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In this section the MFA4Optflux How-to is described. | In this section the MFA4Optflux How-to is described. | ||
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The following set of methods is available in the public version of the plug-in: | The following set of methods is available in the public version of the plug-in: | ||
− | * If the rank of the model stoichiometric matrix | + | * If the rank of the model stoichiometric matrix < unknown rates the system is under-determined. |
** Available Methods: | ** Available Methods: | ||
* Flux Balance Analysis; | * Flux Balance Analysis; | ||
− | + | * Null Space Method; | |
* Tight Bounds Calculation. | * Tight Bounds Calculation. | ||
− | * If the rank of the model stoichiometric matrix | + | * If the rank of the model stoichiometric matrix = unknown rates the system is determined. |
There are no no linear dependencies between the rows. | There are no no linear dependencies between the rows. | ||
** Available Methods: | ** Available Methods: | ||
− | + | * Null Space Method. | |
− | + | * If the rank of the model stoichiometric matrix < number of metabolites the system is over-determined. | |
− | * If the rank of the model stoichiometric matrix | ||
Some rows of the stoichiometric matrix are linear dependent. | Some rows of the stoichiometric matrix are linear dependent. | ||
** Available Methods: | ** Available Methods: | ||
− | + | * Null Space Method. | |
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=== First step === | === First step === | ||
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[[Image:MFACreateFluxMeasures4.png]] | [[Image:MFACreateFluxMeasures4.png]] | ||
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==== Third step b ==== | ==== Third step b ==== | ||
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=== Fourth step === | === Fourth step === | ||
− | Afterwards, select the menu ''Plugins->MFA->MFA Wizard''. | + | Afterwards, select the menu ''Plugins->MFA->MFA Wizard''. A wizard will pop-up. In the first step select the project, the model and respective flux measures. |
[[Image:MFAWizard1.png]] | [[Image:MFAWizard1.png]] | ||
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[[Image:MFAWizard2.png]] | [[Image:MFAWizard2.png]] | ||
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The second wizard step will show general information about the model as shown in the Figure below. | The second wizard step will show general information about the model as shown in the Figure below. | ||
− | [[Image: | + | [[Image:MFAWizard5a.png]] |
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− | + | The third wizard step will show a set of methods to solve the MFA(depending on the type of system). | |
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=== Fourth step - FBA/Linear Programming === | === Fourth step - FBA/Linear Programming === | ||
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Select the the desired flux to optimize and press Finish. | Select the the desired flux to optimize and press Finish. | ||
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− | + | After select the MFA result on the clipboard. | |
− | + | === Fourth step - Null space Method === | |
Select the null space method and press Finish. | Select the null space method and press Finish. | ||
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− | After select the MFA | + | After select the MFA result on the clipboard. |
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=== Fourth step - Tight Bounds === | === Fourth step - Tight Bounds === | ||
Select tight Bounds and press Finish. | Select tight Bounds and press Finish. | ||
− | + | After select the MFA result on the clipboard. | |
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− | After select the MFA | ||
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