> User's Guide
Flux Balance Analysis

The term flux balance analysis is used here to refer to the study of the equation Sv = 0, where S denotes a stoichiometry matrix and v denotes a vector of fluxes.



Process Categories Brief Descriptions
Optimization Used to compute the optimal values of objective functions in various ways.
Flux Variability Used to compute the variability of fluxes in various ways.
Pathway Identification Used to identify reaction pathways.
Flux Space Sampling Used to create and sample flux spaces in various ways.
Data Analysis Used to analyze various FBA data sets.
Utilities Used to perform useful tasks.
Definitions Brief Descriptions
Flux Space The set of flux vectors that satisfy all of the constraints defined for the system Sv = 0.
Stoichiometric Equivalence Equivalent representations of chemical reactions.
Files Brief Descriptions
FBA Reaction Files Used to store all of the reactions of a stoichiometric network.
Reaction-Catalyst Association Files Used to store reaction-catalyst associations for a stoichiometric network.
Constraints Files Used to store a single set of flux constraints.
Constraint Variation Files Used to store multiple sets of flux constraints.
FBA Single-Optimization Output Files Used to store the results of a single optimization.
FBA Multiple-Optimizations Output Files Used to store the results of multiple optimizations.
Objective Function Files Used to store a list of objective functions.
Catalyst Name Files Used to store sets of catalyst names.
Reaction Name Files Used to store sets of reaction names.
Equivalent Reaction Files Used to store the names of stoichiometrically equivalent reactions.
Single-Flux Vector Files Used to store a single flux vector.
Multiple-Flux Vectors Files Used to store multiple flux vectors.
Single-Flux Interval Vector Files Used to store a single vector of flux intervals.
Multiple-Flux Interval Vectors Files Used to store multiple vectors of flux intervals.
Miscellaneous Brief Descriptions
FBA Objective Functions The objective functions used in Flux Balance Analysis.
Reaction Name Data Headers The data headers of output files used by many FBA processes.
FBA Optimization Data Headers The data headers of FBA optimization output files.
Safety Levels Used for error checking.
Constraint Tolerances Used for error checking.
Zero Cutoffs Used for error checking.
Pseudo-Random Number Generator Seeds Used for generating pseudo-random numbers.