An interactive timeline of simulators in membrane computing

As with any fast-emerging research front in computer science, the proliferation of theoretical and practical results within Membrane computing since its appearance in 1998 was astonishing. As a consequence, it became necessary during the subsequent years to produce several surveys collecting the main achievements from a theoretical point of view, along with some specific surveys about simulation tools for this paradigm. As the discipline has reached a certain degree of maturity, more practical applications have arisen, and new collective works are summarising the new software products appeared. However, while these recapitulation efforts remain useful for details about new simulators, they cannot act as exhaustive updated listings, as they become obsolete as soon as new tools are developed. Thus, we considered that it was necessary to provide an interactive tool showing an updated timeline (https://www.gcn.us.es/SimulationMC) about the simulation of the computational devices of membrane computing (a.k.a P systems), aiming to stay updated whenever any new practical work comes out in the discipline. This paper recalls the main stages and milestones within the evolution of simulation tools for different types and variants of P systems, along with their main related applications. In addition, it describes the interactive web tool with the timeline mentioned, where all the references related here have been incorporated. Unlike other survey papers, it is the intent of this work to reinforce this initial collective effort with the web endpoint kept alive and updated.

[1]  Michael Levin,et al.  Modeling regenerative processes with membrane computing , 2017, Inf. Sci..

[2]  Linqiang Pan,et al.  Modeling Logic Gene Networks by Means of Probabilistic Dynamic P Systems , 2013, Int. J. Unconv. Comput..

[3]  Mario J. Pérez-Jiménez,et al.  The Growth of Branching Structures with P Systems , 2006 .

[4]  Mario de Jesús Pérez Jiménez,et al.  A CLIPS Simulator for Recognizer P Systems with Active Membranes , 2004 .

[5]  Mario J. Pérez-Jiménez,et al.  Simulating P Systems on GPU Devices: A Survey , 2015, Fundam. Informaticae.

[6]  Antoni Margalida,et al.  Application of a computational model for complex fluvial ecosystems: The population dynamics of zebra mussel Dreissena polymorpha as a case study , 2014 .

[7]  Apostolos Syropoulos,et al.  A Distributed Simulation of Transition P Systems , 2003, Workshop on Membrane Computing.

[8]  Gheorghe Paun,et al.  Membrane Computing , 2002, Natural Computing Series.

[9]  Giancarlo Mauri,et al.  Analysis and Simulation of Dynamics in Probabilistic P Systems , 2005, DNA.

[10]  José M. García,et al.  Simulating a P system based efficient solution to SAT by using GPUs , 2010, J. Log. Algebraic Methods Program..

[11]  Xiyu Liu,et al.  A Cluster Splitting Technique by Hopfield Networks and P Systems on Simplices , 2017, Neural Processing Letters.

[12]  Florent Jacquemard,et al.  An Analysis of a Public Key Protocol with Membranes , 2005 .

[13]  Mario J. Pérez-Jiménez,et al.  Graphics and P Systems: Experiments with JPLANT , 2008 .

[14]  Mario J. Pérez-Jiménez,et al.  A Model of the Quorum Sensing System in Vibrio fischeri Using P Systems , 2008, Artificial Life.

[15]  Miguel A. Gutiérrez-Naranjo,et al.  A software tool for generating graphics by means of P systems , 2011, Natural Computing.

[16]  Giancarlo Mauri,et al.  Investigating local evolutions in dynamical probabilistic P systems , 2005, Seventh International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC'05).

[17]  Gabriel Ciobanu,et al.  P System Software Simulator , 2002, Fundam. Informaticae.

[18]  Mario J. Pérez-Jiménez,et al.  A uniform family of tissue P systems with cell division solving 3-COL in a linear time , 2008, Theor. Comput. Sci..

[19]  Sean Sedwards,et al.  Modelling Cellular Processes Using Membrane Systems with Peripheral and Integral Proteins , 2006, CMSB.

[20]  Mario J. Pérez-Jiménez,et al.  A fast P system for finding a balanced 2-partition , 2005, Soft Comput..

[21]  Fernando Arroyo,et al.  Structures and Bio-language to Simulate Transition P Systems on Digital Computers , 2000, WMP.

[22]  Mario J. Pérez-Jiménez,et al.  A P-Lingua Programming Environment for Membrane Computing , 2008, Workshop on Membrane Computing.

[23]  Mario J. Pérez-Jiménez,et al.  Probabilistic Guarded P Systems, A New Formal Modelling Framework , 2014, Int. Conf. on Membrane Computing.

