From Optflux
Simao.soares (talk | contribs) (→Reaction KO FBA) |
Simao.soares (talk | contribs) |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}} | {{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}} | ||
| − | [[File:Operations-model-fba.png]] | + | [[File:Operations-model-fba.png]]<br /> |
| − | The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu MSeed > Operations > Model > FBA. | + | The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu Plugin Builder > MSeed > Operations > Model > FBA. |
==Wild-type FBA == | ==Wild-type FBA == | ||
| − | To do a Wild-type simulation go to MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the | + | To do a Wild-type simulation go to Plugin Builder > MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemistry and media to be used in the simulation.<br /> |
| − | A simulation result will be created in the OptFlux workspace. | + | A simulation result will be created in the OptFlux workspace.<br /> |
[[File:Model-fba-wt.png]] | [[File:Model-fba-wt.png]] | ||
==Reaction KO FBA== | ==Reaction KO FBA== | ||
| − | To perform a reaction knock-out simulation go to MSeed > Operations > Model > FBA > Reaction KO and select: | + | To perform a reaction knock-out simulation go to Plugin Builder > MSeed > Operations > Model > FBA > Reaction KO and select: |
*the local model-seed | *the local model-seed | ||
*the biochemisty | *the biochemisty | ||
*media | *media | ||
| − | * | + | *reactions to be turned off in the simulation.<br /> |
A simulation result will be created in the OptFlux workspace.<br /> | A simulation result will be created in the OptFlux workspace.<br /> | ||
[[File:Model-fba-reactions.png]] | [[File:Model-fba-reactions.png]] | ||
| Line 20: | Line 20: | ||
==Gene KO FBA== | ==Gene KO FBA== | ||
N/A | N/A | ||
| + | |||
| + | <br /> | ||
| + | <br />[[MS-howto|''Return to the Model-seed How-to Index'']] | ||
Latest revision as of 18:33, 25 March 2013
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu Plugin Builder > MSeed > Operations > Model > FBA.
Wild-type FBA[edit]
To do a Wild-type simulation go to Plugin Builder > MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemistry and media to be used in the simulation.
A simulation result will be created in the OptFlux workspace.
Reaction KO FBA[edit]
To perform a reaction knock-out simulation go to Plugin Builder > MSeed > Operations > Model > FBA > Reaction KO and select:
- the local model-seed
- the biochemisty
- media
- reactions to be turned off in the simulation.
A simulation result will be created in the OptFlux workspace.
Gene KO FBA[edit]
N/A