I am trying to figure out what the boundary compartment (c_01) is. It was not presented in the yeast_4.02 model, but appears in yeast_5.01 and is the only one having no GO annotations. I have looked at the reactions with the species of the boundary: there is the biomass growth reaction (cytoplasm -> boundary) and quite a few extracellular-to-boundary exchange reactions. I could not find any other reactions involving boundary species. In yeast_4.02 the biomass growth was a cytoplasm -> extracellular reaction, while those extracellular-to-boundary reactions were not present. I am wondering wether in fact the boundary is a fake, used to express boundary conditions for the optimization process? Or is it a real compartment? Is it outside of the cell envelope (between the cell envelope and the extracellular compartment)?
Thank you for your help,
Anna Zhukova
PhD student
Magnome team
Inria Bordeaux Sud-Ouest
351 cours de la Libération
33405 Talence Cedex – France
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Dear yeastnet developers,
I am trying to figure out what the boundary compartment (c_01) is. It was not presented in the yeast_4.02 model, but appears in yeast_5.01 and is the only one having no GO annotations. I have looked at the reactions with the species of the boundary: there is the biomass growth reaction (cytoplasm -> boundary) and quite a few extracellular-to-boundary exchange reactions. I could not find any other reactions involving boundary species. In yeast_4.02 the biomass growth was a cytoplasm -> extracellular reaction, while those extracellular-to-boundary reactions were not present. I am wondering wether in fact the boundary is a fake, used to express boundary conditions for the optimization process? Or is it a real compartment? Is it outside of the cell envelope (between the cell envelope and the extracellular compartment)?
Thank you for your help,
PhD student
Magnome team
Inria Bordeaux Sud-Ouest
351 cours de la Libération
33405 Talence Cedex – France