Team:Valencia UPV/Modeling/fba

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<h1>Modeling Pheromone Production Overview</h1>
<h1>Modeling Pheromone Production Overview</h1>
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            <p>Sexually communication among moths is accomplished chemically by the release of an “odor”: sexual pheromones. Pheromones are molecules that can be carried by a diffusion process in which the random movement of gas molecules transport the chemical away from its source.  Pheromone chemicals obey to the diffusion equation, resulting in a straightforward application of the mathematics of a diffusing source. (referencia Lecture 9)</p><br/>
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<p>Pheromones production rates are estimated when the system is in stationary state with an FBA (Flux Balance Analysis). This can be useful to know about the amount of pheromone that can be produced by the synthetic plant during a certain period of time, once the system has ended its transitory levels of pheromone production.</p>  
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<p>The equation of diffusion that we will use in this project to model the pheromones dispersion will adopt the form of the heat equation, and will be solved by the Euler numeric approximation. <a class="normal-link-page" href="#">See more about heat equation and mathematical expressions for Euler method.</a></p><br/>
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<h2>Flux Balance Analysis</h2>      
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<p>Moths seem to respond to gradients of pheromone concentration attracted towards the source, although there are other factors that lead moths sexually to pheromone sources such as optomotor anemotaxis  (J. N. Perry and C. Wall , A Mathematical Model for the Flight of Pea Moth to Pheromone Traps Through a Crop). However, increasing the pheromone concentration to unnaturally high levels may disrupt male orientation (W. L. Roelofs and R. T. Carde, Responses of Lepidoptera to synthetic sex pheromone chemicals and their analogues). <a class="normal-link-page" href="#">See more about model for moth flight.</a></p><br/>
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<p>Flux balance analysis (FBA) is a mathematical approach for analyzing the flow of metabolites through a metabolic network.  FBA is a widely used for studying biochemical networks, in particular the genome-scale metabolic network reconstructions that have been built in the past decade.  These reconstructions contain all of the known metabolic reactions in an organism or plant, and the genes that encode each enzyme. In our case, FBA will calculate the flow of metabolites through our metabolic network to obtain the major production of pheromone.</p>
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<p>The pheromone diffusion process and moth behavior when they are in presence of our synthetic plants acting as continuously-emitting sources, are modeled in <a class="normal-link-page" href="#">Netlogo</a>.</p>
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<h2>CROBA</h2>
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<p>The COnstraints Based Reconstruction and Analysis (COBRA) approach to systems biology accepts the fact that we do not possess sufficiently detailed parameter data to precisely model, in the biophysical sense, an organism or plant at the genome scale [1].
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The COBRA Toolbox [2] is a freely available Matlab toolbox can be used to perform a variety of COBRA methods, including many FBA-based methods. Models for the COBRA Toolbox are saved in the Systems Biology Markup Language (SBML).</p>
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Revision as of 17:19, 16 September 2014


Modeling Pheromone Production Overview

Pheromones production rates are estimated when the system is in stationary state with an FBA (Flux Balance Analysis). This can be useful to know about the amount of pheromone that can be produced by the synthetic plant during a certain period of time, once the system has ended its transitory levels of pheromone production.

Flux Balance Analysis

Flux balance analysis (FBA) is a mathematical approach for analyzing the flow of metabolites through a metabolic network. FBA is a widely used for studying biochemical networks, in particular the genome-scale metabolic network reconstructions that have been built in the past decade. These reconstructions contain all of the known metabolic reactions in an organism or plant, and the genes that encode each enzyme. In our case, FBA will calculate the flow of metabolites through our metabolic network to obtain the major production of pheromone.

CROBA

The COnstraints Based Reconstruction and Analysis (COBRA) approach to systems biology accepts the fact that we do not possess sufficiently detailed parameter data to precisely model, in the biophysical sense, an organism or plant at the genome scale [1]. The COBRA Toolbox [2] is a freely available Matlab toolbox can be used to perform a variety of COBRA methods, including many FBA-based methods. Models for the COBRA Toolbox are saved in the Systems Biology Markup Language (SBML).

NetLogo is an agent-based programming language and integrated modeling environment. NetLogo is free and open source software, under a GPL license.

NetLogo is an agent-based programming language and integrated modeling environment. NetLogo is free and open source software, under a GPL license.

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