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BioSystemsUM / MEWpy

Metabolic Engineering Workbench
https://mewpy.readthedocs.io
GNU General Public License v3.0
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Kbase ModelSeed #16

Closed pg42866 closed 3 years ago

pg42866 commented 3 years ago

Boa tarde, Envio em anexo o modelo metabólico obtido pela app modelSeed na kbase, o qual segundo o FBA da plataforma indica um fluxo de biomassa de cerca de 19 em meio completo. Contudo, o mewpy indica "None" quando o objetivo definido é a biomassa. M_formicicum_complete_media.SBML (1).zip

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pg42866 commented 3 years ago

Acrescento ainda informação completar de acordo com os resultados obtidos no CobraPy, obrigado pela atenção.

M_formicicum_complete_media 62.564878115599804 Objective

1.0 bio1_biomass = 62.564878115599804

Uptake

Metabolite Reaction Flux C-Number C-Flux cpd00006_e0 EX_cpd00006_e0 0.3511 21 0.16% cpd00007_e0 EX_cpd00007_e0 643.9 0 0.00% cpd00009_e0 EX_cpd00009_e0 45.2 0 0.00% cpd00010_e0 EX_cpd00010_e0 0.3511 21 0.16% cpd00017_e0 EX_cpd00017_e0 17.72 15 5.65% cpd00023_e0 EX_cpd00023_e0 30.91 5 3.28% cpd00027_e0 EX_cpd00027_e0 208.4 6 26.57% cpd00028_e0 EX_cpd00028_e0 0.1756 34 0.13% cpd00030_e0 EX_cpd00030_e0 0.1756 0 0.00% cpd00033_e0 EX_cpd00033_e0 30.85 2 1.31% cpd00034_e0 EX_cpd00034_e0 0.1756 0 0.00% cpd00035_e0 EX_cpd00035_e0 28.34 3 1.81% cpd00039_e0 EX_cpd00039_e0 17.86 6 2.28% cpd00041_e0 EX_cpd00041_e0 345.7 4 29.39% cpd00048_e0 EX_cpd00048_e0 0.1756 0 0.00% cpd00051_e0 EX_cpd00051_e0 15.43 6 1.97% cpd00054_e0 EX_cpd00054_e0 14.41 3 0.92% cpd00058_e0 EX_cpd00058_e0 0.1756 0 0.00% cpd00063_e0 EX_cpd00063_e0 0.1756 0 0.00% cpd00065_e0 EX_cpd00065_e0 2.953 11 0.69% cpd00066_e0 EX_cpd00066_e0 9.667 9 1.85% cpd00067_e0 EX_cpd00067_e0 89.46 0 0.00% cpd00069_e0 EX_cpd00069_e0 7.55 9 1.44% cpd00084_e0 EX_cpd00084_e0 4.94 3 0.31% cpd00099_e0 EX_cpd00099_e0 0.1756 0 0.00% cpd00104_e0 EX_cpd00104_e0 0.1756 10 0.04% cpd00107_e0 EX_cpd00107_e0 23.49 6 3.00% cpd00118_e0 EX_cpd00118_e0 0.1756 4 0.01% cpd00119_e0 EX_cpd00119_e0 4.959 6 0.63% cpd00129_e0 EX_cpd00129_e0 11.53 5 1.23% cpd00132_e0 EX_cpd00132_e0 12.56 4 1.07% cpd00136_e0 EX_cpd00136_e0 0.1756 7 0.03% cpd00149_e0 EX_cpd00149_e0 0.1756 0 0.00% cpd00156_e0 EX_cpd00156_e0 22.04 5 2.34% cpd00161_e0 EX_cpd00161_e0 13.21 4 1.12% cpd00185_e0 EX_cpd00185_e0 4.694 5 0.50% cpd00205_e0 EX_cpd00205_e0 0.1756 0 0.00% cpd00216_e0 EX_cpd00216_e0 0.3511 10 0.07% cpd00220_e0 EX_cpd00220_e0 0.5267 17 0.19% cpd00254_e0 EX_cpd00254_e0 0.1756 0 0.00% cpd00264_e0 EX_cpd00264_e0 0.1756 7 0.03% cpd00305_e0 EX_cpd00305_e0 0.1756 12 0.04% cpd00322_e0 EX_cpd00322_e0 15.13 6 1.93% cpd00357_e0 EX_cpd00357_e0 1.178 10 0.25% cpd00393_e0 EX_cpd00393_e0 0.5267 19 0.21% cpd00731_e0 EX_cpd00731_e0 1.565 6 0.20% cpd01741_e0 EX_cpd01741_e0 1.565 12 0.40% cpd03847_e0 EX_cpd03847_e0 7.824 14 2.33% cpd10515_e0 EX_cpd10515_e0 0.5267 0 0.00% cpd15311_e0 EX_cpd15311_e0 7.794 39 6.46% cpd17041_c0 rxn13782_c0 62.56 0 0.00% cpd17042_c0 rxn13783_c0 62.56 0 0.00% cpd17043_c0 rxn13784_c0 62.56 0 0.00%

Secretion

Metabolite Reaction Flux C-Number C-Flux cpd11416_c0 DM_cpd11416_c0 -62.56 0 0.00% cpd00001_e0 EX_cpd00001_e0 -838.8 0 0.00% cpd00011_e0 EX_cpd00011_e0 -1000 1 44.64% cpd00013_e0 EX_cpd00013_e0 -280.8 0 0.00% cpd00029_e0 EX_cpd00029_e0 -588.5 2 52.54% cpd00047_e0 EX_cpd00047_e0 -7.538 1 0.34% cpd00060_e0 EX_cpd00060_e0 -9.549 5 2.13% cpd00116_e0 EX_cpd00116_e0 -7.714 1 0.34%

vmspereira commented 3 years ago

Olá pg42866,

Sugiro que em vez de carregar o modelo com o REFRAMED utilize o COBRApy. O REFRAMED pode ter tido alguma dificuldade em ler o modelo. Assim, a única alteração que terá de realizar no código em exemplo será, 

from cobra.io import read_sbml_model
model = read_sbml_model(PATH_TO_MODEL)

em vez de: 

from reframed.io.sbml import load_cbmodel
model = load_cbmodel(PATH_TO_MODEL,flavor='cobra')

Se de facto tiver preferência em utilizar o REFRAMED, poderá tentar carregar o modelo sem o parâmetro flavor='cobra' ou bem consultar a documentação do REFRAMED em https://reframed.readthedocs.io.