Metabolic control analysis example - Revision history

Elena.kutumova@biouml.org at 03:48, 16 March 2022

2022-03-16T03:48:36Z

Elena.kutumova@biouml.org at 02:14, 16 March 2022

2022-03-16T02:14:01Z

Elena.kutumova@biouml.org at 09:39, 14 March 2022

2022-03-14T09:39:41Z

Elena.kutumova@biouml.org at 09:29, 14 March 2022

2022-03-14T09:29:11Z

Elena.kutumova@biouml.org at 02:29, 14 March 2022

2022-03-14T02:29:59Z

Elena.kutumova@biouml.org at 10:05, 11 March 2022

2022-03-11T10:05:27Z

Elena.kutumova@biouml.org at 09:53, 11 March 2022

2022-03-11T09:53:29Z

Elena.kutumova@biouml.org at 09:52, 11 March 2022

2022-03-11T09:52:34Z

Elena.kutumova@biouml.org at 09:52, 11 March 2022

2022-03-11T09:52:19Z

Elena.kutumova@biouml.org at 09:36, 11 March 2022

2022-03-11T09:36:01Z

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 ==Reproducing a test case in BioUML==
-To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
+To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analyses</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
 After double click on ''Metabolic Control Analysis'', a new tab with analysis settings opens.

@@ Line 1: / Line 1: @@
 The method description could be found in the section [[Metabolic Control Analysis]]. Here we give an example of the method application and using in BioUML.
 ==Reproducing a test case in BioUML==
 To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
-After double click on ''Metabolic Control Analysis'', a new tab with analysis settings opens (Figure 1).
+After double click on ''Metabolic Control Analysis'', a new tab with analysis settings opens.
 Select a path to the input diagram:
@@ Line 16: / Line 16: @@
 ''data/Collaboration/Demo/Data/Temp/Metabolic Control Analysis Results''
 After you click the ''Run'' button and the calculations are finished, you can see the results presented in six tables, including unscaled elastisities (the matrix ''Ɗ<sub>C<sup>ss</sup></sub>v'' in the description below), unscaled concentration controls (the matrix Γ), unscaled flux controls (the matrix Λ), and scaled versions of these matrices with elements ''e<sub>i,j</sub>'' defined as a product of the corresponding elements in the unscaled matrixes and values of ''c<sub>i,j</sub> / r<sub>i,j</sub>'', where ''c<sub>i,j</sub>'' and ''r<sub>i,j</sub>'' denote steady state values of column and row elements, respectively.
@@ Line 74: / Line 76: @@
 ==References==
 # Reder C. Metabolic control theory: a structural approach. ''Journal of Theoretical Biology''. 1988. V. 135. № 2. p. 175-201.

@@ Line 15: / Line 15: @@
 and a path to save results of analysis, for example:
-''data/Collaboration/Demo/Data/Temp/Metabolic Control Analysis''
+''data/Collaboration/Demo/Data/Temp/Metabolic Control Analysis Results''
 After you click the ''Run'' button and the calculations are finished, you can see the results presented in six tables, including unscaled elastisities (the matrix ''Ɗ<sub>C<sup>ss</sup></sub>v'' in the description below), unscaled concentration controls (the matrix Γ), unscaled flux controls (the matrix Λ), and scaled versions of these matrices with elements ''e<sub>i,j</sub>'' defined as a product of the corresponding elements in the unscaled matrixes and values of ''c<sub>i,j</sub> / r<sub>i,j</sub>'', where ''c<sub>i,j</sub>'' and ''r<sub>i,j</sub>'' denote steady state values of column and row elements, respectively.
@@ Line 21: / Line 21: @@
 Ready analysis results can be found here:
-''data/Examples/DAE models/Data/Metabolic Control Analysis''
+''data/Examples/DAE models/Data/Metabolic Control Analysis Results''
 ==Description of the test case==

@@ Line 2: / Line 2: @@
 ==Reproducing a test case in BioUML==
 To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
-After double click on ''Metabolic Control Analysis'', a new tab with analysis settings opens.
+After double click on ''Metabolic Control Analysis'', a new tab with analysis settings opens (Figure 1).
 Select a path to the input diagram:

@@ Line 1: / Line 1: @@
 The method description could be found in the section [[Metabolic Control Analysis]]. Here we give an example of the method application and using in BioUML.
-==Reproducing a test case==
+==Reproducing a test case in BioUML==
 To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.

@@ Line 7: / Line 7: @@
 After double click on ''Metabolic Control Analysis'', a new tab with analysis settings opens.
-Select a path to an example input diagram:
+Select a path to the input diagram:
 ''data/Examples/DAE models/Data/Diagrams/Geva_Zatorsky_2006_Model_I''

@@ Line 3: / Line 3: @@
 ==Reproducing a test case in BioUML==
-To reproduce a test case below in [[BioUML]] workbench you first need to go to the <b>Analysis</b> tab in navigation pane and then follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
+To reproduce a test case below in [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
 After double click on ''Metabolic Control Analysis'', a new tab with analysis settings opens.