[24]  Andrei George Florea,et al.  Synchronized dispersion of robotic swarms using XP colonies , 2016 .

[25]  Ioan Dumitrache,et al.  Robot Localization Implemented with Enzymatic Numerical P Systems , 2012, Living Machines.

[26]  Alfonso Rodríguez-Patón,et al.  Tissue P systems , 2003, Theor. Comput. Sci..

[27]  Fernando Arroyo,et al.  Towards an Electronic Implementation of Membrane Computing: A Formal Description of Non-deterministic Evolution in Transition P Systems , 2001, DNA.

[28]  Linqiang Pan,et al.  A P_Lingua Based Simulator for P Systems with Symport/Antiport Rules , 2015, Fundam. Informaticae.

[29]  Mario J. Pérez-Jiménez,et al.  A MzScheme Implementation of Transition P Systems , 2002, WMC-CdeA.

[30]  Mario J. Pérez-Jiménez,et al.  A software tool for verification of Spiking Neural P Systems , 2008, Natural Computing.

[31]  Marian Gheorghe,et al.  3-Col problem modelling using simple kernel P systems , 2013, Int. J. Comput. Math..

[32]  Christof Teuscher,et al.  A Reconfigurable Hardware Membrane System , 2003, Workshop on Membrane Computing.

[33]  Mario J. Pérez-Jiménez,et al.  An Efficient Family of P Systems for Packing Items into Bins , 2004, J. Univers. Comput. Sci..

[34]  Mario J. Pérez-Jiménez,et al.  A bio-inspired computing model as a new tool for modeling ecosystems: The avian scavengers as a case study , 2011 .

[35]  Jun Li,et al.  Decoder Design Based on Spiking Neural P Systems , 2016, IEEE Transactions on NanoBioscience.

[36]  Oscar H. Ibarra,et al.  Simulating FAS-induced apoptosis by using P systems , 2007 .

[37]  Andrei George Florea,et al.  A distributed approach to the control of multi-robot systems using XP colonies , 2017, Integr. Comput. Aided Eng..

[38]  Mario J. Pérez-Jiménez,et al.  A Prolog simulator for deterministic P systems with active membranes , 2009, New Generation Computing.

[39]  Natalio Krasnogor,et al.  The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology , 2011, Bioinform..

[40]  Henry N. Adorna,et al.  An Improved GPU Simulator for Spiking Neural P Systems , 2011, 2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications.

[41]  Artiom Alhazov.  Maximally Parallel multiset-rewriting systems: Browsing the Configurations , 2005 .

[42]  Vincenzo Manca,et al.  P Systems for Biological Dynamics , 2006, Applications of Membrane Computing.

[43]  Francesc Solsona,et al.  PSysCal: a parallel tool for calibration of ecosystem models , 2013, Cluster Computing.

[44]  Andrei George Florea,et al.  Membrane Computing for Distributed Control of Robotic Swarms: Emerging Research and Opportunities , 2017 .

[45]  Rudolf Freund,et al.  Implementation of Catalytic P Systems , 2004, CIAA.

[46]  Sean Sedwards,et al.  Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes , 2007, Bioinform..

[47]  A. Moya,et al.  A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES) , 2015, Biology Direct.

[48]  Matteo Cavaliere.  Evolution-Communication P Systems , 2002, WMC-CdeA.

[49]  Luca Bianco,et al.  Psim: A Computational Platform for Metabolic P Systems , 2007, Workshop on Membrane Computing.

[50]  Ravie Chandren Muniyandi,et al.  Implementing Mitogen Activated Protein Kinases Cascade on Membrane Computing Using P-Lingua , 2015, J. Comput. Sci..

[51]  Hiroshi Tanaka,et al.  Artificial Life Applications of a Class of P Systems: Abstract Rewriting Systems on Multisets , 2000, WMP.

[52]  Nepomuceno Chamorro,et al.  A Java Simulator for Basic Transition P Systems , 2004 .

[53]  Pierluigi Frisco,et al.  Conformons-P Systems , 2002, DNA.

[54]  Pierluigi Frisco,et al.  A simulator and an evolution program for conformon-P systems , 2005, Seventh International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC'05).

[55]  Giancarlo Mauri,et al.  Dynamical probabilistic P systems , 2006, Int. J. Found. Comput. Sci..

[56]  Henry N. Adorna,et al.  Simulating Spiking Neural P Systems Without Delays Using GPUs , 2011, Int. J. Nat. Comput. Res..

