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right clicking on the Metabolic Model icon on the clipboard.<br> | right clicking on the Metabolic Model icon on the clipboard.<br> | ||
<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-structural-simplification/CalculateCriticalMenu.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-structural-simplification/CalculateCriticalMenu.png</div> | ||
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In the options you can select the | In the options you can select the | ||
model/project to work, and set up the process.<br> | model/project to work, and set up the process.<br> | ||
<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-structural-simplification/CalculateCriticalOperation.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-structural-simplification/CalculateCriticalOperation.png</div> | ||
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<b>1.Biomass Flux</b><br> | <b>1.Biomass Flux</b><br> | ||
Revision as of 19:55, 16 November 2009
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.
