No / Kernel P systems integrate in a coherent and elegant manner many of the features of different P system variants, successfully used for modelling various applications. In this paper, we present our initial attempt to extend the software framework developed to support kernel P systems: a formal verification tool based on the NuSMV model checker and a large scale simulation environment based on FLAME. The use of these two tools for modelling and analysis of biological systems is illustrated with a synthetic biology example.

yes / This Workshop on Membrane Computing, at the Conference of Unconventional Computation and Natural Computation (UCNC), 12th July 2016, Manchester, UK, is the second event of this type after the Workshop at UCNC 2015 in Auckland, New Zealand*. Following the tradition of the 2015 Workshop the Proceedings are published as technical report. The Workshop consisted of one invited talk and six contributed presentations (three full papers and three extended abstracts) covering a broad spectrum of topics in Membrane Computing, from computational and complexity theory to formal verification, simulation and applications in robotics. All these papers – see below, but the last extended abstract, are included in this volume. The invited talk given by Rudolf Freund, “P SystemsWorking in Set Modes”, presented a general overview on basic topics in the theory of Membrane Computing as well as new developments and future research directions in this area. Radu Nicolescu in “Distributed and Parallel Dynamic Programming Algorithms Modelled on cP Systems” presented an interesting dynamic programming algorithm in a distributed and parallel setting based on P systems enriched with adequate data structure and programming concepts representation. Omar Belingheri, Antonio E. Porreca and Claudio Zandron showed in “P Systems with Hybrid Sets” that P systems with negative multiplicities of objects are less powerful than Turing machines. Artiom Alhazov, Rudolf Freund and Sergiu Ivanov presented in “Extended Spiking Neural P Systems with States” new results regading the newly introduced topic of spiking neural P systems where states are considered. “Selection Criteria for Statistical Model Checker”, by Mehmet E. Bakir and Mike Stannett, presented some early experiments in selecting adequate statistical model checkers for biological systems modelled with P systems. In “Towards Agent-Based Simulation of Kernel P Systems using FLAME and FLAME GPU”, Raluca Lefticaru, Luis F. Macías-Ramos, Ionuţ M. Niculescu, Laurenţiu Mierlă presented some of the advatages of implementing kernel P systems simulations in FLAME. Andrei G. Florea and Cătălin Buiu, in “An Efficient Implementation and Integration of a P Colony Simulator for Swarm Robotics Applications" presented an interesting and efficient implementation based on P colonies for swarms of Kilobot robots. *http://ucnc15.wordpress.fos.auckland.ac.nz/workshop-on-membrane-computingwmc- at-the-conference-on-unconventional-computation-natural-computation/

no / This chapter gives an overview of an integrated software suite, the Infobiotics Workbench, which is based on a novel spatial discrete-stochastic P systems modelling framework. The Workbench incorporates three important features, simu- lation, model checking and optimisation. Its capability for building, analysing and optimising large spatially discrete and stochastic models of multicellular systems makes it a useful, coherent and comprehensive in silico tool in systems and synthetic biology research. / EPSRC / The full text is unavailable due to publisher copyright restrictions on book chapters.

No / The paper presents the use of a membrane computing model for specifying a synthetic biology pulse generator example and discusses some simulation results produced by the tools associated with this model and compare their performances. The results show the potential of the simulation approach over the other analysis tools like model checkers.

Yes / Computational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations). These models incorporate a set of methods for specifying, modeling, testing, and simulating biological systems. In addition, they can be analyzed using algorithmic techniques (e.g., formal verification). This paper shows how formal verification is utilized in systems and synthetic biology through qualitative vs quantitative analysis. Here, we choose two well-known case studies: quorum sensing in P. aeruginosas and pulse generator. The paper reports verification analysis of two systems carried out using some model checking tools, integrated to the Infobiotics Workbench platform, where system models are based on stochastic P systems. / EPSRC

Yes / In this paper we consider four restricted cases of the generalised communicating P systems and study their computational power, by providing improved results, with respect to the number of compartments involved. We illustrate the expressive power of these devices by modelling several problems, such as producer/consumer, work ow patterns, broadcasting problem and comparative operations. We also present some relationships between generalised communicating P systems and P colonies, tissue-like P systems with very simple components. / MG and FI were supported by a grant of the Romanian National Authority for Scientific Research, CNCS-UEFISCDI, project number PN-II-ID-PCE-2011-3-0688, CSVE by grant No. 120558 of the National Research, Development, and Innovation Office, Hungary.

No / A membrane-inspired evolutionary algorithm (MIEA) is a successful instance of a model linking membrane computing and evolutionary algorithms. This paper proposes the analysis of dynamic behaviors of MIEAs by introducing a set of population diversity and convergence measures. This is the first attempt to obtain additional insights into the search capabilities of MIEAs. The analysis is performed on the MIEA, QEPS (a quantum-inspired evolutionary algorithm based on membrane computing), and its counterpart algorithm, QIEA (a quantum-inspired evolutionary algorithm), using a comparative approach in an experimental context to better understand their characteristics and performances. Also the relationship between these measures and fitness is analyzed by presenting a tendency correlation coefficient to evaluate the importance of various population and convergence measures, which is beneficial to further improvements of MIEAs. Results show that QEPS can achieve better balance between convergence and diversity than QIEA, which indicates QEPS has a stronger capacity of balancing exploration and exploitation than QIEA in order to prevent premature convergence that might occur. Experiments utilizing knapsack problems support the above made statement.

No / Evolutionary membrane computing is an important research direction of membrane computing that aims to explore the complex interactions between membrane computing and evolutionary computation. These disciplines are receiving increasing attention. In this paper, an overview of the evolutionary membrane computing state-of-the-art and new results on two established topics in well defined scopes (membrane-inspired evolutionary algorithms and automated design of membrane computing models) are presented. We survey their theoretical developments and applications, sketch the differences between them, and compare the advantages and limitations. (C) 2014 Elsevier Inc. All rights reserved.