diff --git a/docs/src/notebooks/7_community_model.jl b/docs/src/notebooks/7_community_model.jl
index a5ece1c56103d2921b18e7310533c26350ecb777..3ac595469d75db2a3ea78420102d553daed46fca 100644
--- a/docs/src/notebooks/7_community_model.jl
+++ b/docs/src/notebooks/7_community_model.jl
@@ -40,15 +40,15 @@ sol["BIOMASS_Ecoli_core_w_GAM"] # Enolase knockout μ, cannot grow by itself
# ## Build a community model of the cytochrome oxidase knockout and the ATP synthase knockout models
-ex_rxns = filter(looks_like_exchange_reaction, reactions(base_model)) # identify exchange reactions heuristically
-ex_mets = [first(keys(reaction_stoichiometry(base_model, ex_rxn))) for ex_rxn in ex_rxns] # identify exchange metabolites IN THE SAME ORDER as ex_rxns
-[ex_rxns ex_mets]
+ex_rxn_mets = Dict(
+ ex_rxn => first(keys(reaction_stoichiometry(base_model, ex_rxn))) for
+ ex_rxn in filter(looks_like_exchange_reaction, reactions(base_model))
+) # identify exchange reactions heuristically
#
model_names = ["cytbd_ko", "atps4r_ko"]
community_model = join_with_exchanges(
[cytbd_knockout_model, atps4r_knockout_model],
- ex_rxns,
- ex_mets;
+ ex_rxn_mets;
add_biomass_objective = true,
biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"],
model_names = model_names,
@@ -56,9 +56,9 @@ community_model = join_with_exchanges(
# ## Set exchange reaction bounds of community model based on the bounds of the individual models
-env_ex_rxn_idxs = indexin(ex_rxns, reactions(community_model)) # identify the global (environmental exchange reactions)
-cytbd_ex_rxn_idxs = indexin(ex_rxns, reactions(cytbd_knockout_model)) # identify the indices of the corresponding exchange reactions in the original models
-atps4r_ex_rxn_idxs = indexin(ex_rxns, reactions(atps4r_knockout_model))
+env_ex_rxn_idxs = indexin(keys(ex_rxn_mets), reactions(community_model)) # identify the global (environmental exchange reactions)
+cytbd_ex_rxn_idxs = indexin(keys(ex_rxn_mets), reactions(cytbd_knockout_model)) # identify the indices of the corresponding exchange reactions in the original models
+atps4r_ex_rxn_idxs = indexin(keys(ex_rxn_mets), reactions(atps4r_knockout_model))
# In case some exchange reactions are not present in both models, set
# environmental exchange bound to the sum of the individual exchange bounds
@@ -96,8 +96,7 @@ d["community_biomass"] # community μ
community_model = add_model_with_exchanges(
community_model,
eno_knockout_model,
- ex_rxns,
- ex_mets;
+ ex_rxn_mets;
model_name = "eno_ko",
biomass_id = "BIOMASS_Ecoli_core_w_GAM",
)
diff --git a/src/reconstruction/community.jl b/src/reconstruction/community.jl
index c5fcb2415d6135ff56bbf68b8687320cf676dd29..4295e841a2385b89a8d38db182472881f30b3197 100644
--- a/src/reconstruction/community.jl
+++ b/src/reconstruction/community.jl
@@ -63,35 +63,38 @@ end
add_model_with_exchanges(
community::CoreModel,
model::MetabolicModel,
- exchange_rxn_ids::Vector{String},
- exchange_met_ids::Vector{String};
+ exchange_rxn_mets::Dict{String,String};
model_name = "unknown_species",
biomass_id = nothing,
)::CoreModel
-Add `model` to `community`, which is a pre-existing community model with
-`exchange_rxn_ids` and `exchange_met_ids`. The `model_name` is appended to
-each reaction and metabolite, see [`join_with_exchanges`](@ref). If
-`biomass_id` is specified then a biomass metabolite for `model` is also added
-to the resulting model. The column corresponding to the `biomass_id` reaction
-then produces this new biomass metabolite with unit coefficient. Note,
-`exchange_rxn_ids` and `exchange_met_ids` must already exist in the `community`
-model.
+Add `model` to `community`, which is a pre-existing community model with exchange reactions
+and metabolites in the dictionary `exchange_rxn_mets`. The `model_name` is appended to each
+reaction and metabolite, see [`join_with_exchanges`](@ref). If `biomass_id` is specified
+then a biomass metabolite for `model` is also added to the resulting model. The column
+corresponding to the `biomass_id` reaction then produces this new biomass metabolite with
+unit coefficient. Note, `exchange_rxn_ids` and `exchange_met_ids` must already exist in the
+`community` model.
