Flux balance analysis - Revision history

Akberdinir@gmail.com at 11:06, 18 March 2022

2022-03-18T11:06:53Z

Akberdinir@gmail.com: /* FBA via Analysis tab */

2022-03-18T10:55:20Z

‎FBA via Analysis tab

Akberdinir@gmail.com at 10:54, 18 March 2022

2022-03-18T10:54:31Z

Akberdinir@gmail.com: /* FBA via Diagram */

2022-03-18T10:10:07Z

‎FBA via Diagram

Akberdinir@gmail.com: /* FBA via Diagram */

2022-03-18T10:09:55Z

‎FBA via Diagram

Akberdinir@gmail.com: /* FBA via Diagram */

2022-03-18T08:13:30Z

‎FBA via Diagram

Akberdinir@gmail.com: /* FBA via Analysis tab */

2022-03-16T12:10:02Z

‎FBA via Analysis tab

Akberdinir@gmail.com: /* FBA via Analysis tab */

2022-03-16T12:09:20Z

‎FBA via Analysis tab

Akberdinir@gmail.com at 12:06, 16 March 2022

2022-03-16T12:06:48Z

Akberdinir@gmail.com: /* FBA via Diagram */

2022-03-16T12:04:15Z

‎FBA via Diagram

@@ Line 7: / Line 7: @@
 ==FBA via Diagram==
 <font size="3">
-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.
+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.
@@ Line 45: / Line 45: @@
 </font size="3">
 ==FBA via Analysis tab==
@@ Line 89: / Line 91: @@
 <span style="font-size: 90%"> '''Figure 10.''' Resulting "FBC table" tab usage for <i>iMK1321</i> model. The objective function's value of the model is marked red.</span>
 </font size="3">

@@ Line 56: / Line 56: @@
 It is worth noting that the [[Building Flux Balance DataTable (analysis)|Building Flux Balance Data Table]] analysis and "FBC table" tab work only with [[SBML (file format)|SBML]] L3v1 {{Type link|diagram}}s with special <b><i>fbc</i></b> package. Thus, if the {{Type link|diagram}} does not satisfy these conditions it should be transformed before using this analysis. For example, if the {{Type link|diagram}} does not use <b><i>fbc</i></b> package but contains all necessary information about fluxes, it should be preprocessed by [[Recon transformer (analysis)|Recon transformer]] firstly.
-[[File:FBA_viaAnalysis_Fig1.png|1000px]]
+[[File:FBA_viaAnalysis_Fig1_18_03.png|1000px]]
 <span style="font-size: 90%"> '''Figure 6.''' View of <b>Building Flux Balance Data Table</b> analysis. Double-click of the left mouse button the analysis icon (marked red) opens the analysis settings in the <b>Work Space</b> (marked red). It is necessary to specify a path to the diagram, output path for the table and values of lower and upper bounds in mmol*gDCW<sup>-1</sup>*h<sup>-1</sup>.</span>
@@ Line 63: / Line 63: @@
 One click of the left mouse button on the <b><i>Run</i></b> will launch the analysis. The resulting Flux Balance Data Table for FBA will be automatically opened in the <b>Work Space</b> as an output of the analysis.
-[[File:FBA_viaAnalysis_Fig2.png|1000px]]
+[[File:FBA_viaAnalysis_Fig2_18_03.png|1000px]]
 <span style="font-size: 90%"> '''Figure 7.''' Resulting Flux Balance Data Table for <i>iMK1321</i> model. The objective function of the model is marked red.</span>
@@ Line 72: / Line 72: @@
 To start work with the [[Flux Balance Constraint (analysis)|Flux Balance Constraint]] analysis one needs a {{Type link|diagram}} and a special table with data about its fluxes (names, bounds, objective function coefficients, etc.). To open the analysis settings in the <b>Work Space</b> double-click of the left mouse button the analysis icon (marked red).
-[[File:FBA_viaAnalysis_Fig3.png|1000px]]
+[[File:FBA_viaAnalysis_Fig3_18_03.png|1000px]]
 <span style="font-size: 90%"> '''Figure 8.''' <b>[[Flux Balance Constraint (analysis)|Flux Balance Constraint]]</b> analysis in the [[BioUML]].</span>
@@ Line 79: / Line 79: @@
 Analysis enables to select path to the {{Type link|diagram}}, to the data table and to the table with output results. It has also an expert mode where user can select type of the objective function, solver type (GLPK, Apache simplex solver and Gurobi solver are available) and some solver's properties.
-[[File:FBA_viaAnalysis_Fig4.png|1000px]]
+[[File:FBA_viaAnalysis_Fig4_18_03.png|1000px]]
 <span style="font-size: 90%"> '''Figure 9.''' Solver type selection in the FBC analysis.</span>
@@ Line 86: / Line 86: @@
 One click of the left mouse button on the <b><i>Run</i></b> will launch the analysis. The outcome of the FBA will be automatically opened in the <b>Work Space</b> as an output table of the analysis.
-[[File:FBA_viaAnalysis_Fig5.png|1000px]]
+[[File:FBA_viaAnalysis_Fig5_18_03.png|1000px]]
 <span style="font-size: 90%"> '''Figure 10.''' Resulting "FBC table" tab usage for <i>iMK1321</i> model. The objective function's value of the model is marked red.</span>
 </font size="3">

