How to calculate a Critical Genes/Reactions
OptFlux allows the users to define which are the genes or reactions that are essential for the strain to survive, i.e. to keep a value of biomass/ growth significantly different from zero. The essential genes/ reactions can be calculated using Flux Balance Analysis. Also, the software allows the user to load thse genes or reactions from a file (if they are available). The list of essential genes/ reactions can be manually edited, allowing users to add or remove elements, given their knowledge or the purpose of their experiments.
You
can access
the "Calculate Critical Genes/Reactions" option under the "Model Simplification" menu or
right clicking on the Metabolic Model icon on the clipboard.
In the options you can select the
model/project to work, and set up the process.
1.Biomass Flux
Choose the flux related to the biomass / growth.
2.Critical Information
Choose if you want to calculate essential reactions or genes (if GPR information available).
3. Select Environmental Conditions
If you have loaded/created environmental conditions you can select them
to use as constraints in the critical genes/reactions calculation. This means that in this case you will calculate essential genes/reactions in a given environment.
And that's all !! Now you can press OK and check the results in the clipboard.
