> 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. |