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LCSB-BioCore
COBREXA.jl
Commits
30ad20fb
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Commit
30ad20fb
authored
Oct 13, 2021
by
St. Elmo
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small changes to readme
parent
f6d84a8c
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#48294
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README.md
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30ad20fb
...
...
@@ -118,18 +118,17 @@ Dict{String,Float64} with 95 entries:
#### Model variant processing
The main feature of COBREXA.jl is the ability to easily specify and process
many analyses
at once,
in parallel.
L
et's see how the organism would perform if
some reactions were disabled:
many analyses in parallel.
To demonstrate, l
et's see how the organism would perform if
some reactions were disabled
independently
:
```
julia
# convert to a model type that is e
asy
to modify
# convert to a model type that is e
fficient
to modify
m
=
convert
(
StandardModel
,
m
)
# find the model objective value if oxygen and carbon dioxide transports are disabled
screen
(
m
,
# this specifies how to generate the desired model variants
variants
=
[
[],
# one with no modifications
# find the model objective value if oxygen or carbon dioxide transports are disabled
screen
(
m
,
# the base model
variants
=
[
# this specifies how to generate the desired model variants
[],
# one with no modifications, i.e. the base case
[
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
(
"O2t"
,
lower
=
0.0
,
upper
=
0.0
),
...
...
@@ -151,8 +150,10 @@ biomass production much harder:
```
Most importantly, such analyses can be easily specified by automatically
generating long lists of the modifications to apply to the model, and
parallelized:
generating long lists of modifications to be applied to the model, and
parallelized.
Knocking out each reaction in the model is efficiently accomplished:
```
julia
# load the task distribution package, add several worker nodes, and load
...
...
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