[57]  Vincenzo Manca,et al.  Psim: a simulator for biomolecular dynamics based on P systems , 2007, 2007 IEEE Congress on Evolutionary Computation.

[58]  Gabriel Ciobanu,et al.  P Systems Running on a Cluster of Computers , 2003, Workshop on Membrane Computing.

[59]  Mario J. Pérez-Jiménez,et al.  Attacking the Common Algorithmic Problem by Recognizer P Systems , 2004, MCU.

[60]  Artiom Alhazov,et al.  Communicative P Systems with Minimal Cooperation , 2004, Workshop on Membrane Computing.

[61]  Mario J. Pérez-Jiménez,et al.  Modelling gene expression control using P systems: The Lac Operon, a case study , 2008, Biosyst..

[62]  Giancarlo Mauri,et al.  Stochastic Approaches in P Systems for Simulating Biological Systems , 2006 .

[63]  Catalin Buiu,et al.  A software tool for modeling and simulation of numerical P systems , 2011, Biosyst..

[64]  Mario J. Pérez-Jiménez,et al.  A P-Lingua Based Simulator for Spiking Neural P Systems , 2011, Int. Conf. on Membrane Computing.

[65]  Marian Gheorghe,et al.  Membrane-Based Devices Used in Computer Graphics , 2006, Applications of Membrane Computing.

[66]  Mario J. Pérez-Jiménez,et al.  Implementing in Prolog an Effective Cellular Solution to the Knapsack Problem , 2003, Workshop on Membrane Computing.

[67]  Francisco José Romero Campero,et al.  A Tool for Using the SBML Format to Represent P Systems which Model Biological Reaction Networks , 2005 .

[68]  Mario J. Pérez-Jiménez,et al.  A Study of the Robustness of the EGFR Signalling Cascade Using Continuous Membrane Systems , 2005, IWINAC.

[69]  Mario de Jesús Pérez Jiménez,et al.  Attacking the common algorithmic problem by recognizer p systems , 2004 .

[70]  Gheorghe Paun,et al.  Computing with Membranes , 2000, J. Comput. Syst. Sci..

[71]  Theodore Andronikos,et al.  Membrane automata for modeling biomolecular processes , 2017, Natural Computing.

[72]  Mario J. Pérez-Jiménez,et al.  A Formalization of Transition P Systems , 2002, Fundam. Informaticae.

[73]  Mario de Jesús Pérez Jiménez,et al.  Tissue Simulator: A Graphical Tool for Tissue P Systems , 2007 .

[74]  Abdullah Mohd Zin,et al.  Improved Implementation of Simulation for Membrane Computing on the Graphic Processing Unit , 2013 .

[75]  Florentin Ipate,et al.  Towards an Integrated Approach for Model Simulation, Property Extraction and Veri cation of P Systems , 2012 .

[76]  Mario J. Pérez-Jiménez,et al.  MeCoSim: A general purpose software tool for simulating biological phenomena by means of P systems , 2010, 2010 IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA).

[77]  Mario J. Pérez-Jiménez,et al.  Graphical Modeling of Higher Plants Using P Systems , 2006, Workshop on Membrane Computing.

[78]  Mario J. Pérez-Jiménez,et al.  An Overview of P-Lingua 2.0 , 2009, Workshop on Membrane Computing.

[79]  Ravie Chandren Muniyandi,et al.  Accelerated Simulation of Membrane Computing to Solve the N-queens Problem on Multi-core , 2013, SEMCCO.

[80]  Mario J. Pérez-Jiménez,et al.  Parallel simulation of Population Dynamics P systems: updates and roadmap , 2016, Natural Computing.

[81]  Mario J. Pérez-Jiménez,et al.  Accelerated Simulation of P Systems on the GPU: A Survey , 2014, BIC-TA.

[82]  K. Chandrasekaran,et al.  Tools and Simulators for Membrane Computing-A Literature Review , 2016, BIC-TA.

[83]  Giovanni Acampora,et al.  A proposal of multi-agent simulation system for membrane computing devices , 2007, 2007 IEEE Congress on Evolutionary Computation.

[84]  Mario J. Pérez-Jiménez,et al.  Available Membrane Computing Software , 2006, Applications of Membrane Computing.

[85]  Pierluigi Frisco,et al.  The conformon-P system: a molecular and cell biology-inspired computability model , 2004, Theor. Comput. Sci..

[86]  Henry N. Adorna,et al.  A GPU Simulation for Evolution-Communication P Systems with Energy Having no Antiport Rules , 2013 .

