Commit f780aee0 authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
Browse files

slight rewording/commenting

parent 68c02401
Pipeline #48276 passed with stages
in 8 minutes and 26 seconds
...@@ -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,
) )
``` ```
......
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