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<b>1. Gene knockout list</b><br> | <b>1. Gene knockout list</b><br> | ||
| − | Selecting in the Gene list you can add/remove (using the arrows buttons) | + | Selecting in the Gene list you can add/remove (using the arrows |
| + | buttons) to the knockout list (the list of genes to be knocked out, in the right). In the Inactive Reactions list you can see the reactions that will be turned off using that set of genes. <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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| − | ROOM-LP stands for the Regulatory On-Off Minimization Method (ROOM), using a linear programming (LP) relaxation; ROOM-MILP is the original ROOM that uses a Mixed Integer LP (MILP) method; MOMA stands for the Minimization of Metabolic Adjustment method that uses quadratic programming. | + | ROOM-LP stands for the Regulatory On-Off Minimization Method (ROOM), using a linear programming (LP) relaxation; ROOM-MILP is the original ROOM that uses a Mixed Integer LP (MILP) method; MOMA stands for the Minimization of Metabolic Adjustment method that uses quadratic programming.<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 that 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 | + | If you have loaded/created environmental conditions you can select them to use as constraints in the simulation. 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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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/gene-knockout/simulationGeneMutantSolution.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/simulation-mutant/gene-knockout/simulationGeneMutantSolution.png</div> | ||
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