Closed ae-tafur closed 7 months ago
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Running geckoCoreFunctionTests
Done geckoCoreFunctionTests
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as suggested by @edkerk, gene essentially now is considered if growth is < 1e-8.
Main improvements in this PR:
FSEOF implementation in GECKO 2 in summary fix % of the maximum growth and forced the rest of the carbon source towards product target. Nevertheless, original implementation (https://doi.org/10.1128/AEM.00115-10), same as RAVEN have, is the opposite. A maximum theoretical product is calculated, then this value is fixed to a different % of it, to further maximize the growth. Then, here FSEOF implementation is refactored to follow same as RAVEN since the cell will always have growth as objective.
Now:
alpha (values to fix target production) vector from the minimum production to 90% of the maximum theoretical yield, in n steps defined by the user.
k_score (mean of fold changes) is not longer calculated, then an slope value is calculated for each reaction which always increase or decrease while enforcing the objective
Actions are suggested for reactions and gene targets. OE (ever expression) for those reaction that always increase; KD, for those that always decrease; KO, for those that always decrease but in the las step (90% of the maximum theoretical yield) are zero.
Transport reactions, defined as reactions involving (at least) one metabolite name in more than one compartment. are reported in a new table.
Gene targets predicted are checked for gene essentiality while maximizing growth and product target production.
Instructions on merging this PR:
develop
as target branch, and will be resolved with a squash-merge.main
as target branch, and will be resolved with a merge commit.