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LCSB-BioCore
COBREXA.jl
Commits
13ba1ee0
Unverified
Commit
13ba1ee0
authored
May 17, 2021
by
Miroslav Kratochvil
Browse files
switch README to Tulip
Closes
#232
parent
77c2927e
Pipeline
#41884
passed with stages
in 11 minutes and 57 seconds
Changes
1
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2
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README.md
View file @
13ba1ee0
...
...
@@ -69,7 +69,7 @@ add COBREXA
You also need to install your favorite solver supported by
`JuMP.jl`
, typing
e.g.:
```
add
GLPK
add
Tulip
```
When the packages are installed, switch back to the "normal" julia shell by
...
...
@@ -80,7 +80,7 @@ flux balance analysis as follows:
```
julia
using
COBREXA
# loads the package
using
GLPK
# loads the optimization solver
using
Tulip
# loads the optimization solver
# download the model
download
(
"http://bigg.ucsd.edu/static/models/e_coli_core.xml"
,
"e_coli_core.xml"
)
...
...
@@ -89,7 +89,7 @@ download("http://bigg.ucsd.edu/static/models/e_coli_core.xml", "e_coli_core.xml"
model
=
load_model
(
"e_coli_core.xml"
)
# run a FBA
fluxes
=
flux_balance_analysis_dict
(
model
,
GLPK
.
Optimizer
)
fluxes
=
flux_balance_analysis_dict
(
model
,
Tulip
.
Optimizer
)
```
The variable
`fluxes`
will now contain a dictionary of the computed optimal
...
...
@@ -104,7 +104,7 @@ Dict{String,Float64} with 95 entries:
"R_EX_pi_e" => -3.2149
"R_PPC" => 2.50431
"R_O2t" => 21.7995
"R_G6PDH2r" => 4.9599
8
"R_G6PDH2r" => 4.9599
9
"R_TALA" => 1.49698
⋮ => ⋮
```
...
...
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