Difference between revisions of "Flux Balance Constraint (analysis)"

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=== Flux balance Analysis ===
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;Analysis title
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:[[File:Differential-algebraic-equations-Flux-Balance-Constraint-icon.png]] Flux Balance Constraint
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;Provider
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:[[Institute of Systems Biology]]
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;Class
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:{{Class|biouml.plugins.fbc.analysis.FbcAnalysis}}
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;Plugin
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:[[Biouml.plugins.fbc (plugin)|biouml.plugins.fbc (Flux Balance)]]
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=== Flux Balance Analysis ===
  
 
Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network.
 
Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network.
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Metabolic reactions are represented as a stoichiometric matrix ''S''. The flux through all of the reactions in a network is represented by the vector ''v''. Flux Balance Analysis seeks to maximize or minimize an objective function ''Z = c<sup>T</sup>v'', which can be any linear combination of fluxes, where ''c'' is a vector of weights, indicating how much each reaction contributes to the objective function. FBA can thus be defined as the use of linear programming to solve the equation ''Sv = 0'' given a set of upper and lower bounds on ''v'' and a linear combination of fluxes as an objective function.
 
Metabolic reactions are represented as a stoichiometric matrix ''S''. The flux through all of the reactions in a network is represented by the vector ''v''. Flux Balance Analysis seeks to maximize or minimize an objective function ''Z = c<sup>T</sup>v'', which can be any linear combination of fluxes, where ''c'' is a vector of weights, indicating how much each reaction contributes to the objective function. FBA can thus be defined as the use of linear programming to solve the equation ''Sv = 0'' given a set of upper and lower bounds on ''v'' and a linear combination of fluxes as an objective function.
  
# Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, "What is flux balance analysis?". Nature Biotechnology 28, 245–248 2010.
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==== Parameters: ====
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* '''Diagram''' – Path to input diagram
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* '''Data table''' – Path to the table with initial FBC data (bounds, objective function coefficients)
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* '''Output path''' – Path to table with fluxes values
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* '''Optimization type''' (expert) – Type of objective function optimization which will be used (maximize or minimize)
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* '''Solver type''' (expert) – Type of the solver which will be used to find fluxes
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* '''Max iter''' (expert) – Maximal iteration number
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One should use '''Building Flux Balance DataTable''' or '''Score based FBC table builder''' analyses to generate FBC data table.
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==== Example ====
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FBC syntax example: a simple four reaction pathway. The reactions are ''R1, R2, X1, X2'' with fixed species ''IN, OUT, ATP, NADH'' and variable species ''A, B''.
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:: [[File:Differential-algebraic-equations-Flux-Balance-Constraint-fbc_1.png]]
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Using the reagent identity and stoichiometry it is possible to compactly describe this network in terms of its reaction stoichiometry:
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:: [[File:Differential-algebraic-equations-Flux-Balance-Constraint-fbc_2.png]]
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:: [[File:Differential-algebraic-equations-Flux-Balance-Constraint-fbc_3.png]]
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There are capacity constraints in this example:
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:: [[File:Differential-algebraic-equations-Flux-Balance-Constraint-fbc_4.png]]
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In this example the flux through reaction ''R2'' will be maximized. Solving this we find that maximization of flux through ''R2'' gives an optimal solution ''R2 = 1'' with one possible solution for ''v''.
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:: [[File:Differential-algebraic-equations-Flux-Balance-Constraint-fbc_5.png]]
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# Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, "What is flux balance analysis?". Nature Biotechnology 28, 245-248 2010.
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# [http://identifiers.org/combine.specifications/sbml.level-3.version-1.fbc.version-1.release-1 SBML Level 3 Package Specification]
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:DAE models (analyses group)]]
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[[Category:Differential algebraic equations (analyses group)]]
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[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:14, 9 December 2020

Analysis title
Differential-algebraic-equations-Flux-Balance-Constraint-icon.png Flux Balance Constraint
Provider
Institute of Systems Biology
Class
FbcAnalysis
Plugin
biouml.plugins.fbc (Flux Balance)

[edit] Flux Balance Analysis

Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network.

Metabolic reactions are represented as a stoichiometric matrix S. The flux through all of the reactions in a network is represented by the vector v. Flux Balance Analysis seeks to maximize or minimize an objective function Z = cTv, which can be any linear combination of fluxes, where c is a vector of weights, indicating how much each reaction contributes to the objective function. FBA can thus be defined as the use of linear programming to solve the equation Sv = 0 given a set of upper and lower bounds on v and a linear combination of fluxes as an objective function.

[edit] Parameters:

  • Diagram – Path to input diagram
  • Data table – Path to the table with initial FBC data (bounds, objective function coefficients)
  • Output path – Path to table with fluxes values
  • Optimization type (expert) – Type of objective function optimization which will be used (maximize or minimize)
  • Solver type (expert) – Type of the solver which will be used to find fluxes
  • Max iter (expert) – Maximal iteration number

One should use Building Flux Balance DataTable or Score based FBC table builder analyses to generate FBC data table.

[edit] Example

FBC syntax example: a simple four reaction pathway. The reactions are R1, R2, X1, X2 with fixed species IN, OUT, ATP, NADH and variable species A, B.

Differential-algebraic-equations-Flux-Balance-Constraint-fbc 1.png

Using the reagent identity and stoichiometry it is possible to compactly describe this network in terms of its reaction stoichiometry:

Differential-algebraic-equations-Flux-Balance-Constraint-fbc 2.png
Differential-algebraic-equations-Flux-Balance-Constraint-fbc 3.png

There are capacity constraints in this example:

Differential-algebraic-equations-Flux-Balance-Constraint-fbc 4.png

In this example the flux through reaction R2 will be maximized. Solving this we find that maximization of flux through R2 gives an optimal solution R2 = 1 with one possible solution for v.

Differential-algebraic-equations-Flux-Balance-Constraint-fbc 5.png
  1. Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, "What is flux balance analysis?". Nature Biotechnology 28, 245-248 2010.
  2. SBML Level 3 Package Specification
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