A Process Calculus for Spatially-explicit Ecological Models

We propose PALPS, a Process Algebra with Locations for Population Systems. PALPS allows us to produce spatially-explicit, individual-based models and to reason about their behavior. Our calculus has two levels: at the first level we may define the behavior of an individual of a population while, at the second level, we may specify a system as the collection of individuals of various species located in space, moving through their life cycle while changing their location, if they so wish, and interacting with each other in various ways such as preying on each other. Furthermore, we propose a probabilistic temporal logic for reasoning about the behavior of PALPS processes. We illustrate our framework via models of dispersal in metapopulations.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347

Ecological Modelling with the Calculus of Wrapped Compartments

The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions. In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems evolution. As a case study, we model the distribution of height of Croton wagneri, a shrub constituting the endemic predominant species of the dry ecosystem in southern Ecuador. In particular, we consider the plant at different altitude gradients (i.e. at different temperature conditions), to study how it adapts under the effects of global climate change.Comment: A preliminary version of this paper has been presented in CMC13 (LNCS 7762, pp 358-377, 2013

Membrane Computing (Tutorial)

The aim of the tutorial is to give a general overview of the Membrane Computing paradigm [2,5]. Membrane Computing is a quite active research field, initiated by Gh. Păun in 1998 [3]. It is a theoretical machine-oriented model, where the computational devices (known as P systems) are in some sense an abstraction of a living cell. There exist a large number of different definitions of P systems, but most of them share some common features: a membrane structure (defining in a natural way a number of regions or compartments), and an alphabet of objects that are able to evolve and/or move within the membrane structure according to a set of rules (emulating the way substances undergo biochemical reactions in a cell).Ministerio de Ciencia e Innovación TIN2008-04487-EMinisterio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420

A uniform framework for modeling based on P Systems

In this paper, a P systems based general framework for modeling the dynamics of a population biology is presented. Multienvironment probabilistic functional P systems with active membranes provide the syntactical specification, and the semantics is captured by using stochastic or probabilistic strategies implemented through simulation algorithms.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08–TIC-0420

Cellular modelling using P systems and process algebra.

In this paper various molecular chemical interactions are modelled under different computational paradigms. P systems and -calculus are used to describe intra-cellular reactions like protein-protein interactions and gene regulation control

Membrane Computing as a Modeling Framework. Cellular Systems Case Studies

Membrane computing is a branch of natural computing aiming to abstract computing models from the structure and functioning of the living cell, and from the way cells cooperate in tissues, organs, or other populations of cells. This research area developed very fast, both at the theoretical level and in what concerns the applications. After a very short description of the domain, we mention here the main areas where membrane computing was used as a framework for devising models (biology and bio-medicine, linguistics, economics, computer science, etc.), then we discuss in a certain detail the possibility of using membrane computing as a high level computational modeling framework for addressing structural and dynamical aspects of cellular systems. We close with a comprehensive bibliography of membrane computing applications

Towards Probabilistic Model Checking on P Systems Using PRISM

This paper presents the use of P systems and π-calculus to model interacting molecular entities and how they are translated into a probabilistic and symbolic model checker called PRISM.Ministerio de Educación y Ciencia TIN2005-09345-C04-01Junta de Andalucía TIC-58

Parallel Graph Rewriting Systems

In this paper we introduce a new theoretical paradigm, called PGR systems, which can be used to model in a discrete manner some natural phenomena occurring in-vivo/in-vitro en- vironments. PGR systems make use of graphs to describe the spatial structure of space of individuals, while the system dynamics caused by the movement/interaction of individuals is captured by the parallel applications of some graph rewriting rules. In this frame, an il- lustrative example is studied and based on it, an eloquent comparison between the abstract rewriting machines and PGR systems is done. Several further ideas to overcome the global computational effort needed for simulations, but still maintaining the overall ability for mod- eling are finally proposed

An Overview of P-Lingua 2.0

P–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–like P systems. It is able to handle input files (either in XML or in P–Lingua format) defining P systems from a number of different 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 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–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.Ministerio de Educación y Ciencia TIN2006-13425Junta de Andalucía TIC04200

MeCoSim: A general purpose software tool for simulating biological phenomena by means of P Systems

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.Ministerio de Educación y Ciencia TIN2009–13192Junta de Andalucía P08–TIC-0420