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MetaPlab: A Computational Framework for Metabolic P Systems [chapter]

Alberto Castellini, Vincenzo Manca
2009 Lecture Notes in Computer Science  
In this work the formalism of Metabolic P systems has been employed as a basis of a new computational plugin-based framework for modeling biological networks.  ...  This software architecture supports MP systems dynamics in a virtual laboratory, called MetaPlab.  ...  Metabolic P systems, namely MP systems, are a class of P systems proved to be significant and successful for modeling biological phenomena related to metabolism (matter transformation, assimilation and  ... 
doi:10.1007/978-3-540-95885-7_12 fatcat:umiujwrk6ffdni6cjdgejd2rmi

Goldbeter's Mitotic Oscillator Entirely Modeled by MP Systems [chapter]

Vincenzo Manca, Luca Marchetti
2010 Lecture Notes in Computer Science  
MP systems are a class of P systems introduced for modeling metabolic processes. Here we apply an algorithm, we call Log-Gain Stoichiometric Stepwise Regression (LGSS), to Golbeter's oscillator.  ...  By means of a suitable MATLAB implementation of LGSS, we automatically generated 700 MP models (τ varying from 10 −3 min to 700 · 10 −3 min with increments of 10 −3 min).  ...  , or P metabolic systems, represent metabolic processes in a discrete mathematical framework.  ... 
doi:10.1007/978-3-642-18123-8_22 fatcat:llqsvgihujaijfhhehjrnosew4

Metabolic P System Flux Regulation by Artificial Neural Networks [chapter]

Alberto Castellini, Vincenzo Manca, Yasuhiro Suzuki
2010 Lecture Notes in Computer Science  
Metabolic P systems are an extension of P systems employed for modeling biochemical systems in a discrete and deterministic perspective.  ...  This methodology, based on backpropagation with weight elimination for neural network training and on an heuristic algorithm for computing tuning indexes, has achieved encouraging results in a synthetic  ...  In particular, metabolic P systems, or MP systems, suggest a deterministic strategy, based on the generalization of chemical laws, for computing the amount of objects moved by rules at each computational  ... 
doi:10.1007/978-3-642-11467-0_15 fatcat:375hu25pifcwhi5umldwlk6hxa

Metabolic approximation of real periodical functions

Vincenzo Manca, Luca Marchetti
2010 The Journal of Logic and Algebraic Programming  
MP systems are a class of P systems introduced for modeling metabolic processes. Here approximation of real functions is approached by using MP systems.  ...  An example is presented which provides a good approximation of sine and cosine functions based on a surprisingly simple MP system.  ...  MP systems Metabolic P systems or P metabolic systems (shortly MP systems) represent metabolic processes in a discrete mathematical framework.  ... 
doi:10.1016/j.jlap.2010.03.005 fatcat:snmfpezoczflfktgsmtpdup7bu

Regulation and Covering Problems in MP Systems [chapter]

Giuditta Franco, Vincenzo Manca, Roberto Pagliarini
2010 Lecture Notes in Computer Science  
In this paper we report some partial results and related open problems regarding the efficient computation of regulation fluxes in metabolic P systems.  ...  By means of Log-gain theory the system dynamics can be linearized, in such a way to be described by a recurrence equations system, of which we point out a few algebraic properties, involving covering problems  ...  their own evolution, is new of metabolic P systems.  ... 
doi:10.1007/978-3-642-11467-0_18 fatcat:dym53g7m55bbjbysildiwtiblq

From P to MP Systems [chapter]

Vincenzo Manca
2010 Lecture Notes in Computer Science  
Metabolic P systems (MP systems) represent metabolic processes in a discrete mathematical framework based on P systems.  ...  MP systems are presented, with a special emphasis to their roots and to their relationship with P systems, which provided the right conceptual framework for their development.  ...  As it will results evident from the next section, the letter P of MP systems comes from the theoretical framework of P systems introduced by Pȃun, in the context of membrane computing [39] .  ... 
doi:10.1007/978-3-642-11467-0_7 fatcat:bjch5plzp5fkxgtfq6emuuv23y

A P-Simulator with Carriers of Cellular Respiration and Mitochondrial Oxidative Metabolism

Lamia Hassaan Ahmed, Amr Ahmed Badr, Ibrahim Farag Abd El-Rahaman
2011 Journal of clean energy technologies  
The results of the system meet the values of cellular metabolism and correctly vary according to the inputs. Index Terms-Natural Computing, P Simulator, P Systems, P Systems with carriers.  ...  The functions done by the cell and its mitochondrion to produce energy can be simulated by computer programs. One approach is a membrane system which is also called P system.  ...  It is a deterministic P system developed to model dynamics of biological phenomena related to metabolism. It added a new plugin based framework for processing metabolic P systems.  ... 
doi:10.7763/ijcte.2011.v3.348 fatcat:tupeqqyzvjdffdd2sghhbhlnou

Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology [chapter]

Jonathan Blakes, Jamie Twycross, Savas Konur, Francisco Jose Romero-Campero, Natalio Krasnogor, Marian Gheorghe
2013 Emergence, Complexity and Computation  
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.  ...  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  ...  Some of the most well-studied P systems with relevance for modelling biological systems are presented below. • Deterministic and non-deterministic P systems consisting of a broad range of models: -Metabolic  ... 
doi:10.1007/978-3-319-03191-0_1 fatcat:vz4edynpzbglxiyg23evljxeqi

A Review of Membrane Computing Models for Complex Ecosystems and a Case Study on a Complex Giant Panda System

Yingying Duan, Haina Rong, Dunwu Qi, Luis Valencia-Cabrera, Gexiang Zhang, Mario J. Pérez-Jiménez
2020 Complexity  
Then, a discussion follows on the use of P systems for ecosystem modelling.  ...  In this paper, a comprehensive survey of membrane computing models for ecosystems is given, taking a giant panda ecosystem as an example to assess the model performance.  ...  It is a computational framework for metabolic P systems. is framework consists of the following four layers: (i) MP graph, which takes MP systems as inputs and visualizes them; (ii) MP store data structure  ... 
doi:10.1155/2020/1312824 fatcat:uvkxmicof5cqhkt74az6n6hcki

Deterministic and stochastic P systems for modelling cellular processes

Marian Gheorghe, Vincenzo Manca, Francisco J. Romero-Campero
2009 Natural Computing  
This paper presents two approaches based on metabolic and stochastic P systems, together with their associated analysis methods, for modelling biological systems and illustrates their use through two case  ...  with the aim of producing a coherent, robust and efficient computational mechanism, called P system, that mimics the behaviour of some cellular processes [26].  ...  The authors would like to thank the anonymous referees for their valuable comments. FJRC would like to acknowledge EPSRC grant EP/E017215/1 and BBSRC grants BB/F01855X/1 and BB/D019613/1.  ... 
doi:10.1007/s11047-009-9158-4 fatcat:n3f3i4rbj5azvkoemy37oiafja

An interactive timeline of simulators in membrane computing

Luis Valencia-Cabrera, David Orellana-Martín, Miguel Ángel Martínez-del-Amor, Mario J. Pérez-Jiménez
2019 Journal of Membrane Computing  
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.  ...  A good example of this transition from the previous works was MetaPlab [151] , a computational framework for MP systems, moving several steps forward wit respect to the first simulator [55] based on  ... 
doi:10.1007/s41965-019-00016-z fatcat:qfooqodxefbcbadrr4ealb53my