Load a few packages and functions.
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import pandas
pandas.options.display.max_rows = 12
import escher
from cameo import models, fba
from cameo.exceptions import Infeasible
First we load a model from the BiGG database (and make a copy of it).
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model = models.bigg.e_coli_core.copy()
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print(model.objective)
Run flux balance analysis.
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result = fba(model)
The predicted growth rate is $0.87 \ h^{-1}$.
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result.objective_value
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Take a look at the predicted metabolic fluxes.
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result.data_frame
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result.data_frame.describe()
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active_fluxes = result.data_frame[result.data_frame.flux != 0].sort_values(by='flux')
active_fluxes
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model.reactions.ATPS4r
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import escher
import jupyter
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escher.__version__
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!pip show jupyter
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escher.Builder('e_coli_core.Core metabolism', reaction_data=active_fluxes.flux.to_dict()).display_in_notebook()
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result.display_on_map('e_coli_core.Core metabolism')
model.genes.get_by_id('<geneID>').knock_out() where
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gene_essentiality = {}
for gene in model.genes:
mutant = model.copy()
mutant.genes.get_by_id(gene.id).knock_out()
try:
print(gene, fba(mutant).objective_value)
gene_essentiality[gene] = fba(mutant).objective_value
except Infeasible:
print(gene, 0)
gene_essentiality[gene] = 0
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