View source for Flux Balance Constraint (analysis)

;Analysis title
:[[File:Default-analysis-icon.png]] Flux Balance Constraint
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.fbc.analysis.FbcAnalysis}}
;Plugin
:[[Biouml.plugins.fbc (plugin)|biouml.plugins.fbc (Flux Balance)]]

=== 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 = 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.

==== Parameters: ====

* '''Diagram path''' – Path to input diagram
* '''Data Table Path''' – Path to FBC data table
* '''Result path''' – Path to resulting element
* '''Type Objective Function''' (expert) – TypeObjectiveFunction

==== 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''.

:: [[File:DAE-models-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:

:: [[File:DAE-models-Flux-Balance-Constraint-fbc_2.png]]

:: [[File:DAE-models-Flux-Balance-Constraint-fbc_3.png]]

There are capacity constraints in this example:

:: [[File:DAE-models-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''.

:: [[File:DAE-models-Flux-Balance-Constraint-fbc_5.png]]

# Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, "What is flux balance analysis?". Nature Biotechnology 28, 245–248 2010.
# [http://identifiers.org/combine.specifications/sbml.level-3.version-1.fbc.version-1.release-1 SBML Level 3 Package Specification]

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