add more metabolite in the medium

[chengyong-jia777]

Hi,

I am just intersted in the MICOM. I found that the metabolic flux is really dependent on the medium table you input. I used the American diet as medium to get the metabolite flux. But I want to add more metabolite flux beside these metabolites such as more bile acids. I checked the code in https://github.com/micom-dev/media/blob/main/recipes/vmh_eu_average.ipynb. I just found the flux for

"# mucin
for met in annotations.loc[annotations.metabolite.str.contains("core"), "metabolite"]:
diet.loc[met, "flux"] = 1

primary BAs

for met in ["gchola", "tchola"]:
diet.loc[met, "flux"] = 1

fiber

diet.loc["cellul", "flux"] = 0.1

anaerobic

diet.loc["o2", "flux"] = 0.001

diet.reset_index(inplace=True)
diet["reaction"] = "EX_" + diet.metabolite + "(e)"
diet"

is really abritory. Could you please let me if I want to add more metabolite beside the medium in the list. Could I just added the metabolite flux arbitory? I think it is really not easy to understand. Anyway, thanks for the great contribution on the method.

Best,
Joshua Jia