Editing MFA4OptFlux

== MFA4OptFlux Plug-in How-to ==

 In this section the MFA4Optflux How-to is described. 

Assuming the pseudo-steady state hypothesis we have

     A*v = 0
     An*Vn+Am*Vm = 0, where "m" represents measured fluxes matrices

  The following set  of methods is available in the public version of the plug-in:
      
          * If the rank of the model stoichiometric matrix (An) <  unknown rates the system is under-determined.
            ** Available Methods: 
                     * Flux Balance Analysis;
                     * Null Space Method;
                     * Tight Bounds Calculation.
          * If the rank of the model stoichiometric matrix (An) ==  unknown rates the system is determined. 
            There are no no linear dependencies between the rows.
            ** Available Methods:
                     * Null Space Method.
          * If  the rank of the model stoichiometric matrix (An) < number of metabolites the system is over-determined. 
            Some rows of the stoichiometric matrix are linear dependent.
            ** Available Methods:
                     * Null Space Method.

===  First step ===

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]]


[[Image:MFAloadProject1.png]]

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

[[Image:MFAloadProject2.png]]

To finish up press Ok.

=== Second step === 

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

[[Image: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.

[[Image: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.

[[Image:MFACreateFluxMeasures3.png]]

=== Third step a ===

Enter the values displayed bellow.

[[Image:MFACreateFluxMeasures4.png]]

==== Third step b ====

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)''. 

[[Image:MFACreateFluxMeasures5.png]]

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

[[Image:MFACreateFluxMeasures6.png]]

=== Fourth step ===

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

[[Image:MFAWizard1.png]]

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

[[Image:MFAWizard2.png]]

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

[[Image:MFAWizard3.png]]

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

[[Image:MFAWizard4a.png]]

=== Fourth step - FBA/Linear Programming ===

Select the the desired flux to optimize and press Finish.

[[Image:MFAWizard4af.png]]

After select the MFA Solution datatype on the clipboard.

[[Image:MFAWizard5a.png]]

=== Fourth step - Null space Method ===

Select the null space method and press Finish.

[[Image:MFAWizard4b.png]]

After select the MFA Solution datatype on the clipboard.

[[Image:MFAWizard6a.png]]

=== Fourth step - Tight Bounds ===

Select tight Bounds and press Finish.

[[Image:MFAWizard4c.png]]

After select the MFA Solution datatype on the clipboard.

[[Image:MFAWizard7a.png]]