Commit 7f22afea authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
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clean up the notebook with atom exchanges

parent 486efbb9
Pipeline #43055 passed with stages
in 8 minutes and 32 seconds
......@@ -59,13 +59,14 @@ fluxes = flux_balance_analysis_dict(
# It is sometimes interesting to keep track of the atoms entering and leaving
# the system through boundary reactions. This can be inspected by calling
# [`atom_exchange`](@ref). That gives you the flux of individual atoms entering
# and leaving the system through boundary reactions (e.g. exchange reactions),
# based on `fluxes`:
# [`atom_exchange`](@ref). That gives you the flux of individual atoms getting
# consumed and produced by all reactions, based on `fluxes`. We erase the
# reaction that consumes the atoms for creating biomass, to see how much mass
# the "rest" of the reaction produces for it:
fluxes_without_biomass = copy(fluxes);
delete!(fluxes_without_biomass, "BIOMASS_Ecoli_core_w_GAM");
atom_exchange(model, fluxes)
atom_exchange(model, fluxes_without_biomass)
# ## Inspecting the flux solution: `metabolite_fluxes`
......
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