KBase COBRA Model¶
[2]:
import cobra
import logging
import cobrakbase
logger = logging.getLogger(__name__)
[3]:
kbase = cobrakbase.KBaseAPI()
[4]:
ws = "filipeliu:narrative_1561151919387"
cobra_model = kbase.get_from_ws('GCF_000005845.2.gf.mdl', ws)
[5]:
cobra_model
[5]:
| Name | GCF_000005845.2.mdl |
| Memory address | 0x07f5c1b91be20 |
| Number of metabolites | 1287 |
| Number of reactions | 1566 |
| Number of groups | 0 |
| Objective expression | 1.0*bio1 - 1.0*bio1_reverse_b18f7 |
| Compartments | c0, e0 |
Run default FBA with solution of 298.498 (complete media)¶
[7]:
cobra_model.summary()
[7]:
Objective
1.0 bio1 = 298.49841109986005
Uptake
| Metabolite | Reaction | Flux | C-Number | C-Flux |
|---|---|---|---|---|
| cpd00007_e0 | EX_cpd00007_e0 | 973.9 | 0 | 0.00% |
| cpd00023_e0 | EX_cpd00023_e0 | 716.4 | 5 | 7.07% |
| cpd00024_e0 | EX_cpd00024_e0 | 1000 | 5 | 9.87% |
| cpd00030_e0 | EX_cpd00030_e0 | 0.9243 | 0 | 0.00% |
| cpd00034_e0 | EX_cpd00034_e0 | 0.9243 | 0 | 0.00% |
| cpd00039_e0 | EX_cpd00039_e0 | 85.2 | 6 | 1.01% |
| cpd00041_e0 | EX_cpd00041_e0 | 47.14 | 4 | 0.37% |
| cpd00048_e0 | EX_cpd00048_e0 | 0.9243 | 0 | 0.00% |
| cpd00051_e0 | EX_cpd00051_e0 | 73.64 | 6 | 0.87% |
| cpd00054_e0 | EX_cpd00054_e0 | 96 | 3 | 0.57% |
| cpd00058_e0 | EX_cpd00058_e0 | 0.9243 | 0 | 0.00% |
| cpd00063_e0 | EX_cpd00063_e0 | 0.9243 | 0 | 0.00% |
| cpd00065_e0 | EX_cpd00065_e0 | 14.09 | 11 | 0.31% |
| cpd00066_e0 | EX_cpd00066_e0 | 46.12 | 9 | 0.82% |
| cpd00069_e0 | EX_cpd00069_e0 | 36.02 | 9 | 0.64% |
| cpd00079_e0 | EX_cpd00079_e0 | 500 | 6 | 5.92% |
| cpd00080_e0 | EX_cpd00080_e0 | 1000 | 3 | 5.92% |
| cpd00099_e0 | EX_cpd00099_e0 | 0.9243 | 0 | 0.00% |
| cpd00106_e0 | EX_cpd00106_e0 | 992.5 | 4 | 7.84% |
| cpd00107_e0 | EX_cpd00107_e0 | 137.5 | 6 | 1.63% |
| cpd00118_e0 | EX_cpd00118_e0 | 0.9243 | 4 | 0.01% |
| cpd00119_e0 | EX_cpd00119_e0 | 23.66 | 6 | 0.28% |
| cpd00130_e0 | EX_cpd00130_e0 | 80.22 | 4 | 0.63% |
| cpd00149_e0 | EX_cpd00149_e0 | 0.9243 | 0 | 0.00% |
| cpd00156_e0 | EX_cpd00156_e0 | 105.1 | 5 | 1.04% |
| cpd00161_e0 | EX_cpd00161_e0 | 402.2 | 4 | 3.17% |
| cpd00182_e0 | EX_cpd00182_e0 | 43.14 | 10 | 0.85% |
| cpd00184_e0 | EX_cpd00184_e0 | 4.706 | 10 | 0.09% |
| cpd00205_e0 | EX_cpd00205_e0 | 0.9243 | 0 | 0.00% |
| cpd00254_e0 | EX_cpd00254_e0 | 0.9243 | 0 | 0.00% |
