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Applications of Membrane Computing in Systems and Synthetic BiologyMembrane System-Based Models for Specifying Dynamical Population Systems

Applications of Membrane Computing in Systems and Synthetic Biology: Membrane System-Based Models... [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 Algorithm (DCBA), which has been engineered into software simulation tools. In particular, MeCoSim (Membrane Computing Simulator) is a GUI developed in the framework of P-Lingua that can be used as a simulation environment for running virtual experiments. The parameters of each scenario to be simulated can be easily adjusted in a visual way, as well as the settings for the desired output format, thus facilitating the validation of the designed models against real data. The simulation of PDP systems is data intensive for large models. Therefore, the development of efficient simulators for this field is needed. In fact, the computational power of GPUs is currently being used to accelerate simulations of PDP systems. We illustrate the modelling framework presented with a case study concerning pandemics.] http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png

Applications of Membrane Computing in Systems and Synthetic BiologyMembrane System-Based Models for Specifying Dynamical Population Systems

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Publisher
Springer International Publishing
Copyright
© Springer International Publishing Switzerland 2014
ISBN
978-3-319-03190-3
Pages
97 –132
DOI
10.1007/978-3-319-03191-0_4
Publisher site
See Chapter on Publisher Site

Abstract

[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 Algorithm (DCBA), which has been engineered into software simulation tools. In particular, MeCoSim (Membrane Computing Simulator) is a GUI developed in the framework of P-Lingua that can be used as a simulation environment for running virtual experiments. The parameters of each scenario to be simulated can be easily adjusted in a visual way, as well as the settings for the desired output format, thus facilitating the validation of the designed models against real data. The simulation of PDP systems is data intensive for large models. Therefore, the development of efficient simulators for this field is needed. In fact, the computational power of GPUs is currently being used to accelerate simulations of PDP systems. We illustrate the modelling framework presented with a case study concerning pandemics.]

Published: Dec 18, 2013

Keywords: Infected Individual; Asymptomatic Individual; Inference Engine; Infected People; Evolution Rule

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