Commit e957ee8b authored by St. Elmo's avatar St. Elmo
Browse files

can't download a file in Documenter.jl

parent 9c9b6bc3
using Documenter, COBREXA
# download core model
download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
# download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
makedocs(modules = [COBREXA],
clean = false,
......@@ -27,4 +27,4 @@ makedocs(modules = [COBREXA],
)
# delete core model
rm("e_coli_core.json")
\ No newline at end of file
rm("e_coli_core.json")
......@@ -24,6 +24,7 @@ using COBREXA
using JuMP
using Tulip
download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
model = read_model("e_coli_core.json")
biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
......@@ -121,5 +122,6 @@ set_optimizer(cbm, Tulip.Optimizer)
@objective(cbm, Max, v[model[biomass]])
optimize!(cbm)
sol = map_fluxes(v, model)
sol = map_fluxes(v, model)
rm("e_coli_core.json") # hide
```
......@@ -51,12 +51,11 @@ using COBREXA
using JuMP
using Tulip
download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
model = read_model("e_coli_core.json")
biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
optimizer = Tulip.Optimizer
sol = fba(model, biomass, optimizer)
rm("e_coli_core.json") # hide
```
......@@ -9,8 +9,10 @@ read_model(file_location::String)
```@example ioexample
using COBREXA
download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
model = read_model("e_coli_core.json")
rm("e_coli_core.json") # hide
model # pretty printing
```
......@@ -27,4 +29,4 @@ rm("e_coli_core2.json") # hide
```
## IO Problems?
Please let me know when you run into model import/export problems by filing an issue.
\ No newline at end of file
Please let me know when you run into model import/export problems by filing an issue.
......@@ -12,7 +12,9 @@ using COBREXA
using JuMP
using Tulip
download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
model = read_model("e_coli_core.json")
rm("e_coli_core.json") # hide
optimizer = Tulip.Optimizer
biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
cons = Dict("EX_glc__D_e" => (-12.0, -12.0))
......@@ -20,4 +22,4 @@ sol = fba(model, biomass, optimizer, constraints=cons) # classic flux balance an
cons["BIOMASS_Ecoli_core_w_GAM"] = (sol["BIOMASS_Ecoli_core_w_GAM"], sol["BIOMASS_Ecoli_core_w_GAM"]*0.99)
samples = hit_and_run(100_000, model, optimizer; keepevery=10, samplesize=5000, constraints=cons)
```
\ No newline at end of file
```
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment