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<br> | <br> | ||
<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 | + | Selecting in the Gene list you can add/remove (using the arrows buttons) genes 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 knocking out that set of genes. <br> |
| − | 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 | ||
<br> | <br> | ||
<b>2. Select Simulation Method</b><br> | <b>2. Select Simulation Method</b><br> | ||
| − | OptFlux can use several simulation methods, namely:<br> | + | OptFlux can use several simulation methods for knockout simulations, namely:<br> |
Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA<br> | Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA<br> | ||
<br> | <br> | ||
| − | 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> | + | 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> | ||
<br> | <br> | ||
<b>3. Objective Function Configuration</b><br> | <b>3. Objective Function Configuration</b><br> | ||
| − | Here you can select the | + | Here you can select the reaction to optimize (biomass, by default), and you can also define if you will be maximizing or minimizing that flux.<br> |
| − | you can also define if you maximizing or minimizing that flux.<br> | ||
<br> | <br> | ||
<i><b>4. Select Environmental Conditions</b></i><br> | <i><b>4. Select Environmental Conditions</b></i><br> | ||
| − | If you have | + | If you have created [[Environmental conditions|environmental conditions]] you can select them to be used as constraints in the simulation. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced.<br> |
<br> | <br> | ||
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> | ||
<br> | <br> | ||
Revision as of 19:53, 17 November 2009
How to do a mutant simulation - Reaction Deletions
You
can access
the "Gene Mutant" option under the "Simulation -> Mutants Simulation" menu or
right clicking on the Metabolic Model icon on the clipboard.
In the Gene Mutant Simulation you can select the model/project to work, and set up your configuration.
1. Gene knockout list
Selecting in the Gene list you can add/remove (using the arrows buttons) genes 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 knocking out that set of genes.
2. Select Simulation Method
OptFlux can use several simulation methods for knockout simulations, namely:
Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA
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.
3. Objective Function Configuration
Here you can select the reaction to optimize (biomass, by default), and you can also define if you will be maximizing or minimizing that flux.
4. Select Environmental Conditions
If you have created environmental conditions you can select them to be used as constraints in the simulation. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced.
And that's all!! You can press OK and the results will be loaded into the clipboard.
