> User's Guide > Flux Balance Analysis > Flux Space Sampling |
FBA Space
Variation-Coordinate Direction Hit-and-Run Analysis
This process is used to generate random points in multiple flux spaces. See the coordinate directions hit-and-run algorithm for additional information. This process must be supplied with the following:
The random flux vectors generated by this process are the result of multiple "random walks" through flux space - one walk along the axis of each free variable. Stated differently, n walks are made through an n dimensional flux space (where n is the number of free variables) to create the next random point. Each random point can be written to a specified output file, or each i-th random point can be written using the optional points-per-point keyword. 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-CD Hit-and-Run |
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 defining multiple flux spaces. See Multiple-Flux Interval Vectors Files for further information. |
Initial Point File | The name of the file containing the initial flux vectors in the interiors of the provided flux spaces. See Multiple-Flux Vectors Files for further information. |
System Solution File | The solution to the system of linear equations formed by the specified stoichiometric network. See Linear System Solution Files for additional information. |
Iterations | The number of random flux vectors to be written to each of the specified output files. |
Output File Name File | The name of a file containing the desired names of the files to which the random flux vectors will be written. See File Name Files and Multiple-Flux Vectors Files for additional information. |
Obstructed Moves File Name | The desired name of the file to which the number of obstructed moves per flux space will be written. |
Optional Keywords | Possible Values |
Data Headers | The data headers of the specified output file. The default value is all reaction names. See Reaction Name Data Headers for further information. |
File Format | The desired format of the specified output file. The default value is Text. See File Formats for additional information. |
Constraint Tolerance | The amount by which a generated point may lay outside of the defined constraints. The default value is 1E-9. See Constraint Tolerances for more information. |
Points Per Point | The number of random points to generate for each point written to the specified output file. The default value is 1. |
Minimum Chord Length | The minimum length of an unobstructed direction. The default value is 1E-6. |
Seed | The seed for the pseudo-random number generator. The default value is the current time in milliseconds. |
Maximum Obstructed Moves | The number of obstructed moves to allow before the process is terminated prematurely. The default value is 0. |
ExamplesClick here for an example. |