[87]  Mario J. Pérez-Jiménez,et al.  Implementing Enzymatic Numerical P Systems for AI Applications by Means of Graphic Processing Units , 2013 .

[88]  Giancarlo Mauri,et al.  Tau Leaping Stochastic Simulation Method in P Systems , 2006, Workshop on Membrane Computing.

[89]  Mario J. Pérez-Jiménez,et al.  Evolutionary response of a native butterfly to concurrent plant invasions: Simulation of population dynamics , 2017 .

[90]  Mario J. Pérez-Jiménez,et al.  On Descriptive Complexity of P Systems , 2004, Workshop on Membrane Computing.

[91]  U. Tappeiner,et al.  Using a new PDP modelling approach for land-use and land-cover change predictions: A case study in the Stubai Valley (Central Alps) , 2016 .

[92]  Gheorghe Paun.  P Systems with Active Membranes: Attacking NP-Complete Problems , 2001, J. Autom. Lang. Comb..

[93]  Andrei George Florea,et al.  Development of a Software Simulator for P colonies - Applications in Robotics , 2016, Int. J. Unconv. Comput..

[94]  Linqiang Pan,et al.  The Computational Complexity of Tissue P Systems with Evolutional Symport/Antiport Rules , 2018, Complex..

[95]  Andrei George Florea,et al.  Lulu - a software simulator for P colonies. Use case scenarios and demonstration videos , 2015 .

[96]  Mario J. Pérez-Jiménez,et al.  Cellular Solutions to Some Numerical NP-Complete Problems: A Prolog Implementation , 2005 .

[97]  Anne C. Elster,et al.  Parallel Simulation of Probabilistic P Systems on Multicore Platforms , 2012 .

[98]  Feng Qi,et al.  Optimization Spiking Neural P System for Solving TSP , 2017, MLICOM.

[99]  David W. Corne,et al.  Dynamics of HIV infection studied with cellular automata and conformon-P systems , 2008, Biosyst..

[100]  Ioan I. Ardelean,et al.  Modeling Respiration in Bacteria and Respiration/Photosynthesis Interaction in Cyanobacteria Using a P System Simulator , 2006, Applications of Membrane Computing.

[101]  Marian Gheorghe,et al.  Modular Assembly of Cell Systems Biology Models Using P Systems , 2009, Int. J. Found. Comput. Sci..

[102]  Mario J. Pérez-Jiménez,et al.  Robot path planning using rapidly-exploring random trees: A membrane computing approach , 2018, 2018 7th International Conference on Computers Communications and Control (ICCCC).

[103]  Mario J. Pérez-Jiménez,et al.  Data Modeling with Membrane Systems: Applications to Real Ecosystems , 2017 .

[104]  Mario J. Pérez-Jiménez,et al.  A P-Lingua based simulator for tissue P systems , 2010, J. Log. Algebraic Methods Program..

[105]  Taishin Y. Nishida.  Membrane Algorithms , 2005, Workshop on Membrane Computing.

[106]  Luis F. Macías-Ramos,et al.  Agent-Based Simulation of Kernel P Systems with Division Rules Using FLAME , 2016, Int. Conf. on Membrane Computing.

[107]  José M. García,et al.  Simulation of P Systems with Active Membranes on CUDA , 2010, 2009 International Workshop on High Performance Computational Systems Biology.

[108]  Oscar H. Ibarra,et al.  On spiking neural P systems , 2006, Natural Computing.

[109]  Henry N. Adorna,et al.  A Spiking Neural P System Simulator Based on CUDA , 2011, Int. Conf. on Membrane Computing.

[110]  Ioan I. Ardelean,et al.  Modelling biological processes by using a probabilistic P system software , 2004, Natural Computing.

[111]  Dan V. Nicolau,et al.  A C Library for Simulating P Systems , 2002, Fundam. Informaticae.

[112]  Gheorghe Paun,et al.  The Oxford Handbook of Membrane Computing , 2010 .

[113]  Taishin Yasunobu Nishida,et al.  Membrane Algorithms: Approximate Algorithms for NP-Complete Optimization Problems , 2006, Applications of Membrane Computing.

[114]  Mario J. Pérez-Jiménez,et al.  Population Dynamics P System (PDP) Models: A Standardized Protocol for Describing and Applying Novel Bio-Inspired Computing Tools , 2013, PloS one.

[115]  Andrei George Florea,et al.  Modelling multi-robot interactions using a generic controller based on numerical P systems and ROS , 2017, 2017 9th International Conference on Electronics, Computers and Artificial Intelligence (ECAI).