(New page: <b>How to do a mutant simulation - Reaction Deletions</b><br> <br> You can access the "Gene Mutant" option under the "Simulation -> Mutants Simulation" menu or right clicking on the Met...) |
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Revision as of 19:36, 16 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) 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.
2. Select Simulation Method
OptFlux can use several simulation methods, 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 flux to optimize (biomass, by default), and
you can also define if you maximizing or minimizing that flux.
4. Select Environmental Conditions
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.
And that's all!! You can press OK and the results will be loaded into the clipboard.
