Standard FBA example¶
[1]:
import cobra
from cobra.flux_analysis import (
single_gene_deletion, single_reaction_deletion, double_gene_deletion,
double_reaction_deletion)
from cobra.flux_analysis.parsimonious import pfba
import cobrakbase
import escher
from escher import Builder
from modelseedpy import MSPackageManager,FBAHelper
cobrakbase 0.2.8
[2]:
kbase_api = cobrakbase.KBaseAPI()
model = kbase_api.get_from_ws("E_iML1515.kb",40576)
media = kbase_api.get_from_ws("Btheta_Ecoli_minimal_media",40576)
pkgmgr = MSPackageManager.get_pkg_mgr(model)
pkgmgr.getpkg("KBaseMediaPkg").build_package(media)
FBAHelper.set_objective_from_target_reaction(model, "bio1")
solution=model.optimize()
model.summary()
[2]:
Objective
1.0 bio1 = 0.1680011696126881
Uptake
| Metabolite | Reaction | Flux | C-Number | C-Flux |
|---|---|---|---|---|
| cpd00009_e0 | EX_cpd00009_e0 | 0.1621 | 0 | 0.00% |
| cpd00013_e0 | EX_cpd00013_e0 | 1.814 | 0 | 0.00% |
| cpd00027_e0 | EX_cpd00027_e0 | 5 | 6 | 100.00% |
| cpd00030_e0 | EX_cpd00030_e0 | 0.0001161 | 0 | 0.00% |
| cpd00034_e0 | EX_cpd00034_e0 | 5.729E-05 | 0 | 0.00% |
| cpd00048_e0 | EX_cpd00048_e0 | 0.04231 | 0 | 0.00% |
| cpd00058_e0 | EX_cpd00058_e0 | 0.0001191 | 0 | 0.00% |
| cpd00063_e0 | EX_cpd00063_e0 | 0.0008744 | 0 | 0.00% |
| cpd00099_e0 | EX_cpd00099_e0 | 0.0008744 | 0 | 0.00% |
| cpd00149_e0 | EX_cpd00149_e0 | 4.2E-06 | 0 | 0.00% |
| cpd00205_e0 | EX_cpd00205_e0 | 0.03279 | 0 | 0.00% |
| cpd00244_e0 | EX_cpd00244_e0 | 5.426E-05 | 0 | 0.00% |
| cpd00254_e0 | EX_cpd00254_e0 | 0.001457 | 0 | 0.00% |
| cpd10515_e0 | EX_cpd10515_e0 | 0.001387 | 0 | 0.00% |
| cpd10516_e0 | EX_cpd10516_e0 | 0.001312 | 0 | 0.00% |
| cpd11574_e0 | EX_cpd11574_e0 | 1.176E-06 | 0 | 0.00% |
Secretion
| Metabolite | Reaction | Flux | C-Number | C-Flux |
|---|---|---|---|---|
| cpd01042_c0 | DM_cpd01042_c0 | -3.746E-05 | 7 | 0.00% |
| cpd15380_c0 | DM_cpd15380_c0 | -0.0001127 | 5 | 0.00% |
| cpd00001_e0 | EX_cpd00001_e0 | -0.7985 | 0 | 0.00% |
| cpd00029_e0 | EX_cpd00029_e0 | -3.722 | 2 | 32.22% |
| cpd00036_e0 | EX_cpd00036_e0 | -0.05605 | 4 | 0.97% |
| cpd00047_e0 | EX_cpd00047_e0 | -8.048 | 1 | 34.83% |
| cpd00067_e0 | EX_cpd00067_e0 | -13.43 | 0 | 0.00% |
| cpd00116_e0 | EX_cpd00116_e0 | -3.36E-07 | 1 | 0.00% |
| cpd00363_e0 | EX_cpd00363_e0 | -3.693 | 2 | 31.97% |
| cpd02701_c0 | SK_cpd02701_c0 | -3.36E-07 | 15 | 0.00% |
[5]:
deletion_results = cobra.flsingle_gene_deletion(model)
deletion_results
[5]:
| growth | status | |
|---|---|---|
| ids | ||
| (b1123) | 0.168001 | optimal |
| (b1134) | 0.168001 | optimal |
| (b0158) | 0.168001 | optimal |
| (b0775) | 0.000000 | optimal |
| (b1683) | 0.168001 | optimal |
| ... | ... | ... |
| (b4386) | 0.168001 | optimal |
| (b0867) | 0.168001 | optimal |
| (b1463) | 0.168001 | optimal |
| (b0688) | 0.168001 | optimal |
| (b1475) | 0.168001 | optimal |
1515 rows × 2 columns
[4]:
file = open('CentralCarbon.json',)
ccmap = file.read()
builder = Builder(map_json=ccmap)
builder.reaction_scale=[
{ "type": 'value', "value": 0, "color": '#dcdcdc', "size": 10 },
{ "type": 'value', "value": 0.000001, "color": '#9696ff', "size": 25 },
{ "type": 'value', "value": 1, "color": '#ff0000', "size": 35 },
{ "type": 'value', "value": 20, "color": '#209123', "size": 50 },
]
builder.model = model
builder.reaction_data = solution.fluxes
builder
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