carrascomj / carrascomj/mmodes
MMODES is not able to recognise metabolites to plot in my GEM
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Description
I have been trying to use MMODES to do a simulation using my GEM tracking the acetate and propionate production over time. However when I try to run the model I get this error:
"Metabolite ac_e won't be plotted. Check your spelling of this metabolite.
Metabolite ppa_e won't be plotted. Check your spelling of this metabolite.
Metabolites weren't properly supplied in 'mets_to_plot' parameter. Plot won't be generated!"
I have used the exact same metabolite names as in the SBML file and I have used all different variations of the name as well already. The rest of my code looks like this:
"from mmodes import Consortium, dMetabolite
cons = Consortium(mets_to_plot = ['ac_e', 'ppa_e'])
glc = dMetabolite(id = 'glc__D_e', Km = 14.8, Vmax = 0.13)
path_to_model = "C:/Users/Sam/Jupyter notebooks/prevotella_ruminicola_1_v7_biomass.xml"
cons.add_model(path_to_model, 0.03, dMets = {glc.id: glc})
medium = {'ala__L_e': 0.938846598,
'arab__L_e': 0.666427627,
'arg__L_e': 0.133660701,
'asn__L_e': 0.400330802,
'ca2_e': 1000,
'cl_e': 1000,
'cobalt2_e': 1000,
'cu2_e': 1000,
'cys__L_e': 0.114920408,
'fe2_e': 1000,
'fe3_e': 1000,
'gal_e': 0.075513967,
'glc__D_e': 2.725243655,
'gln__L_e': 0.080568485,
'glu__L_e': 1.597816364,
'glucan4_e': 0.320930655,
'gly_e': 0.268595078,
'h2_e': 1000,
'h2o_e': 1000,
'h2s_e': 1000,
'h_e': 1000,
'his__L_e': 0.124559013,
'ile__L_e': 0.211165444,
'k_e': 1000,
'leu__L_e': 1.148366562,
'lys__L_e': 0.098373937,
'met__L_e': 0.233929798,
'mg2_e': 1000,
'mn2_e': 1000,
'nh4_e': 1000,
'no2_e': 1000,
'no3_e': 1000,
'phe__L_e': 0.310015056,
'pi_e': 0.005244478,
's_e': 1000,
'ser__D_e': 0.317276246,
'so3_e': 1000,
'so4_e': 0.004273279,
'thr__L_e': 0.261179221,
'tyr__L_e': 0.218417727,
'urea_e': 0.629166662,
'val__L_e': 0.385856944,
'xyl__D_e': 0.877945961,
'zn2_e': 1000,
'sucr_e': 0.834726132,
'lnlc_e': 0.610370885,
'gtp_e': 0.007734655,
'man_e': 0.021731242,
'ctp_e': 0.00730785,
'atp_e': 0.006289719,
'utp_e': 0.005932755,
'datp_e': 0.001147315,
'dttp_e': 0.001147552,
'dgtp_e': 0.001012678,
'dctp_e': 0.001016235, 'ac_e' : 0, 'ppa_e':0}
cons.media = cons.set_media(medium)
cons.run(maxT = 10, stepChoiceLevel = (0, 1, 10), outf = "output_test2.tsv", outp = "plot_test2.png", verbose=True)"
How can I fix this? Thank you in advance!
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