> User's Guide > Flux Balance Analysis > Flux Space Sampling
FBA Space Variation-Initial Point Generator

This process is used to generate initial points for algorithms that randomly sample flux vectors from the interior of multiple flux spaces. This process uses the initial point generation technique described in the geometry section of the User's Guide.

The flux intervals supplied to this process must be the intervals on which each flux truly lies. If they are not, the results produced by this process will be incorrect. For all but the simplest systems, these intervals must be computed beforehand using one of the flux variability processes. The flux space must also be bounded, so infinite lower or upper bounds on fluxes are not allowed. These restrictions result from the way in which the positioning space is created for each flux. The extreme points used to define each positioning space are:

(P, V)
( Pmax , Vmin )
( 1.0 , Vmin + 0.001 L )
( 0.5 , Vmin + 0.010 L )
( 0.1 , Vmin + 0.050 L )
( 0.0 , Vmin + 0.500 L )
( 0.1 , Vmin + 0.950 L )
( 0.5 , Vmin + 0.990 L )
( 1.0 , Vmin + 0.999 L )
( Pmax , Vmax )

where Vmin and Vmax are the lower and upper bounds on each flux, respectively, and L = Vmax - Vmin. If the range of a flux is zero, that is L = 0, a P-V space will not be created for it. The value for Pmax can be specified by the user, since the default value is sometimes too high for some linear program solvers. The largest value that still produces a feasible solution should be chosen.

Here is the set of keywords this process understands, along with a description of their possible corresponding values. See the command line documentation for more information about keyword-value pairs.


Required Keywords Possible Values
Process FBA Space Variation-Initial Point Generator
Reaction File The name of an FBA Reaction File containing a stoichiometric network.
Flux Interval File The name of a text file containing the intervals of fluxes from multiple flux spaces. See Multiple-Flux Interval Vectors Files for further information.
Program Solver The name of the program solver to be used to compute the minimum value of Σ Ci. See Program Solvers for further information.
Optional Keywords Possible Values
Flux Vector File Name The desired name of the file to which the computed flux vectors will be written. See Multiple-Flux Vectors Files for further information.
P Max The numerical value of positioning variables at the edges of the convex polytope. The default is 1E15.
Average C File Name The desired name of the file to which the average C values for each vector will be written.
Zero Cutoff The amount by which an upper and lower flux bound can differ, but their range still be considered zero. See Zero Cutoffs for further information.
Constraint Tolerance The amount by which the linear program solver is allowed to violate the defined flux intervals. See Constraint Tolerances for further information.
Safety Level The safety level at which the optimizations will be performed. See Safety Levels for further information.
Program Solver Parameter File The name of the file containing parameters for the linear program solver. See Program Solver Parameter Files for further information.

Examples

Click here for an example.