@@ Line 10: / Line 10: @@
-[[File:FBA_viaDiagram_Fig1.png|1000px]]
+[[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>
@@ Line 18: / Line 18: @@
 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.png|1000px]]
+[[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>
@@ Line 26: / Line 26: @@
 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.png|1000px]]
+[[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>
@@ Line 33: / Line 33: @@
 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.
-[[File:FBA_viaDiagram_Fig4.png|1000px]]
+[[File:FBA_viaDiagram_Fig4_18_03.png|1000px]]
 <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>
@@ Line 40: / Line 40: @@
 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.png|1000px]]
+[[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>

@@ Line 8: / Line 8: @@
 <font size="3">
 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.png|1000px]]

@@ Line 7: / Line 7: @@
 ==FBA via Diagram==
 <font size="3">
-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].
+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.png|1000px]]

← Older revision		Revision as of 08:13, 18 March 2022
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	</font size="3">		</font size="3">
−
−

	==FBA via Analysis tab==		==FBA via Analysis tab==

@@ Line 49: / Line 49: @@
 ==FBA via Analysis tab==
 <font size="3">
-FBA can be also conducted via the [[Flux Balance Constraint (analysis)|Flux Balance Constraint]] analysis in the [[BioUML]].
+FBA can be also conducted via the [[Flux Balance Constraint (analysis)|Flux Balance Constraint]] (FBC) analysis in the [[BioUML]].
 Firstly, move to <b>Analysis</b> tab in the <b>Tree Area</b> by a single click with the right mouse button on the corresponding tab.

← Older revision		Revision as of 12:09, 16 March 2022
Line 78:		Line 78:


−	Analysis enables to select path to the {{Type link\|diagram}}, to the data table and to the table with output results. ~~Also it~~ has an expert mode where user can select type of the objective function, solver type (GLPK, Apache simplex solver and Gurobi solver are available) and some solver's properties.	+	Analysis enables to select path to the {{Type link\|diagram}}, to the data table and to the table with output results. It has also an expert mode where user can select type of the objective function, solver type (GLPK, Apache simplex solver and Gurobi solver are available) and some solver's properties.

	[[File:FBA_viaAnalysis_Fig4.png\|1000px]]		[[File:FBA_viaAnalysis_Fig4.png\|1000px]]

@@ Line 15: / Line 15: @@
 <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 below) 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.
+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.png|1000px]]
@@ Line 27: / Line 27: @@
 [[File:FBA_viaDiagram_Fig3.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 below.</span>
+<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>