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The BiGG Models website server
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"copy" reactions in BiGG models #296

Closed acenieuw closed 5 years ago

acenieuw commented 6 years ago

Hi,

I am analysing pipelines to construct metabolic models and comparing the outcome to established BiGG models. However, I've noticed that in some models (for example model iNF517) "copy" reactions are present. So reactions that are called "reactionname_copy1" and "reactionname_copy2". There is no difference in gene protein association with the original gene and the second copy nor is there a difference with stoichiometrics.

What is the purpose of a copy gene?

zakandrewking commented 6 years ago

sorry it's not well documented. When the same reaction appears multiple times in a model, then we have to append this _copy# to it on export. BiGG wants to ensure that identical reactions get merged together, but we keep the multiple copies because they often have different bounds and gene reaction rules that we cannot merge without changing the way the model simulates

let me know if that makes sense

zakandrewking commented 6 years ago

TODO documentation