| Line 20: | Line 20: | ||
<i><b>3.Select Environmental Conditions</b></i><br> | <i><b>3.Select Environmental Conditions</b></i><br> | ||
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> | 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> | ||
| − | + | <br> | |
| + | <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> | <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> | ||
<br> | <br> | ||
<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> | ||
Revision as of 19:30, 16 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 reaction.
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.
3.Select Environmental Conditions
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.
