FBA Constraint
Variation-Catalyst Deletion
This process is used to compute the effects of varying the
constraints in a stoichiometric network while simultaneously deleting
sets of catalysts. The following steps are executed during this
process:
1. |
If a constraints file is
specified, the flux constraints it contains are applied. |
2. |
An output file is opened with the next
name specified in the output file name file. |
3. |
The next set of flux constraints contained
in the constraint variation file are applied. These
constraints will override any pre-existing constraints. |
4. |
The next set of catalyst names contained
in the specified catalyst deletion file are retrieved, and
the fluxes of the reactions for which they are required are
constrained to the interval [0, 0]. These constraints must not
conflict with the current set of constraints from the constraint
variation file, or else the process will halt prematurely. |
5. |
The specified objective function is
optimized in the specified direction, and the results are written to
the next line of the current output file. |
6. |
If another set of catalyst names is
present in the catalyst deletion file, Steps 4 and 5 are
repeated. |
7. |
The current output file is closed, and the
flux constraints are returned to the state achieved immediately
after Step 1. |
8. |
If another set of flux constraints is
present in the constraint variation file, Steps 2-7 are
repeated. |
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.
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