Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
LCSB-BioCore
COBREXA.jl
Commits
f780aee0
Commit
f780aee0
authored
Oct 13, 2021
by
Miroslav Kratochvil
Browse files
slight rewording/commenting
parent
68c02401
Pipeline
#48276
passed with stages
in 8 minutes and 26 seconds
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
README.md
View file @
f780aee0
...
@@ -127,14 +127,17 @@ m = convert(StandardModel, m)
...
@@ -127,14 +127,17 @@ m = convert(StandardModel, m)
# find the model objective value if oxygen and carbon dioxide transports are disabled
# find the model objective value if oxygen and carbon dioxide transports are disabled
screen
(
m
,
screen
(
m
,
# this specifies how to generate the desired model variants
variants
=
[
variants
=
[
[],
# no modifications
[],
#
one with
no modifications
[
with_changed_bound
(
"O2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable oxygen
[
with_changed_bound
(
"O2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable oxygen
[
with_changed_bound
(
"CO2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable CO2
[
with_changed_bound
(
"CO2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable CO2
[
with_changed_bound
(
"O2t"
,
lower
=
0.0
,
upper
=
0.0
),
[
with_changed_bound
(
"O2t"
,
lower
=
0.0
,
upper
=
0.0
),
with_changed_bound
(
"CO2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable both
with_changed_bound
(
"CO2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable both
],
],
analysis
=
x
->
flux_balance_analysis_dict
(
x
,
Tulip
.
Optimizer
)[
"BIOMASS_Ecoli_core_w_GAM"
],
# this specifies what to do with the model variants (received as the argument `x`)
analysis
=
x
->
flux_balance_analysis_dict
(
x
,
Tulip
.
Optimizer
)[
"BIOMASS_Ecoli_core_w_GAM"
],
)
)
```
```
You should receive a result showing that missing oxygen transport makes the
You should receive a result showing that missing oxygen transport makes the
...
@@ -164,17 +167,17 @@ worker_list = workers()
...
@@ -164,17 +167,17 @@ worker_list = workers()
# run the processing in parallel for many model variants
# run the processing in parallel for many model variants
res
=
screen
(
m
,
res
=
screen
(
m
,
variants
=
[
variants
=
[
#
specify
one variant for each reaction in the model, with that reaction knocked out
#
create
one variant for each reaction in the model, with that reaction knocked out
[
with_changed_bound
(
reaction_id
,
lower
=
0.0
,
upper
=
0.0
)]
[
with_changed_bound
(
reaction_id
,
lower
=
0.0
,
upper
=
0.0
)]
for
reaction_id
in
reactions
(
m
)
for
reaction_id
in
reactions
(
m
)
],
],
analysis
=
model
->
begin
analysis
=
model
->
begin
# we need to check if the
model
even found a feasible solution,
which
# we need to check if the
optimizer
even found a feasible solution,
# may not be the case if we knock out important reactions
#
which
may not be the case if we knock out important reactions
sol
=
flux_balance_analysis_dict
(
model
,
Tulip
.
Optimizer
)
sol
=
flux_balance_analysis_dict
(
model
,
Tulip
.
Optimizer
)
isnothing
(
sol
)
?
nothing
:
sol
[
"BIOMASS_Ecoli_core_w_GAM"
]
isnothing
(
sol
)
?
nothing
:
sol
[
"BIOMASS_Ecoli_core_w_GAM"
]
end
,
end
,
# run the screening in parallel on all workers
from
the list
# run the screening in parallel on all workers
in
the list
workers
=
worker_list
,
workers
=
worker_list
,
)
)
```
```
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment