Build Metabolic ModelΒΆ
[1]:
import modelseedpy
from modelseedpy import MSBuilder, MSGenome
[2]:
genome = MSGenome.from_fasta('GCF_000005845.2_ASM584v2_protein.faa', split=' ')
[3]:
print('Number of features:', len(genome.features))
Number of features: 4285
[4]:
from modelseedpy.helpers import get_template
from modelseedpy.core.mstemplate import MSTemplateBuilder
template = MSTemplateBuilder.from_dict(get_template('template_core')).build()
template
[4]:
| ID | CoreModelTemplateV2 |
| Memory address | 0x07fcbc3ca95e0 |
| Number of metabolites | 161 |
| Number of species | 187 |
| Number of reactions | 197 |
| Number of biomasses | 2 |
| Number of roles | 20552 |
| Number of complexes | 9423 |
[5]:
model = MSBuilder.build_metabolic_model('ecoli.core', genome, gapfill_media=None, template=template, allow_all_non_grp_reactions=True, annotate_with_rast=True)
model
[5]:
| Name | ecoli.core |
| Memory address | 0x07fcbc00f94c0 |
| Number of metabolites | 148 |
| Number of reactions | 155 |
| Number of groups | 0 |
| Objective expression | 1.0*bio1 - 1.0*bio1_reverse_b18f7 |
| Compartments | c0, e0 |
[6]:
model.objective = 'bio1'
model.medium = {
'EX_cpd00067_e0': 1000,
'EX_cpd00027_e0': 1,
'EX_cpd00007_e0': 1000,
'EX_cpd00001_e0': 1000,
'EX_cpd00009_e0': 1000,
}
model.summary()
[6]:
Objective
1.0 bio1 = 0.05181669326590254
Uptake
| Metabolite | Reaction | Flux | C-Number | C-Flux |
|---|---|---|---|---|
| cpd00007_e0 | EX_cpd00007_e0 | 4.049 | 0 | 0.00% |
| cpd00009_e0 | EX_cpd00009_e0 | 0.2184 | 0 | 0.00% |
| cpd00027_e0 | EX_cpd00027_e0 | 1 | 6 | 100.00% |
Secretion
| Metabolite | Reaction | Flux | C-Number | C-Flux |
|---|---|---|---|---|
| cpd00001_e0 | EX_cpd00001_e0 | -4.656 | 0 | 0.00% |
| cpd00011_e0 | EX_cpd00011_e0 | -3.684 | 1 | 100.00% |
| cpd00067_e0 | EX_cpd00067_e0 | -0.737 | 0 | 0.00% |
| cpd11416_c0 | SK_cpd11416_c0 | -0.05182 | 0 | 0.00% |
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