Merge pull request #515 from LCSB-BioCore/develop

develop→master for 1.1 release

Project.toml

 name = "COBREXA"
 uuid = "babc4406-5200-4a30-9033-bf5ae714c842"
 authors = ["The developers of COBREXA.jl"]
-version = "1.0.6"
+version = "1.1"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -40,12 +40,12 @@ julia = "1"
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 OSQP = "ab2f91bb-94b4-55e3-9ba0-7f65df51de79"
 SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
-GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
 
 [targets]
 test = ["Aqua", "Downloads", "OSQP", "SHA", "Test", "Tulip", "GLPK"]

docs/src/advanced/2_custom_model.md

@@ -73,8 +73,8 @@ function COBREXA.objective(m::CircularModel)
 end
 
 COBREXA.bounds(m::CircularModel) = (
-    spzeros(n_reactions(m)), # lower bounds
-    sparse(ones(n_reactions(m))), # upper bounds
+    zeros(n_reactions(m)), # lower bounds
+    ones(n_reactions(m)), # upper bounds
 )
 
 function COBREXA.stoichiometry(m::CircularModel)

src/analysis/flux_balance_analysis.jl

@@ -5,28 +5,28 @@ A variant of FBA that returns a vector of fluxes in the same order as reactions
 of the model, if the solution is found.
 
 Arguments are passed to [`flux_balance_analysis`](@ref).
+
+This function is kept for backwards compatibility, use [`flux_vector`](@ref)
+instead.
 """
-function flux_balance_analysis_vec(args...; kwargs...)::Union{Vector{Float64},Nothing}
-    optmodel = flux_balance_analysis(args...; kwargs...)
-    is_solved(optmodel) || return nothing
-    value.(optmodel[:x])
-end
+flux_balance_analysis_vec(args...; kwargs...)::Maybe{Vector{Float64}} =
+    flux_vector(flux_balance_analysis(args...; kwargs...))
 
 """
     flux_balance_analysis_dict(model::MetabolicModel, args...)::Union{Dict{String, Float64},Nothing}
 
 A variant of FBA that returns a dictionary assigning fluxes to reactions, if
 the solution is found. Arguments are passed to [`flux_balance_analysis`](@ref).
+
+This function is kept for backwards compatibility, use [`flux_dict`](@ref)
+instead.
 """
-function flux_balance_analysis_dict(
+flux_balance_analysis_dict(
     model::MetabolicModel,
     args...;
     kwargs...,
-)::Union{Dict{String,Float64},Nothing}
-    v = flux_balance_analysis_vec(model, args...; kwargs...)
-    isnothing(v) && return nothing
-    Dict(zip(reactions(model), v))
-end
+)::Maybe{Dict{String,Float64}} =
+    flux_dict(model, flux_balance_analysis(model, args...; kwargs...))
 
 """
     flux_balance_analysis(

src/analysis/flux_variability_analysis.jl

@@ -140,18 +140,11 @@ mins, maxs = flux_variability_analysis_dict(
 ```
 """
 function flux_variability_analysis_dict(model::MetabolicModel, optimizer; kwargs...)
-    vs = flux_variability_analysis(
-        model,
-        optimizer;
-        kwargs...,
-        ret = m -> JuMP.value.(m[:x]),
-    )
+    fluxes = flux_variability_analysis(model, optimizer; kwargs..., ret = flux_vector)
     rxns = reactions(model)
+    dicts = zip.(Ref(rxns), fluxes)
 
-    return (
-        Dict(zip(rxns, [Dict(zip(rxns, fluxes)) for fluxes in vs[:, 1]])),
-        Dict(zip(rxns, [Dict(zip(rxns, fluxes)) for fluxes in vs[:, 2]])),
-    )
+    return (Dict(rxns .=> Dict.(dicts[:, 1])), Dict(rxns .=> Dict.(dicts[:, 2])))
 end
 
 """
@@ -166,9 +159,5 @@ function _max_variability_flux(opt_model, rid, ret)
     @objective(opt_model, sense, var)
     optimize!(opt_model)
 
-    if is_solved(opt_model)
-        return ret(opt_model)
-    else
-        return nothing
-    end
+    is_solved(opt_model) ? ret(opt_model) : nothing
 end

src/analysis/minimize_metabolic_adjustment.jl

@@ -69,7 +69,7 @@ minimize_metabolic_adjustment(flux_ref::Vector{Float64}) =
     end
 
 """
-    minimize_metabolic_adjustment(flux_ref_dict::Dict{String, Float64}) 
+    minimize_metabolic_adjustment(flux_ref_dict::Dict{String, Float64})
 
 Overload of [`minimize_metabolic_adjustment`](@ref) that works with a
 dictionary of fluxes.
@@ -87,30 +87,22 @@ minimize_metabolic_adjustment(flux_ref_dict::Dict{String,Float64}) =
 Perform minimization of metabolic adjustment (MOMA) and return a vector of fluxes in the
 same order as the reactions in `model`. Arguments are forwarded to
 [`minimize_metabolic_adjustment`](@ref) internally.
-"""
-function minimize_metabolic_adjustment_analysis_vec(args...; kwargs...)
-    opt_model = minimize_metabolic_adjustment_analysis(args...; kwargs...)
-
-    isnothing(opt_model) && return nothing
 
-    return value.(opt_model[:x])
-end
+This function is kept for backwards compatibility, use [`flux_vector`](@ref)
+instead.
+"""
+minimize_metabolic_adjustment_analysis_vec(args...; kwargs...) =
+    flux_vector(minimize_metabolic_adjustment_analysis(args...; kwargs...))
 
 """
-    minimize_metabolic_adjustment_analysis_dict(args...; kwargs...)
+    minimize_metabolic_adjustment_analysis_dict(model::MetabolicModel, args...; kwargs...)
 
 Perform minimization of metabolic adjustment (MOMA) and return a dictionary mapping the
 reaction IDs to fluxes. Arguments are forwarded to [`minimize_metabolic_adjustment`](@ref)
 internally.
-"""
-function minimize_metabolic_adjustment_analysis_dict(
-    model::MetabolicModel,
-    args...;
-    kwargs...,
-)
-    opt_fluxes = minimize_metabolic_adjustment_analysis_vec(model, args...; kwargs...)
 
-    isnothing(opt_fluxes) && return nothing
-
-    return Dict(zip(reactions(model), opt_fluxes))
-end
+This function is kept for backwards compatibility, use [`flux_vector`](@ref)
+instead.
+"""
+minimize_metabolic_adjustment_analysis_dict(model::MetabolicModel, args...; kwargs...) =
+    flux_dict(model, minimize_metabolic_adjustment_analysis(model, args...; kwargs...))

src/analysis/modifications/moment.jl

@@ -29,18 +29,10 @@ that active site number and unit issues are prevented.
 
 # Example
 ```
-sol = flux_balance_analysis_dict(
-    model,
-    Tulip.Optimizer;
-    modifications = [
-        add_moment_constraints(
-            ksas,
-            protein_mass_fraction
-        ),
-        change_constraint("EX_glc__D_e", lb = -1000),
-    ],
+flux_balance_analysis(
+    ...,
+    modifications = [ add_moment_constraints(my_kcats, 0.6) ],
 )
-```
 """
 add_moment_constraints(kcats::Dict{String,Float64}, protein_mass_fraction::Float64) =
     (model, opt_model) -> begin

