Skip to content

Commit

Permalink
cleanup wording
Browse files Browse the repository at this point in the history
  • Loading branch information
exaexa committed Nov 22, 2024
1 parent a4dd3b3 commit 89461ba
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion docs/src/examples/05g-gapfilling.jl
Original file line number Diff line number Diff line change
@@ -103,7 +103,7 @@ x2 = gap_filling_analysis(
other_filled_reactions = [k for (k, v) in x2.fill_flags if v != 0]

#md # !!! warning "Why is the gapfilling algorithm adding seemingly unneeded reactions?"
#md # By default, COBREXA does not do any "cleaning" on the universal model; all reactions that are present in that model will be potentially utilized in the new model, and all of them will need to respect their original bounds in the universal model. That becomes an issue with **reactions that are bounded to non-zero flux** (such as the `ATPM` reaction in the E. coli "core" model) -- since their flux is marked as necessarily non-zero to make any model feasible; they will need to be in the fill set, because otherwise their flux would be equal zero.
#md # By default, COBREXA does not do any "cleaning" on the universal model; all reactions that are present in that model will be potentially utilized in the new model, and all of them will need to respect their original bounds in the universal model. That becomes an issue with **reactions that are bounded to non-zero flux** (such as the `ATPM` reaction in the E. coli "core" model) -- since their flux is required to be non-zero in any feasible model solution, they will also need to be in the fill set, because otherwise their flux would be zero.
#md #
#md # As the simplest solution, all realistic uses of gapfilling should carefully check the set of universal reactions, and ideally exclude all exchanges and pseudoreactions.

0 comments on commit 89461ba

Please sign in to comment.