcitypublishing.com/IJUC/IJUCcontents/IJUCv9n5-6contents.html},
	author = {Luis Valencia-Cabrera and Manuel Garc{\'\i}a-Quismondo and Mario J. P{\'e}rez-Jim{\'e}nez and Yansen Su and Hui Yu and Linqiang Pan}
}
@article {898,
	title = {Implementing Enzymatic Numerical P Systems for AI Applications by means of Graphic Processing Units},
	journal = {Beyond Artificial Intelligence: Contemplations, Expectations, Applications},
	year = {2013},
	month = {10/2012},
	pages = {137-157},
	publisher = {Springer Verlag},
	chapter = {14},
	address = {Berlin, Germany},
	isbn = {978-3642344213},
	doi = {http://dx.doi.org/10.1007/978-3-642-34422-0_10},
	url = {http://www.amazon.com/Beyond-Artificial-Intelligence-Contemplations-Expectations/dp/3642344216},
	author = {Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@article {963,
	title = {Analysing Gene Networks with PDP Systems. Arabidopsis thaliana, a Case Study},
	journal = {Eleventh Brainstorming Week on Membrane Computing (11BWMC)},
	year = {2013},
	month = {08/2013},
	pages = {257-272},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	abstract = {Gene Regulatory Networks (GRNs) are a useful tool for biologists to understand
the interactions among genes in living organisms. A special kind of GRNs known
as Logic Networks (LNs) has been recently introduced. These networks consider that
the state of one or more genes can in
uence another one. In a previous work, we proposed
a Membrane Computing model which simulates the dynamics of LNs by drawing
on the improved LAPP algorithm. In this paper we provide a case study for our LN
model on a network which regulates the circadian rhythms of long{term studied plant
Arabidopsis thaliana. We outline the software tools employed and propose a methodology
for analysing LNs on our Membrane Computing model. At the end of the paper, some
conclusions and future work are included.},
	keywords = {bioinformatics, Gene networks, Genetics, LAPP, Logic networks, MeCoSim, Membrane computing, Modelling, Software engineering},
	isbn = {978-84-940691-9-2},
	url = {http://www.gcn.us.es/files/11bwmc/257_valencia_cabrera.pdf},
	author = {Luis Valencia-Cabrera and Manuel Garc{\'\i}a-Quismondo and Mario J. P{\'e}rez-Jim{\'e}nez and Yansen Su and Hui Yu and Linqiang Pan}
}
@article {959,
	title = {Kernel P Systems - Version I},
	journal = {Eleventh Brainstorming Week on Membrane Computing (11BWMC)},
	year = {2013},
	month = {08/2013},
	pages = {97-124},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	abstract = {A basic P system, called kernel P system4 (kP system for short), combining
features of dierent P systems introduced and studied so far is dened and discussed. The
structure of such systems is dened as a dynamic graph, similar to tissue-like P systems,
the objects are organised as multisets, and the rules in each compartment, rewriting and
communication together with system structure changing rules, are applied in accordance
with a specic execution strategy. The denition of kP systems is introduced and some
examples illustrate this concept. Two classes of P systems, namely neural-like and generalised
communicating P systems are simulated by kP systems. Some case studies prove
the expressive power of these systems.},
	isbn = {978-84-940691-9-2},
	url = {http://www.gcn.us.es/files/11bwmc/097_gheorghe_ipate.pdf},
	author = {Marian Gheorghe and Florentin Ipate and Ciprian Dragomir and Laurentiu Mierla and Luis Valencia-Cabrera and Manuel Garc{\'\i}a-Quismondo and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@proceedings {964,
	title = {Proceedings of the Eleventh Brainstorming Week on Membrane Computing (11BWMC)},
	journal = {Eleventh Brainstorming Week on Membrane Computing (11BWMC)},
	year = {2013},
	month = {08/2013},
	pages = {x+272},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	isbn = {978-84-940691-9-2},
	url = {http://www.gcn.us.es/files/11bwmc/contents.pdf},
	author = {Luis Valencia-Cabrera and Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Miguel A. Mart{\'\i}nez-del-Amor and Gheorghe Paun 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}
}
@proceedings {871,
	title = {Proceedings of the Tenth Brainstorming Week on Membrane Computing},
	journal = {Tenth Brainstorming Week on Membrane Computing},
	volume = {II},
	year = {2012},
	month = {30/01/2012},
	pages = {xiv+292},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Espa{\~n}a},
	url = {http://www.gcn.us.es/10BWMC/10BWMCvolII/bravol2012II.pdf},
