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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.
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| − | 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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| − | ** Available Methods:
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| − | * Flux Balance Analysis;
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| − | <!-- * Null Space Method; -->
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| − | * 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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| − | There are no no linear dependencies between the rows.
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| − | ** Available Methods:
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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 (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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| − | ** Available Methods:
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| − | * Least squares estimate
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| − | <!-- * Null Space Method; -->
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| | === First step === | | === First step === |
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| | In this how-to the following Metatool model will be used: [[Media:MFAmetatool.txt]] | | In this how-to the following Metatool model will be used: [[Media:MFAmetatool.txt]] |
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| − | [[Image:MFAloadProject1.png]]
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| − | After name the project and load the [[Media:MFAmetatool.txt]] model.
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| − | [[Image:MFAloadProject2.png]]
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| − | To finish up press Ok.
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| | === Second step === | | === Second step === |
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| | In Menu '''Plugins''' choose ''Plugins->MFA->Create Measured Values'' as shown in the following Figure. | | In Menu '''Plugins''' choose ''Plugins->MFA->Create Measured Values'' as shown in the following Figure. |
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| − | [[Image:MFACreateFluxMeasures1.png]]
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| | 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. | | 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. |
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| − | [[Image:MFACreateFluxMeasures2.png]]
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| | The file has to respect the following format: | | The file has to respect the following format: |
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| | If the flux measured list is empty the following dialog will be shown. | | If the flux measured list is empty the following dialog will be shown. |
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| − | [[Image:MFACreateFluxMeasures3.png]]
| + | === Third step === |
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| − | === Third step a === | |
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| | Enter the values displayed bellow. | | Enter the values displayed bellow. |
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| − | [[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.
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| | ==== Third step b ==== | | ==== Third step b ==== |
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| − | 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)''. | + | In order to visualize the flux values click on the respective the ''Flux Measures (Instance <Number>)''. In this example it is called ''Flux Measures (Instance 0)''. |
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| − | [[Image:MFACreateFluxMeasures5.png]]
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| − | The flux measures can also be saved by pressing the "Save" button.
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| − | [[Image:MFACreateFluxMeasures6.png]]
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| − | | |
| − | === Fourth step ===
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| − | Afterwards, select the menu ''Plugins->MFA->MFA Wizard''.
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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]]
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| − | 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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