View source for Flux balance analysis

==FBA via Diagram==
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If the {{Type link|diagram}} contains fluxes properties written as fbc extension of the SBML "FBC table" tab can be used. Advantage of this tab usage is lack of necessity in creation table with data about fluxes: it will be created automatically using {{Type link|diagram}}. The step-by-step instruction of the analysis will be demonstrated on the <i>[https://ict.biouml.org/bioumlweb/#de=data/Collaboration/FBA%20models/Data/Geobacillus%20icigianus/iMK1321_Model iMK1321]</i> model for <i>Geobacillus icigianus</i> developed by our research group and [https://doi.org/10.3390/microorganisms8071002 recently published]. <b><i>Note:</i></b> opening of the large-size diagram may take a while due to the size and layouting of the diagram.


[[File:FBA_viaDiagram_Fig1_18_03.png|1000px]]

<span style="font-size: 90%"> '''Figure 1.''' View of the <i>iMK1321</i> model diagram in BioUML. Double-click of the left mouse button the diagram icon (marked red as 1) opens the diagram in the <b>Work Space</b> (marked red as 2).</span>


<h5> Flux Balance tab in the Operations Field</h5>
To launch the analysis, move to the <b><i>Flux Balance</i></b> tab in the <b>Operations Field</b> (Figure 1, marked red at the bottom) and push the corresponding button in upper left corner of the tab (marked red as 3). It will lead to pop-up window where a specification of the analysis settings is required. 

[[File:FBA_viaDiagram_Fig2_18_03.png|1000px]]

<span style="font-size: 90%"> '''Figure 2.''' Solver type selection and specification of the optimization (maximize or minimize the objective function's value) in BioUML. One-click of the left mouse button <b><i>Ok</i></b> button runs the FBA.</span>


<h5> Optimal solution in the tab</h5>
The outcome of the FBA will be automatically presented upon completion of the analysis in the <b><i>Flux Balance</i></b> tab.

[[File:FBA_viaDiagram_Fig3_18_03.png|1000px]]

<span style="font-size: 90%"> '''Figure 3.''' Results of the FBA in corresponding tab for <i>iMK1321</i> model. The flux distribution of the model is marked red at the bottom.</span>


The flux distribution can be saved as a table via one-click of the left mouse button the save icon in upper left corner of the tab (Figure 3, marked red as 1). It will lead to pop-up window where a specification of the path and name of the table file are required. 

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<span style="font-size: 90%"> '''Figure 4.''' Specification of the path and name of the table file with the output flux distribution of the model.</span>


As a result, the table will be automatically opened in the <b>Work Space</b>. The table consists of two columns: reaction ID and optimal value of the reaction flux obtained by FBA.

[[File:FBA_viaDiagram_Fig5_18_03.png|1000px]]

<span style="font-size: 90%"> '''Figure 5.''' Resulting FBA table usage for <i>iMK1321</i> model.</span>

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