> User's Guide > Flux Balance Analysis > Flux Space Sampling
Coordinate Direction Hit-and-Run Analysis

This process is used to generate random points in flux space. See the coordinate directions hit-and-run algorithm for additional information.

This process must be supplied with the following:

  1. An initial flux vector that lies in the interior of flux space. This can be obtained with the Initial Point Generator.
  2. The flux intervals for each reaction. This should be the same Flux Interval File that was supplied to the Initial Point Generator.
  3. The solution to Sv = 0. This can be obtained with the FBA System Solver if Mathematica is available. If Mathematica is not available, the Network Information Gatherer can be used to generate the system of equations corresponding to Sv = 0, so that the solution can be obtained with another program of your choice.

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.

It should be noted that this process uses many parameters, and the default values may be inappropriate in many situations. If inappropriate parameters are used, this process may fail to complete execution, or the generated points may not be uniformly distributed thoughout the flux space.

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 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 each flux in the specified stoichiometric network. See Single-Flux Interval Vector Files for further information.
Initial Point File The name of the file containing the initial flux vector from the interior of the defined flux space. See Single-Flux Vector 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 the specified output file.
Output File Name The desired name of the file to which the random flux vectors will be written. See Multiple-Flux Vectors Files for additional information.
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.
Zero Cutoff The zero cutoff for the coefficients of linear combinations.
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.

Examples

Click here for an example.