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LCSB-BioCore
COBREXA.jl
Commits
870f492f
Commit
870f492f
authored
Aug 16, 2021
by
Miroslav Kratochvil
Browse files
fix the remove_reaction plurality in notebook
parent
6f7d15c0
Pipeline
#45434
passed with stages
in 28 minutes and 49 seconds
Changes
1
Pipelines
1
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Side-by-side
docs/src/notebooks/7_community_model.jl
View file @
870f492f
...
...
@@ -26,15 +26,15 @@ using Tulip
base_model
=
load_model
(
CoreModel
,
"e_coli_core.json"
)
# base from from which the knockouts will be constructed
cytbd_knockout_model
=
remove_reaction
s
(
base_model
,
"CYTBD"
)
# knockout the CYTBD (cytochrome oxidase) reaction
cytbd_knockout_model
=
remove_reaction
(
base_model
,
"CYTBD"
)
# knockout the CYTBD (cytochrome oxidase) reaction
sol
=
flux_balance_analysis_dict
(
cytbd_knockout_model
,
Tulip
.
Optimizer
)
sol
[
"BIOMASS_Ecoli_core_w_GAM"
]
# Cytochrome oxidase knockout μ (growth rate)
#
atps4r_knockout_model
=
remove_reaction
s
(
base_model
,
"ATPS4r"
)
# knockout the ATP synthase reaction
atps4r_knockout_model
=
remove_reaction
(
base_model
,
"ATPS4r"
)
# knockout the ATP synthase reaction
sol
=
flux_balance_analysis_dict
(
atps4r_knockout_model
,
Tulip
.
Optimizer
)
sol
[
"BIOMASS_Ecoli_core_w_GAM"
]
# ATP synthase knockout μ
#
eno_knockout_model
=
remove_reaction
s
(
base_model
,
"ENO"
)
# knockout the enolase reaction
eno_knockout_model
=
remove_reaction
(
base_model
,
"ENO"
)
# knockout the enolase reaction
sol
=
flux_balance_analysis_dict
(
eno_knockout_model
,
Tulip
.
Optimizer
)
sol
[
"BIOMASS_Ecoli_core_w_GAM"
]
# Enolase knockout μ, cannot grow by itself
...
...
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