MFA4OptFlux

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MFA4OptFlux Plug-in How-to[edit]

In this section the MFA4Optflux How-to is described. 

Assuming the pseudo-steady state hypothesis we have

    A*v = 0, where A is the stoichiometric matrix and v is the flux matrix
    Ac*Vc+Am*Vm = 0, where  the subfix "m" represents measured fluxes matrices 
    and the subfix "c" is related with the fluxes that are going to be calculated.
 The following set  of methods is available in the public version of the plug-in:
     
         * If the rank of the model stoichiometric matrix (Ac) <  unknown rates the system is under-determined.
           ** Available Methods: 
                    * Flux Balance Analysis;
                    * Tight Bounds Calculation.
         * If the rank of the model stoichiometric matrix (Ac) ==  unknown rates the system is determined. 
           There are no no linear dependencies between the rows.
           ** Available Methods:
                    * The Vc is calculated by the following expression: Vc = -(Ac^-1)*Am*Vm  
         * If  the rank of the model stoichiometric matrix (Ac) < number of metabolites the system is over-determined. 
           Some rows of the stoichiometric matrix are linear dependent.
           ** Available Methods:
                    * Least squares estimate

First step[edit]

Load a metabolic model, see How to create a new model/project from SBML and How to create a new model/project from text files.

In this how-to the following Metatool model will be used: Media:MFAmetatool.txt‎


MFAloadProject1.png

After name the project and load the Media:MFAmetatool.txt‎ model.

MFAloadProject2.png

To finish up press Ok.

Second step[edit]

In Menu Plugins choose Plugins->MFA->Create Measured Values as shown in the following Figure.

MFACreateFluxMeasures1.png

A Dialog will pop-up asking the measured flux values. Enter the set of measured values or load a set of flux values from a file.

MFACreateFluxMeasures2.png

The file has to respect the following format:

  <Reaction_ID> <Delimiter><Measured Value>

Note: The reaction order can be different from the model and any lines only with the Reaction_ID will be ignored.

  If the flux measured list is empty the following dialog will be shown.

MFACreateFluxMeasures3.png

Third step a[edit]

Enter the values displayed bellow.

MFACreateFluxMeasures4.png

Note: to delete a flux value first select the desired flux value and press Enter. After erase the flux value by pressing backspace or delete (depending on the cursor position) and press Enter again.

Third step b[edit]

In order to visualize the flux values click on the respective Flux Measures (Instance <Number>) object. In this example it is called Flux Measures (Instance 0).

MFACreateFluxMeasures5.png

The flux measures can also be saved by pressing the "Save" button.

MFACreateFluxMeasures6.png

Fourth step[edit]

Afterwards, select the menu Plugins->MFA->MFA Wizard.

MFAWizard1.png

A wizard will pop-up. In the first step select the project, the model and respective flux measures.

MFAWizard2.png

The second wizard step will show general information about the model as shown in the Figure below.

MFAWizard3.png

The third wizard step will show a set of methods to solve the MFA(depending on the type of system) as displayed in the Figure below..

MFAWizard4aa.png

Fourth step - FBA/Linear Programming[edit]

Select the the desired flux to optimize and press Finish.

MFAWizard4af.png

After select the MFA Solution datatype on the clipboard.

MFAWizard5a.png

Fourth step - Tight Bounds[edit]

Select tight Bounds and press Finish.

MFAWizard4cc.png

After select the MFA Solution datatype on the clipboard.

MFAWizard7a.png

Determined and Over-determined cases[edit]

These cases are analogous to the previous shown scenario. The following examples will use the model used in the under-determined scenario and some previously illustrated steps will be omitted.

Determined system example[edit]

Create the following flux measures, as shown below.

MFACreateFluxMeasures4determined.png

Execute the MFA Wizard and press next trough out the steps as shown in the Figures below.

MFAWizard1Determined.png

MFAWizard2Determined.png

MFAWizard3Determined.png

After select the MFA Solution datatype on the clipboard.

MFASolutionDetermined.png

Over-determined system example[edit]

Create the following flux measures, as shown below.

MFACreateFluxMeasures4overdetermined.png

MFAWizard2OverDetermined.png

MFAWizard3OverDetermined.png

After select the MFA Solution datatype on the clipboard.

MFASolutionOverDetermined.png