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BIOMD0000000455 - Smallbone2013 - Metabolic Control Analysis - Example 2

 

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Reference Publication
Publication ID: http://arxiv.org/pdf...
Kieran Smallbone
Metabolic Control Analysis: Rereading Reder
Quantitative Methods
Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, UK.  [more]
Model
Original Model: BIOMD0000000455.xml.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1305030001
Submission Date: 03 May 2013 12:37:47 UTC
Last Modification Date: 31 May 2013 16:09:21 UTC
Creation Date: 01 May 2013 12:00:00 UTC
Encoders:  Vijayalakshmi Chelliah
   Kieran Smallbone
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:hasTaxon Taxonomy cellular organisms
set #3
bqbiol:isVersionOf Gene Ontology regulation of binding
Notes
Smallbone2013 - Metabolic Control Analysis - Example 2

Metabolic control analysis (MCA) is a biochemical formalism, defining how variables, such as fluxes and concentrations, depend on network parameters. In this paper, owing to its limitations, it is shown with three example models (MODEL1305030000-2) that the algorithm with slight modification can be applied to all models.

This model is described in the article:

Kieran Smallbone
Quantitative Methods; Tue, 28 May 2013.

Abstract:

Metabolic control analysis is a biochemical formalism defined by Kacser and Burns in 1973, and given firm mathematical basis by Reder in 1988. The algorithm defined by Reder for calculating the control matrices is still used by software programs today, but is only valid for some biochemical models. We show that, with slight modification, the algorithm may be applied to all models.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: http://arxiv.org/pdf... Submission Date: 03 May 2013 12:37:47 UTC Last Modification Date: 31 May 2013 16:09:21 UTC Creation Date: 01 May 2013 12:00:00 UTC
Mathematical expressions
Reactions
v1 v2 v3 v4
v5      
Physical entities
Compartments Species
cell x1 x2 x3
y1 y2 y3
y4 y5 y6
Reactions (5)
 
 v1 [y1] + [x2] ↔ [x1] + [x3];   {y1} , {x2} , {x1} , {x3}
 
 v2 [y4] + [x3] ↔ [y5] + [x2];   {y4} , {x3} , {y5} , {x2}
 
 v3 [x1] ↔ [y2];   {x1} , {y2}
 
 v4 [x1] ↔ [y3];   {x1} , {y3}
 
 v5 [x3] ↔ [y6];   {x3}
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 x1
Compartment: cell
Initial concentration: 0.05625738310526
 
 x2
Compartment: cell
Initial concentration: 0.76876151899652
 
 x3
Compartment: cell
Initial concentration: 4.23123848100348
 
 y1
Compartment: cell
Initial concentration: 10.0
Constant
 
 y2
Compartment: cell
Initial concentration: 0.0
Constant
 
 y3
Compartment: cell
Initial concentration: 0.0
Constant
 
 y4
Compartment: cell
Initial concentration: 1.0
Constant
 
 y5
Compartment: cell
Initial concentration: 1.0
Constant
 
 y6
Compartment: cell
Initial concentration: 0.0
Constant
 
v1 (2)
 
   e1
Value: 1.0   (Units: dimensionless)
Constant
 
   p1
Value: 10.0   (Units: dimensionless)
Constant
 
v2 (2)
 
   e2
Value: 1.0   (Units: dimensionless)
Constant
 
   p2
Value: 10.0   (Units: dimensionless)
Constant
 
v3 (2)
 
   e3
Value: 1.0   (Units: dimensionless)
Constant
 
   p3
Value: 50.0   (Units: dimensionless)
Constant
 
v4 (2)
 
   e4
Value: 1.0   (Units: dimensionless)
Constant
 
   p4
Value: 10.0   (Units: dimensionless)
Constant
 
v5 (2)
 
   e5
Value: 1.0   (Units: dimensionless)
Constant
 
   p5
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000455

Curator's comment: (updated: 31 May 2013 16:51:42 BST)

As there are no plots to reproduce as curation figure, Table 2 that provides the steady-state concentrations of variables and fluxes, are reproduced here - using Copasi v4.8 (Build 35).

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