Unverified Commit 60a1abab authored by Miroslav Kratochvil's avatar Miroslav Kratochvil Committed by GitHub
Browse files

Merge pull request #426 from LCSB-BioCore/mo-fix-notebook

Fix docs
parents fe477a48 7585e9e8
Pipeline #45205 passed with stages
in 34 minutes and 18 seconds
......@@ -121,17 +121,18 @@ flux_variability_summary((fva_mins, fva_maxs))
# value of the minimized flux and the associated biomass growth rate is returned instead
# of every flux.
biomass_idx = first(indexin(["BIOMASS_Ecoli_core_w_GAM"], reactions(model))) # index of biomass function
biomass_idx = first(indexin(["R_BIOMASS_Ecoli_core_w_GAM"], reactions(model))) # index of biomass function
vs = flux_variability_analysis(
model,
Gurobi.Optimizer;
Tulip.Optimizer;
bounds = objective_bounds(0.50), # biomass can vary up to 50% less than optimum
modifications = [
change_optimizer_attribute("IPM_IterationsLimit", 500),
change_constraint("EX_glc__D_e", -10, -10),
change_constraint("EX_o2_e", 0.0, 0.0),
change_constraint("R_EX_glc__D_e", -10, -10),
change_constraint("R_EX_o2_e", 0.0, 0.0),
],
ret = m -> (COBREXA.JuMP.objective_value(m), COBREXA.JuMP.value(m[:x][25])), # m is the model and m[:x] extracts the fluxes from the model
ret = m ->
(COBREXA.JuMP.objective_value(m), COBREXA.JuMP.value(m[:x][biomass_idx])), # m is the model and m[:x] extracts the fluxes from the model
)
#
fva_mins = Dict(rxn => flux for (rxn, flux) in zip(reactions(model), vs[:, 1]))
......
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