	author = {Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Gheorghe Paun and Luis Valencia-Cabrera}
}
@article {895,
	title = {Modeling logic gene networks by means of probabilistic dynamic P systems},
	journal = {Asian Conference on Membrane Computing},
	year = {2012},
	month = {10/2012},
	pages = {30-60},
	address = {Wuhan, China},
	author = {Manuel Garc{\'\i}a-Quismondo and Luis Valencia-Cabrera and Yansen Su and Mario J. P{\'e}rez-Jim{\'e}nez and Linqiang Pan and Hui Yu},
	editor = {Linqiang Pan and Gheorghe Paun and Tao Song}
}
@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 {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 {854,
	title = {Simulating large-scale ENPS models by means of GPU},
	journal = {Tenth Brainstorming Week on Membrane Computing},
	volume = {I},
	year = {2012},
	month = {02/2012},
	pages = {137-152},
	publisher = {F{\'e}nix Editora},
	address = {Seville, Spain},
	abstract = {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.},
	keywords = {Enzymatic Numerical P Systems, GPU, simulation},
	url = {http://www.gcn.us.es/10BWMC/10BWMCvolI/papers/Simulating_complex_ENPS_models_by_means_of_GPU_complete.pdf},
	author = {Manuel Garc{\'\i}a-Quismondo and Ana B. Pavel and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@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 {846,
	title = {Implementing ENPS by means of GPUs for AI applications},
	journal = {Interdisciplinary Aspects of Artificial Intelligence},
	year = {2011},
	month = {12/2011},
	pages = {27-33},
	publisher = {University of West Bohemia, Pilsen},
	address = {Pilsen, Czech Republic},
	abstract = {A P system represents a distributed and parallel computing model in which basic data
structures are, for instance, multisets and strings. Enzymatic Numerical P Systems are a type of
P systems whose basic data structures are sets of numerical variables. Separately, GPGPU is a
novel technological paradigm which focuses on the development of tools for graphic cards to solve
general purpose problems. This paper proposes an ENPS simulator based on GPUs and presents
general concepts about its design and some future ideas and perspectives.},
	keywords = {CUDA, ENPS, GPU, Membrane computing, simulation},
	url = {http://beyondai.zcu.cz/files/BAI2011_proceedings.pdf},
	author = {Manuel Garc{\'\i}a-Quismondo and Luis F. Mac{\'\i}as-Ramos and Mario J. P{\'e}rez-Jim{\'e}nez}
}
@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 {682,
	title = {Solving Sudoku with Membrane Computing},
	journal = {2010 IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications BIC-TA},
	volume = {I},
	year = {2010},
	month = {09/2010},
	pages = {610-615 },
	publisher = {IEEE, Inc.},
	address = {Changsha, China},
	isbn = {978-1-4244-6438-8},
	url = {http://www.ieee.org/conferences_events/conferences/conferencedetails/index.html?Conf_ID=16823},
	author = {Daniel D{\'\i}az-Pernil and Carlos M. Fern{\'a}ndez-M{\'a}rquez and Manuel Garc{\'\i}a-Quismondo and Miguel A. Guti{\'e}rrez-Naranjo and Miguel A. Mart{\'\i}nez-del-Amor},
	editor = {K. Li and Z. Tang and R. Li and Atulya Nagar and R. Thamburaj}
}
@article {634,
	title = {A Cellular Sudoku Solver},
	journal = {Eighth Brainstorming  Week on Membrane Computing},
	year = {2010},
	month = {02/2010},
	pages = {77-88},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Spain},
	isbn = {978-84-614-2357-6},
	url = {http://www.gcn.us.es/8BWMC/volume/06sudokuMiguel.pdf},
	attachments = {http://www.gcn.us.es/biblio/files/files/06sudokuMiguel.pdf},
	author = {Daniel D{\'\i}az-Pernil and Carlos M. Fern{\'a}ndez-M{\'a}rquez and Manuel Garc{\'\i}a-Quismondo and Miguel A. Guti{\'e}rrez-Naranjo and Miguel A. Mart{\'\i}nez-del-Amor}
}
@article {638,
	title = {How Does a P System Sound? },
	journal = {Eighth Brainstorming  Week on Membrane Computing},
	year = {2010},
	month = {02/2010},
	pages = {123-132},
	publisher = {F{\'e}nix Editora},
	address = {Sevilla, Spain},
	isbn = {978-84-614-2357-6},
	url = {http://www.gcn.us.es/8BWMC/volume/10music.pdf},
	attachments = {http://www.gcn.us.es/biblio/files/files/10music.pdf},
	author = {Manuel Garc{\'\i}a-Quismondo and Miguel A. Guti{\'e}rrez-Naranjo and Daniel Ram{\'\i}rez-Mart{\'\i}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 {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 {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 {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}
}