# Example
```
-community = add_model_with_exchanges(community, model, exchange_rxn_ids, exchange_met_ids; model_name="species_2", biomass_id="BIOMASS_Ecoli_core_w_GAM")
+community = add_model_with_exchanges(community,
+ model,
+ exchange_rxn_mets;
+ model_name="species_2",
+ biomass_id="BIOMASS_Ecoli_core_w_GAM")
```
"""
function add_model_with_exchanges(
community::CoreModel,
model::MetabolicModel,
- exchange_rxn_ids::Vector{String},
- exchange_met_ids::Vector{String};
+ exchange_rxn_mets::Dict{String,String};
model_name = "unknown_species",
biomass_id = nothing,
)::CoreModel
+ exchange_rxn_ids = keys(exchange_rxn_mets)
+ exchange_met_ids = values(exchange_rxn_mets)
exchange_met_community_inds = indexin(exchange_met_ids, metabolites(community))
exchange_rxn_community_inds = indexin(exchange_rxn_ids, reactions(community))
if any(isnothing.(exchange_met_community_inds)) ||
@@ -171,36 +174,33 @@ end
"""
join_with_exchanges(models::Vector{M},
- exchange_rxn_ids::Vector{String},
- exchange_met_ids::Vector{String};
+ exchange_rxn_mets::Dict{String, String};
add_biomass_objective=false,
biomass_ids::Vector{String},
model_names=String[]
)
-Return a `CoreModel` representing the community model of `models` joined through
-their `exchange_rxn_ids` and `exchange_met_ids`. These exchange reactions and
-metabolites link to environmental metabolites and reactions.
-Optionally specify `model_names` to append a specific name to each reaction
-and metabolite of an organism for easier reference (default is `species_i` for
-each model index i in `models`). Note, the bounds of the environmental variables
-are all set to zero. Thus, to run a simulation you need to constrain them
-appropriately. All the other bounds are inherited from the models used to
-construct the community model.
-
-If `add_biomass_objective` is true then `biomass_ids` needs to be supplied as
-well. This creates a model with an extra reaction added to the end of the
-stoichiometric matrix (last column) that can be assigned as the objective
-reaction. It also creates biomass "metabolites" that can be used in this
-objective reaction. Note, this reaction is unspecified, further action needs to
-be taken to specify it, e.g. assign weights to the last column of the
-stoichiometric matrix in the rows corresponding to the biomass metabolites.
-
-To further clarify how this `join` works. Suppose you have 2 organisms with
-stoichiometric matrices Sâ‚ and Sâ‚‚ and you want to link them with
-`exchange_met_ids = [emâ‚, emâ‚‚, em₃, ...]` and `exchange_rxn_ids = [erâ‚, erâ‚‚,
-er₃, ...]`. Then a new community stoichiometric matrix is constructed that looks
-like this:
+Return a `CoreModel` representing the community model of `models` joined through their
+exchange reactions and metabolites in the dictionary `exchange_rxn_mets`, which maps
+exchange reactions to their associated metabolite. These exchange reactions and metabolites
+link model metabolites to environmental metabolites and reactions. Optionally specify
+`model_names` to append a specific name to each reaction and metabolite of an organism for
+easier reference (default is `species_i` for each model index i in `models`). Note, the
+bounds of the environmental variables are all set to zero. Thus, to run a simulation you
+need to constrain them appropriately. All the other bounds are inherited from the models
+used to construct the community model.
+
+If `add_biomass_objective` is true then `biomass_ids` needs to be supplied as well. This
+creates a model with an extra reaction added to the end of the stoichiometric matrix (last
+column) that can be assigned as the objective reaction. It also creates biomass
+"metabolites" that can be used in this objective reaction. Note, this reaction is
+unspecified, further action needs to be taken to specify it, e.g. assign weights to the last
+column of the stoichiometric matrix in the rows corresponding to the biomass metabolites.
