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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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Assuming the pseudo-steady state hypothesis we have
 
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    A*v = 0, where A is the stoichiometric matrix and v is the flux matrix
 
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    Ac*Vc+Am*Vm = 0, where  the subfix "m" represents measured fluxes matrices
 
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    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:
 
   The following set  of methods is available in the public version of the plug-in:
 
        
 
        
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           * If the rank of the model stoichiometric matrix (Ac) <  unknown rates the system is under-determined.
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           * 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;
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                <!-- * Null Space Method; -->
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                    * Null Space Method;
 
                     * Tight Bounds Calculation.
 
                     * Tight Bounds Calculation.
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           * If the rank of the model stoichiometric matrix (Ac) ==  unknown rates the system is determined.  
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           * If the rank of the model stoichiometric matrix =  unknown rates the system is determined.  
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            There are no no linear dependencies between the rows.
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There are no no linear dependencies between the rows.
 
             ** Available Methods:
 
             ** Available Methods:
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                <!-- * Null Space Method; -->
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                    * Null Space Method.
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                    * The Vc is calculated by the following expression: Vc = -(Ac^-1)*Am*Vm 
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           * If  the rank of the model stoichiometric matrix < number of metabolites the system is over-determined.  
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           * If  the rank of the model stoichiometric matrix (Ac) < number of metabolites the system is over-determined.  
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Some rows of the stoichiometric matrix are linear dependent.
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            Some rows of the stoichiometric matrix are linear dependent.
 
 
             ** Available Methods:
 
             ** Available Methods:
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                     * Least squares estimate
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                     * Null Space Method.
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                  <!-- * 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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'''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 ====
 
==== Third step b ====
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=== Fourth step ===
 
=== Fourth step ===
  
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Afterwards, select the menu ''Plugins->MFA->MFA Wizard''.  
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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.
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[[Image:MFAWizard1.png]]
 
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A wizard will pop-up. In the first step select the project, the model and respective flux measures.
 
  
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[[Image:MFAWizard2.png]]
 
  
 
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.
  
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[[Image:MFAWizard3.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) as displayed in the Figure below..
 
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[[Image:MFAWizard4aa.png]]
 
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<!-- [[Image:MFAWizard4a.png]] -->
 
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=== Fourth step - FBA/Linear Programming ===
 
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Select the the desired flux to optimize and press Finish.
 
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[[Image:MFAWizard4af.png]]
 
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After select the MFA Solution datatype on the clipboard.
 
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[[Image:MFAWizard5a.png]]
 
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<!-- === Fourth step - Null space Method ===
 
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Select the null space method and press Finish.
 
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[[Image:MFAWizard4b.png]]
 
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After select the MFA Solution datatype on the clipboard.
 
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[[Image:MFAWizard6a.png]]
 
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-->
 
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=== Fourth step - Tight Bounds ===
 
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Select tight Bounds and press Finish.
 
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[[Image:MFAWizard4cc.png]]
 
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After select the MFA Solution datatype on the clipboard.
 
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[[Image:MFAWizard7a.png]]
 
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=== Determined and Over-determined cases ===
 
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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.
 
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==== Determined system example ====
 
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Create the following flux measures, as shown below.
 
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[[Image:MFACreateFluxMeasures4determined.png]]
 
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Execute the MFA Wizard and press next trough out the steps as shown in the Figures below.
 
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[[Image:MFAWizard1Determined.png]]
 
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[[Image:MFAWizard2Determined.png]]
 
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[[Image:MFAWizard3Determined.png]]
 
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After select the MFA Solution datatype on the clipboard.
 
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[[Image:MFASolutionDetermined.png]]
 
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==== Over-determined system example ====
 
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Create the following flux measures, as shown below.
 
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[[Image:MFACreateFluxMeasures4overdetermined.png]]
 
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[[Image:MFAWizard2OverDetermined.png]]
 
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[[Image:MFAWizard3OverDetermined.png]]
 
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After select the MFA Solution datatype on the clipboard.
 
  
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[[Image:MFASolutionOverDetermined.png]]
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The third wizard step will show a set of methods to solve the MFA.

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