| cpd00264_e0 | EX_cpd00264_e0 | 0.9243 | 7 | 0.01% |
| cpd00268_e0 | EX_cpd00268_e0 | 12.75 | 0 | 0.00% |
| cpd00276_e0 | EX_cpd00276_e0 | 1000 | 6 | 11.84% |
| cpd00277_e0 | EX_cpd00277_e0 | 1000 | 10 | 19.74% |
| cpd00305_e0 | EX_cpd00305_e0 | 0.9243 | 12 | 0.02% |
| cpd00311_e0 | EX_cpd00311_e0 | 49.9 | 10 | 0.98% |
| cpd00322_e0 | EX_cpd00322_e0 | 72.18 | 6 | 0.85% |
| cpd00355_e0 | EX_cpd00355_e0 | 1.849 | 11 | 0.04% |
| cpd00367_e0 | EX_cpd00367_e0 | 178.4 | 9 | 3.17% |
| cpd00644_e0 | EX_cpd00644_e0 | 1.849 | 9 | 0.03% |
| cpd00794_e0 | EX_cpd00794_e0 | 483.8 | 12 | 11.46% |
| cpd01080_e0 | EX_cpd01080_e0 | 25.43 | 18 | 0.90% |
| cpd03847_e0 | EX_cpd03847_e0 | 44.79 | 14 | 1.24% |
| cpd10516_e0 | EX_cpd10516_e0 | 3.697 | 0 | 0.00% |
| cpd11590_e0 | EX_cpd11590_e0 | 39.07 | 8 | 0.62% |
| cpd15500_e0 | EX_cpd15500_e0 | 1.849 | 51 | 0.19% |
| cpd17041_c0 | rxn13782_c0 | 298.5 | 0 | 0.00% |
| cpd17042_c0 | rxn13783_c0 | 298.5 | 0 | 0.00% |
| cpd17043_c0 | rxn13784_c0 | 298.5 | 0 | 0.00% |
Secretion
| Metabolite | Reaction | Flux | C-Number | C-Flux |
|---|---|---|---|---|
| cpd00009_e0 | EX_cpd00009_e0 | -1000 | 0 | 0.00% |
| cpd00011_e0 | EX_cpd00011_e0 | -1000 | 1 | 2.57% |
| cpd00012_e0 | EX_cpd00012_e0 | -129.7 | 0 | 0.00% |
| cpd00033_e0 | EX_cpd00033_e0 | -168 | 2 | 0.86% |
| cpd00047_e0 | EX_cpd00047_e0 | -1000 | 1 | 2.57% |
| cpd00067_e0 | EX_cpd00067_e0 | -1000 | 0 | 0.00% |
| cpd00092_e0 | EX_cpd00092_e0 | -121.3 | 4 | 1.25% |
| cpd00100_e0 | EX_cpd00100_e0 | -467.5 | 3 | 3.60% |
| cpd00108_e0 | EX_cpd00108_e0 | -754.3 | 6 | 11.63% |
| cpd00117_e0 | EX_cpd00117_e0 | -562.5 | 3 | 4.34% |
| cpd00122_e0 | EX_cpd00122_e0 | -1000 | 8 | 20.56% |
| cpd00129_e0 | EX_cpd00129_e0 | -495.4 | 5 | 6.36% |
| cpd00137_e0 | EX_cpd00137_e0 | -1000 | 6 | 15.42% |
| cpd00139_e0 | EX_cpd00139_e0 | -2.773 | 2 | 0.01% |
| cpd00211_e0 | EX_cpd00211_e0 | -40.43 | 4 | 0.42% |
| cpd00222_e0 | EX_cpd00222_e0 | -1000 | 6 | 15.42% |
| cpd00226_e0 | EX_cpd00226_e0 | -1000 | 5 | 12.85% |
| cpd00396_e0 | EX_cpd00396_e0 | -74.09 | 6 | 1.14% |
| cpd01015_e0 | EX_cpd01015_e0 | -297.7 | 1 | 0.76% |
| cpd15499_e0 | EX_cpd15499_e0 | -1.849 | 51 | 0.24% |
| cpd11416_c0 | SK_cpd11416_c0 | -298.5 | 0 | 0.00% |
Get media object from KBase¶
cobrakbase.core.kbasebiochem.media.Media
[8]:
media = kbase.get_from_ws('Carbon-D-Glucose', ws)
print(type(media))