+
+To further clarify how this `join` works. Suppose you have 2 organisms with stoichiometric
+matrices Sâ‚ and Sâ‚‚ and you want to link them with `exchange_rxn_mets = Dict(erâ‚ => emâ‚, erâ‚‚
+=> em₂, er₃ => em₃, ...)`. Then a new community stoichiometric matrix is constructed that
+looks like this:
```
_ er₠er₂ er₃ ... b_
|Sâ‚ |
@@ -213,13 +213,12 @@ S = emâ‚‚| |
bmâ‚‚|_ _|
```
-The exchange reactions in each model get linked to environmental metabolites,
-`emáµ¢`, and these get linked to environmental exchanges, `eráµ¢`. These `eráµ¢`
-behave like normal single organism exchange reactions. When
-`add_biomass_objective` is true each model's biomass becomes a pseudo-metabolite
-(`bmáµ¢`). These can be weighted in column `b`, called the `community_biomass`
-reaction in the community model, if desired. Refer to the tutorial if this is
-unclear.
+The exchange reactions in each model get linked to environmental metabolites, `emáµ¢`, and
+these get linked to environmental exchanges, `eráµ¢`. These `eráµ¢` behave like normal single
+organism exchange reactions. When `add_biomass_objective` is true each model's biomass
+becomes a pseudo-metabolite (`bmáµ¢`). These can be weighted in column `b`, called the
+`community_biomass` reaction in the community model, if desired. Refer to the tutorial if
+this is unclear.
# Example
```
@@ -227,15 +226,14 @@ m1 = load_model(core_model_path)
m2 = load_model(CoreModel, core_model_path)
# need to list ALL the exchanges that will form part of the entire model
-exchange_rxn_ids = filter(looks_like_exchange_reaction, reactions(m1))
-exchange_met_ids = [first(keys(reaction_stoichiometry(m1, ex_rxn))) for ex_rxn in exchange_rxn_ids]
+exchange_rxn_mets = Dict(k => first(keys(reaction_stoichiometry(m1, ex_rxn)))
+ for filter(looks_like_exchange_reaction, reactions(m1)))
biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"]
community = join_with_exchanges(
[m1, m2],
- exchange_rxn_ids,
- exchange_met_ids;
+ exchange_rxn_mets;
add_biomass_objective = true,
biomass_ids = biomass_ids,
)
@@ -243,18 +241,20 @@ community = join_with_exchanges(
"""
function join_with_exchanges(
models::Vector{M},
- exchange_rxn_ids::Vector{String},
- exchange_met_ids::Vector{String};
+ exchange_rxn_mets::Dict{String,String};
add_biomass_objective = true,
biomass_ids = String[],
model_names = String[],
)::CoreModel where {M<:MetabolicModel}
+ exchange_rxn_ids = keys(exchange_rxn_mets)
+ exchange_met_ids = values(exchange_rxn_mets)
if add_biomass_objective && isempty(biomass_ids)
throw(
DomainError(
"biomass_ids",
- "Please add supply the string ids of the biomass functions when `add_biomass_objective` is true.",
+ "Please add supply the string ids of the biomass functions when
+ `add_biomass_objective` is true.",
),
)
end
diff --git a/test/reconstruction/community.jl b/test/reconstruction/community.jl
index 449513eebd2501efcb94336e4ddcdd9edbf090be..a2f18a4a830822a2a891e33de22f500b2de5331c 100644
--- a/test/reconstruction/community.jl
+++ b/test/reconstruction/community.jl
@@ -1,11 +1,9 @@
@testset "Detailed community stoichiometrix matrix check" begin
m1 = test_toyModel()
m2 = test_toyModel()
- ex_rxn_ids = ["EX_m1(e)", "EX_m3(e)"]
- ex_met_ids = ["m1[e]", "m3[e]"]
+ ex_rxn_mets = Dict("EX_m1(e)" => "m1[e]", "EX_m3(e)" => "m3[e]")
- c1 =
- join_with_exchanges([m1, m2], ex_rxn_ids, ex_met_ids; add_biomass_objective = false)
+ c1 = join_with_exchanges([m1, m2], ex_rxn_mets; add_biomass_objective = false)
# test of stoichs are the same
@test all(c1.S[1:6, 1:7] .== c1.S[7:12, 8:14])
@@ -28,8 +26,7 @@
c2 = join_with_exchanges(
