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<b>How to do a wild type simulation</b><br> | <b>How to do a wild type simulation</b><br> | ||
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| − | OptFlux allows the user to perform a simulation of the wild-type strain, i.e. of the model with no genetic modifications.<br> | + | OptFlux allows the user to perform a simulation of the "wild-type" strain, i.e. of the model with no genetic modifications.<br> |
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Access the "Wild Type" option either through the "Simulation" menu or right clicking on the model icon in the clipboard.<br> | Access the "Wild Type" option either through the "Simulation" menu or right clicking on the model icon in the clipboard.<br> | ||
| − | + | [[Image:Menu WT.png]] | |
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| − | All the wild-type simulations are performed using Flux-Balance Analysis (FBA), where a Linear Programming problem is defined by the maximization of one flux of the model, usually the biomass formation | + | All the wild-type simulations are performed using Flux-Balance Analysis (FBA), where a Linear Programming problem is defined by the maximization of one flux of the model, usually the biomass formation.<br> |
| − | <div style="display: block; text-align: left;"> | + | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/simulate-wild-type-strain/simulationWildTypeOperationGui.png</div> |
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<b>2.Objective Function Configuration</b><br> | <b>2.Objective Function Configuration</b><br> | ||
| − | In the objective function section, you have select a reaction (typically the biomass/ growth reaction, selected by default) to maximize or minimize.<br> | + | In the objective function section, you have select a reaction (typically the biomass/ growth reaction, selected by default) to maximize or minimize the corresponding flux.<br> |
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<i><b>3.Select Environmental Conditions</b></i><br> | <i><b>3.Select Environmental Conditions</b></i><br> | ||
| − | If you have | + | If you have created environmental conditions you can select them to be used as constraints in the optimization. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced.<br> |
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<div style="display: block; text-align: left;">And that's all!! You can press OK and the results will be loaded into the clipboard.<br> | <div style="display: block; text-align: left;">And that's all!! You can press OK and the results will be loaded into the clipboard.<br> | ||
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<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/simulate-wild-type-strain/simulationWildTypeSolution.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/simulate-wild-type-strain/simulationWildTypeSolution.png</div> | ||
Latest revision as of 15:36, 18 November 2009
How to do a wild type simulation
OptFlux allows the user to perform a simulation of the "wild-type" strain, i.e. of the model with no genetic modifications.
Access the "Wild Type" option either through the "Simulation" menu or right clicking on the model icon in the clipboard.
All the wild-type simulations are performed using Flux-Balance Analysis (FBA), where a Linear Programming problem is defined by the maximization of one flux of the model, usually the biomass formation.
1.Select Project and Model
Choose the Project and the Metabolic Model to do the simulation.
Attention: Optflux supports multiple-projects and each project can contain an Original Metabolic Model and several Simplified Metabolic Models.
2.Objective Function Configuration
In the objective function section, you have select a reaction (typically the biomass/ growth reaction, selected by default) to maximize or minimize the corresponding flux.
3.Select Environmental Conditions
If you have created environmental conditions you can select them to be used as constraints in the optimization. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced.
