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License: GNU General Public License v3.0

Python 99.66% Shell 0.34%
linear-programming answer-set-programming bioinformatics metabolic-models metabolic-network metabolic-reconstruction flux-balance-analysis gap-filling

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fluto's Issues

scope is not accurate for reactions with a shared metabolite in reactants and products

The following case leads to a more permissive scope than expected:

---> S # S is a seed/nutrient
S + I --> I + T

Because of N!=M in the scope rules, a reactant of a reaction does not have to be producible if it is also a product of the (same) reaction. It is more permissive than the strict Ebenhöh-Hendorf scope definition.

In the example above, the recycling of I would be allowed by default and all four compounds would be in the scope of S. The Ebenhöh-Hendorf scope definition expects only Sto be producible.

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