<class 'cobrakbase.core.kbasebiochem.media.Media'>
Run FBA with Carbon-D-Glucose media¶
FBAModel.medium = dict or Media
FBAModel.mediuminherits default cobra medium setter but also acceptscobrakbase.core.kbasebiochem.media.Media
[12]:
cobra_model.medium = media
cobra_model.summary()
[12]:
Objective
1.0 bio1 = 0.6971420881250999
Uptake
| Metabolite | Reaction | Flux | C-Number | C-Flux |
|---|---|---|---|---|
| cpd00009_e0 | EX_cpd00009_e0 | 0.5661 | 0 | 0.00% |
| cpd00013_e0 | EX_cpd00013_e0 | 5.975 | 0 | 0.00% |
| cpd00027_e0 | EX_cpd00027_e0 | 5 | 6 | 100.00% |
| cpd00030_e0 | EX_cpd00030_e0 | 0.002159 | 0 | 0.00% |
| cpd00034_e0 | EX_cpd00034_e0 | 0.002159 | 0 | 0.00% |
| cpd00048_e0 | EX_cpd00048_e0 | 0.1551 | 0 | 0.00% |
| cpd00058_e0 | EX_cpd00058_e0 | 0.002159 | 0 | 0.00% |
| cpd00063_e0 | EX_cpd00063_e0 | 0.002159 | 0 | 0.00% |
| cpd00099_e0 | EX_cpd00099_e0 | 0.002159 | 0 | 0.00% |
| cpd00149_e0 | EX_cpd00149_e0 | 0.002159 | 0 | 0.00% |
| cpd00205_e0 | EX_cpd00205_e0 | 0.002159 | 0 | 0.00% |
| cpd00254_e0 | EX_cpd00254_e0 | 0.002159 | 0 | 0.00% |
| cpd10516_e0 | EX_cpd10516_e0 | 0.008635 | 0 | 0.00% |
| cpd17041_c0 | rxn13782_c0 | 0.6971 | 0 | 0.00% |
| cpd17042_c0 | rxn13783_c0 | 0.6971 | 0 | 0.00% |
| cpd17043_c0 | rxn13784_c0 | 0.6971 | 0 | 0.00% |
Secretion
| Metabolite | Reaction | Flux | C-Number | C-Flux |
|---|---|---|---|---|
| cpd00001_e0 | EX_cpd00001_e0 | -17.75 | 0 | 0.00% |
| cpd00007_e0 | EX_cpd00007_e0 | -0.0216 | 0 | 0.00% |
| cpd00011_e0 | EX_cpd00011_e0 | -2.538 | 1 | 99.41% |
| cpd00067_e0 | EX_cpd00067_e0 | -4.865 | 0 | 0.00% |
| cpd15378_e0 | EX_cpd15378_e0 | -0.002159 | 7 | 0.59% |
| cpd11416_c0 | SK_cpd11416_c0 | -0.6971 | 0 | 0.00% |
[13]:
media.get_media_constraints()
[13]:
{'cpd00149_e0': (-100, 100),
'cpd00099_e0': (-100, 100),
'cpd00067_e0': (-100, 100),
'cpd00063_e0': (-100, 100),
'cpd00058_e0': (-100, 100),
'cpd00048_e0': (-100, 100),
'cpd00034_e0': (-100, 100),
'cpd00030_e0': (-100, 100),
'cpd00013_e0': (-100, 100),
'cpd00009_e0': (-100, 100),
'cpd00001_e0': (-100, 100),
'cpd00007_e0': (-10, 100),
'cpd00205_e0': (-100, 100),
'cpd00254_e0': (-100, 100),
'cpd00971_e0': (-100, 100),
'cpd10515_e0': (-100, 100),
'cpd10516_e0': (-100, 100),
'cpd11574_e0': (-100, 100),
'cpd00244_e0': (-100, 100),
'cpd00027_e0': (-5, 100)}
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