Applications of Membrane Computing in Systems and Synthetic Biology

Part of the Emergence, Complexity and Computation Book Series (volume 7)

Editors: Frisco, Pierluigi; Gheorghe, Marian; Pérez-Jiménez, Mario J.

DOI: 10.1007/978-3-319-03191-0

ISBN: 978-3-319-03190-3

Publisher: Springer International Publishing - Springer Journals

Dec 18, 2013

Available

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

Blakes, Jonathan; Twycross, Jamie; Konur, Savas; Romero-Campero, Francisco Jose; Krasnogor, Natalio; Gheorghe, Marian

Pages: 1 –41

[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, simulation, model checking and optimisation. Its capability for...
Available

Statistical Model Checking of Membrane Systems with Peripheral Proteins: Quantifying the Role of Estrogen in Cellular Mitosis and DNA Damage

Cavaliere, Matteo; Mazza, Tommaso; Sedwards, Sean

Pages: 43 –63

[Systems biology is a natural application of membrane systems, allowing the analysis of biological systems using the formal technique of model checking. To overcome the intractable model size of typical biological systems, statistical model checking may be used to efficiently estimate the...
Available

Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis

Cazzaniga, Paolo; Besozzi, Daniela; Pescini, Dario; Mauri, Giancarlo

Pages: 65 –96

[In this chapter we present an application of membrane systems to the study of intracellular diffusive processes. In particular, a class of membrane systems, called τ\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb}...
Available

Membrane System-Based Models for Specifying Dynamical Population Systems

Colomer-Cugat, M. A.; García-Quismondo, M.; Macías-Ramos, L. F.; Martínez-del-Amor, M. A.; Pérez-Hurtado, I.; Pérez–Jiménez, M. J.; Riscos-Núñez, A.; Valencia-Cabrera, L.

Pages: 97 –132

[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...
Available

Membrane Systems and Tools Combining Dynamical Structures with Reaction Kinetics for Applications in Chronobiology

Hinze, Thomas; Behre, Jörn; Bodenstein, Christian; Escuela, Gabi; Grünert, Gerd; Hofstedt, Petra; Sauer, Peter; Hayat, Sikander; Dittrich, Peter

Pages: 133 –173

[This chapter addresses three coordinated chronobiological studies demonstrating the convergence of experimental observations, fine-grained spatio-temporal modelling, and predictive simulation. Due to the discrete manner of molecular assembly in cell signalling and gene regulation, we define a...
Available

Biochemical Networks Discrete Modeling Inspired by Membrane Systems

Jack, John; Păun, Andrei; Păun, Mihaela

Pages: 175 –221

[The ideas expressed in this work pertain to biochemical modeling. We explore our technique, the Nondeterministic Waiting Time algorithm, for modeling molecular signaling cascades. The algorithm is presented with pseudocode along with an explanation of its implementation. We discuss several...
Available

MP Modelling for Systems Biology: Two Case Studies

Marchetti, Luca; Manca, Vincenzo; Pagliarini, Roberto; Bollig-Fischer, Aliccia

Pages: 223 –245

[Metabolic P systems (MP systems), based on Păun’s P systems, were introduced for modelling metabolic systems by means of suitable multiset rewriting grammars. The initial modelling framework has been widely extended in last years and equipped with a new regression algorithm which derives MP...
Available

Modelling and Analysis of E. coli Respiratory Chain

Ţurcanu, Adrian; Mierlă, Laurenţiu; Ipate, Florentin; Stefanescu, Alin; Bai, Hao; Holcombe, Mike; Coakley, Simon

Pages: 247 –266

[In this chapter we present some results obtained in the study of the bacterium E. coli related to its behavior at different level of oxygen in the environment. The biological model is expressed in terms of different molecules and their reactions. First, an agent-based model of E. coli is...

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