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Team:Valencia UPV/Modeling/fba
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<h3>Flux Balance Analysis</h3><br/> | <h3>Flux Balance Analysis</h3><br/> | ||
| - | <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> | + | <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><br/> |
| - | <h3> | + | <h3>COBRA</h3> <br/> |
<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]. | <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]. | ||
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> | 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> | ||
Revision as of 20:52, 12 October 2014
Modeling Pheromone Production Overview
Pheromones production rates can be estimated using constrained-based modelling of metabolic networks.This can be useful to know about the amount of pheromone that can be produced by the synthetic plant.
Constraint-based modelling
Constraint-based modelling is based on the fact that cells are subject to constraints that limit their behaviour (Palsson, 2006). In principle, if all constraints operating under a given set of circumstances were known, the actual state of a metabolic network could be elucidated. So by imposing the known constraints, it is possible to determine which functional states can and cannot be achieved by a cell.
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.
COBRA
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).
References
[Llaneras08] Llaneras F, Picó J (2008). Stoichiometric Modelling of Cell Metabolism. Journal of Bioscience and Bioengineering, 105:1.
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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