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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 | + | 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> | ||
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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.<br> | + | 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 reaction.<br> |
<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/simulate-wild-type-strain/simulationWildTypeOperationGui.png</div> | <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 | + | In the objective function section, you have select a reaction (typically the biomass/ growth reaction, selected by default) to maximize or minimize.<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 created environmental conditions you can select them to | + | If you have loaded/created environmental conditions you can select them to use as constraints in the optimization. These can used to define the values of extra-cellular/ drain fluxes, i.e. the way external metabolites are consumed or produced.<br> |
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