renumber to 7

docs/src/notebooks/6_community_model.jl

-# # Building and analysing a small community model
-
-#md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/@__NAME__.ipynb)
-#md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/@__NAME__.ipynb)
-
-# Here we will use `COBREXA` to build and analyze a small community model  
-# consisting of three *E. coli* mutants using the `CoreModel`. We will use an
-# objective function that enforces equal growth rates.
-
-# ## Load the base model
-
-!isfile("e_coli_core.json") &&
-    download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json");
-
-using COBREXA
-using Tulip
-
-# ## Load the models and inspect fba solutions
-
-base_model = load_model(CoreModel, "e_coli_core.json")
-
-cytbd_knockout = remove_reactions(base_model, "CYTBD")
-sol = flux_balance_analysis_dict(cytbd_knockout, Tulip.Optimizer)
-println("Cytochrome oxidase knockout μ = ", sol["BIOMASS_Ecoli_core_w_GAM"])
-
-atps4r_knockout = remove_reactions(base_model, "ATPS4r")
-sol = flux_balance_analysis_dict(atps4r_knockout, Tulip.Optimizer)
-println("ATP synthase knockout μ = ", sol["BIOMASS_Ecoli_core_w_GAM"])
-
-eno_knockout = remove_reactions(base_model, "ENO")
-sol = flux_balance_analysis_dict(eno_knockout, Tulip.Optimizer)
-println("Enolase knockout μ = ", sol["BIOMASS_Ecoli_core_w_GAM"])
-# notice that the enolase mutant cannot grow by itself.
-
-# ## Build a community model of the Cytochrome oxidase and ATP synthase knockouts 
-
-ex_rxns = filter(looks_like_exchange_reaction, reactions(base_model))
-ex_mets = [first(keys(reaction_stoichiometry(base_model, ex_rxn))) for ex_rxn in ex_rxns]
-
-models = [cytbd_knockout, atps4r_knockout]
-community_model = join_with_exchanges(models, ex_rxns, ex_mets; 
-        add_biomass_objective=true, 
-        biomass_ids=["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"], 
-        model_names=["cytbd_ko", "atps4r_ko"]
-        )     
-
-# ## Set bounds of community model
-
-env_ex_rxn_idxs = indexin(ex_rxns, reactions(community_model))
-cytbd_ex_rxn_idxs = indexin(ex_rxns, reactions(cytbd_knockout))
-atps4r_ex_rxn_idxs = indexin(ex_rxns, reactions(atps4r_knockout))
-
-for (env_ex, m2_ex, m1_ex) in zip(env_ex_rxn_idxs, cytbd_ex_rxn_idxs, atps4r_ex_rxn_idxs)
-    # in case some exchange reactions are not present in both models
-    m2lb = isnothing(m2_ex) ? 0.0 : atps4r_knockout.xl[m2_ex]
-    m2ub = isnothing(m2_ex) ? 0.0 : atps4r_knockout.xu[m2_ex]
-
-    m1lb = isnothing(m1_ex) ? 0.0 : cytbd_knockout.xl[m1_ex]
-    m1ub = isnothing(m1_ex) ? 0.0 : cytbd_knockout.xu[m1_ex]
-
-    change_bounds!(community_model, [env_ex]; xl= [m1lb + m2lb], xu = [m1ub + m2ub])
-end
-
-# ## Add objective function to community model
-
-biomass_ids = ["cytbd_ko_BIOMASS_Ecoli_core_w_GAM", "atps4r_ko_BIOMASS_Ecoli_core_w_GAM"]
-add_objective!(
-    community_model,
-    biomass_ids;
-    objective_column_index = first(
-        indexin(["community_biomass"], reactions(community_model)),
-    ),
-)
-
-# ## Perform community FBA
-
-d = flux_balance_analysis_dict(
-    community_model,
-    Tulip.Optimizer;
-    modifications = [change_optimizer_attribute("IPM_IterationsLimit", 1000)],
-)
-println("Community μ = ", d["community_biomass"])
-# The growth rate is limited to the slowest organism as per the objective function
-
-# ## Add the Enolase knockout to the community model
-
-community_model = add_model_with_exchanges(
-    community_model,
-    eno_knockout,
-    ex_rxns,
-    ex_mets;
-    model_name = "eno_ko",
-    biomass_id = "BIOMASS_Ecoli_core_w_GAM",
-)
-
-# ## update the biomass reaction to include the new mutant
-
-biomass_ids = ["cytbd_ko_BIOMASS_Ecoli_core_w_GAM", "atps4r_ko_BIOMASS_Ecoli_core_w_GAM", "eno_ko_BIOMASS_Ecoli_core_w_GAM"]
-add_objective!(
-    community_model,
-    biomass_ids;
-    objective_column_index = first(
-        indexin(["community_biomass"], reactions(community_model)),
-    ),
-)
-
-d = flux_balance_analysis_dict(
-    community_model,
-    Tulip.Optimizer;
-    modifications = [change_optimizer_attribute("IPM_IterationsLimit", 1000)],
-)
-println("Community μ = ", d["community_biomass"])   
-# Notice that the high communal growth rate is 0, due to the enolase knockout.
-
-# ## Allow the mutants to share pyruvate and rescue each other
-
-pyr_exs = ["cytbd_ko_EX_pyr_e", "atps4r_ko_EX_pyr_e", "eno_ko_EX_pyr_e"]
-change_bounds!(community_model, pyr_exs; xl = repeat([-1000.0], inner=3), xu = repeat([1000.0], inner=3))
-
-d = flux_balance_analysis_dict(
-    community_model,
-    Tulip.Optimizer;
-    modifications = [change_optimizer_attribute("IPM_IterationsLimit", 1000)],
-)
-println("Community μ = ", d["community_biomass"])