FBA Constraint
Variation-Reaction Deletion
This process is used to compute the effects of varying the
constraints in a stoichiometric network while simultaneously deleting sets of
reactions. 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 reaction names contained
in the specified reaction deletion file are retrieved, and
the fluxes of their corresponding reactions 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 reaction names is
present in the reaction 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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