Comments (1)
Dear Baudoin,
thank you very much for your question. While it is true that SBML is a very powerful language, it is indeed lacking essential elements that are necessary for 13C MFA. These include, on the structural level, the atom transitions and, on a quantitative level, measurement information. For both, precise syntactical specifications are absolutely crucial. Also, the extremely useful paradigm of “configurations” does not exist in SBML. More about our reasoning is detailed in our paper
To get a better understanding of how small the common denominator between SBML and FluxML is, I suggest to take a FluxML Model with several configurations (e.g. the model from the Parallel Labeling Experiments section of th paper, right before the multiply_fml.py script is applied), convert it to SBML, convert it back to FluxML and compare with the original file.
So there was no technical issue with SBML, it is more about how reasonable it is to write an SBML package for 13C MFA. In conclusion we are not planning to create such an SBML package.
Martin
from fluxml.
Related Issues (19)
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