[m1, m2],
- ex_rxn_ids,
- ex_met_ids;
+ ex_rxn_mets;
add_biomass_objective = true,
biomass_ids = ["biomass1", "biomass1"],
)
@@ -54,22 +51,22 @@ end
m1 = load_model(model_paths["e_coli_core.json"])
m2 = load_model(CoreModel, model_paths["e_coli_core.json"])
- exchange_rxn_ids = filter(looks_like_exchange_reaction, reactions(m2))
- exchange_met_ids =
- [first(keys(reaction_stoichiometry(m2, ex_rxn))) for ex_rxn in exchange_rxn_ids]
+ exchange_rxn_mets = Dict(
+ ex_rxn => first(keys(reaction_stoichiometry(m2, ex_rxn))) for
+ ex_rxn in filter(looks_like_exchange_reaction, reactions(m2))
+ )
biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"]
community = join_with_exchanges(
[m1, m2],
- exchange_rxn_ids,
- exchange_met_ids;
+ exchange_rxn_mets;
add_biomass_objective = true,
biomass_ids = biomass_ids,
)
- env_ex_inds = indexin(exchange_rxn_ids, reactions(community))
- m2_ex_inds = indexin(exchange_rxn_ids, reactions(m2))
+ env_ex_inds = indexin(keys(exchange_rxn_mets), reactions(community))
+ m2_ex_inds = indexin(keys(exchange_rxn_mets), reactions(m2))
community.xl[env_ex_inds] .= m2.xl[m2_ex_inds]
community.xu[env_ex_inds] .= m2.xu[m2_ex_inds]
@@ -92,23 +89,23 @@ end
m1 = load_model(CoreModel, model_paths["e_coli_core.json"])
m2 = load_model(CoreModel, model_paths["iJO1366.mat"])
- exchange_rxn_ids = filter(looks_like_exchange_reaction, reactions(m2))
- exchange_met_ids =
- [first(keys(reaction_stoichiometry(m2, ex_rxn))) for ex_rxn in exchange_rxn_ids]
+ exchange_rxn_mets = Dict(
+ ex_rxn => first(keys(reaction_stoichiometry(m2, ex_rxn))) for
+ ex_rxn in filter(looks_like_exchange_reaction, reactions(m2))
+ )
biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ec_iJO1366_core_53p95M"]
community = join_with_exchanges(
[m1, m2],
- exchange_rxn_ids,
- exchange_met_ids;
+ exchange_rxn_mets;
add_biomass_objective = true,
biomass_ids = biomass_ids,
)
- env_ex_inds = indexin(exchange_rxn_ids, reactions(community))
- m2_ex_inds = indexin(exchange_rxn_ids, reactions(m2))
- m1_ex_inds = indexin(exchange_rxn_ids, reactions(m1))
+ env_ex_inds = indexin(keys(exchange_rxn_mets), reactions(community))
+ m2_ex_inds = indexin(keys(exchange_rxn_mets), reactions(m2))
+ m1_ex_inds = indexin(keys(exchange_rxn_mets), reactions(m1))
for (env_ex, m2_ex, m1_ex) in zip(env_ex_inds, m2_ex_inds, m1_ex_inds)
m2lb = isnothing(m2_ex) ? 0.0 : m2.xl[m2_ex]
@@ -144,22 +141,22 @@ end
@testset "Community model modifications" begin
m1 = load_model(CoreModel, model_paths["e_coli_core.json"])
- exchange_rxn_ids = filter(looks_like_exchange_reaction, reactions(m1))
- exchange_met_ids =
- [first(keys(reaction_stoichiometry(m1, ex_rxn))) for ex_rxn in exchange_rxn_ids]
+ exchange_rxn_mets = Dict(
+ ex_rxn => first(keys(reaction_stoichiometry(m1, ex_rxn))) for
+ ex_rxn in filter(looks_like_exchange_reaction, reactions(m1))
+ )
biomass_ids = ["BIOMASS_Ecoli_core_w_GAM"]
community = join_with_exchanges(
[m1],
- exchange_rxn_ids,
- exchange_met_ids;
+ exchange_rxn_mets;
add_biomass_objective = true,
biomass_ids = biomass_ids,
)
- env_ex_inds = indexin(exchange_rxn_ids, reactions(community))
- m1_ex_inds = indexin(exchange_rxn_ids, reactions(m1))
+ env_ex_inds = indexin(keys(exchange_rxn_mets), reactions(community))
+ m1_ex_inds = indexin(keys(exchange_rxn_mets), reactions(m1))
community.xl[env_ex_inds] .= m1.xl[m1_ex_inds]
community.xu[env_ex_inds] .= m1.xu[m1_ex_inds]
@@ -168,8 +165,7 @@ end
community = add_model_with_exchanges(
community,
m2,
- exchange_rxn_ids,
- exchange_met_ids;
+ exchange_rxn_mets;
model_name = "species_2",
biomass_id = "BIOMASS_Ecoli_core_w_GAM",
)