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<b>1. Reaction knockout list</b><br> | <b>1. Reaction knockout list</b><br> | ||
| − | Selecting in the Reaction list you can add/remove (using the arrows buttons) | + | Selecting in the Reaction list you can add/remove (using the arrows buttons) to the knockout list (the list of reactions to be deleted, on the right).<br> |
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<b>2. Select Simulation Method</b><br> | <b>2. Select Simulation Method</b><br> | ||
| − | OptFlux can use several simulation methods | + | OptFlux can use several simulation methods, namely:<br> |
Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA<br> | Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA<br> | ||
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<b>3. Objective Function Configuration</b><br> | <b>3. Objective Function Configuration</b><br> | ||
| − | Here you can select the | + | Here you can select the flux to optimize (biomass, by default), and you can also define if you maximizing or minimizing the flux.<br> |
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<i><b>4. Select Environmental Conditions</b></i><br> | <i><b>4. 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 constrains in the simulation. These can be 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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And that's all !! You can press OK and the results will be loaded into the clipboard.<br> | 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;">http://sites.google.com/site/optfluxhowtos/howtos/simulation-mutant/reaction-delection/simulationReactionMutantSolution.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/simulation-mutant/reaction-delection/simulationReactionMutantSolution.png</div> | ||
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