src/analysis/parsimonious_flux_balance_analysis.jl

@@ -100,14 +100,12 @@ Perform parsimonious flux balance analysis on `model` using `optimizer`.
 Returns a vector of fluxes in the same order as the reactions in `model`.
 Arguments are forwarded to [`parsimonious_flux_balance_analysis`](@ref)
 internally.
-"""
-function parsimonious_flux_balance_analysis_vec(args...; kwargs...)
-    opt_model = parsimonious_flux_balance_analysis(args...; kwargs...)
-
-    isnothing(opt_model) && return nothing
 
-    return value.(opt_model[:x])
-end
+This function is kept for backwards compatibility, use [`flux_vector`](@ref)
+instead.
+"""
+parsimonious_flux_balance_analysis_vec(args...; kwargs...) =
+    flux_vector(parsimonious_flux_balance_analysis(args...; kwargs...))
 
 """
     parsimonious_flux_balance_analysis_dict(model::MetabolicModel, args...; kwargs...)
@@ -115,11 +113,9 @@ end
 Perform parsimonious flux balance analysis on `model` using `optimizer`.
 Returns a dictionary mapping the reaction IDs to fluxes. Arguments are
 forwarded to [`parsimonious_flux_balance_analysis`](@ref) internally.
-"""
-function parsimonious_flux_balance_analysis_dict(model::MetabolicModel, args...; kwargs...)
-    opt_fluxes = parsimonious_flux_balance_analysis_vec(model, args...; kwargs...)
-
-    isnothing(opt_fluxes) && return nothing
 
-    return Dict(zip(reactions(model), opt_fluxes))
-end
+This function is kept for backwards compatibility, use [`flux_dict`](@ref)
+instead.
+"""
+parsimonious_flux_balance_analysis_dict(model::MetabolicModel, args...; kwargs...) =
+    flux_dict(model, parsimonious_flux_balance_analysis(model, args...; kwargs...))

src/base/solver.jl

@@ -32,29 +32,23 @@ function make_optimization_model(model::MetabolicModel, optimizer; sense = MOI.M
 end
 
 """
-    is_solved(optmodel)
+    is_solved(opt_model)
 
-Return `true` if `optmodel` solved successfully (solution is optimal or locally
+Return `true` if `opt_model` solved successfully (solution is optimal or locally
 optimal).  Return `false` if any other termination status is reached.
 Termination status is defined in the documentation of `JuMP`.
 """
-function is_solved(optmodel)
-    termination_status(optmodel) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED] ? true : false
-end
+is_solved(opt_model) = termination_status(opt_model) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED]
 
 """
-    optimize_objective(optmodel)::Union{Float64,Nothing}
+    optimize_objective(opt_model)::Maybe{Float64}
 
 Shortcut for running JuMP `optimize!` on a model and returning the objective
 value, if solved.
 """
-function optimize_objective(optmodel)::Maybe{Float64}
-    optimize!(optmodel)
-    if is_solved(optmodel)
-        objective_value(optmodel)
-    else
-        nothing
-    end
+function optimize_objective(opt_model)::Maybe{Float64}
+    optimize!(opt_model)
+    solved_objective_value(opt_model)
 end
 
 """
@@ -88,3 +82,43 @@ function set_optmodel_bound!(
     isnothing(lb) || set_normalized_rhs(opt_model[:lbs][vidx], -lb)
     isnothing(ub) || set_normalized_rhs(opt_model[:ubs][vidx], ub)
 end
+
+
+"""
+    solved_objective_value(opt_model)::Maybe{Float64}
+
+Returns the current objective value of a model, if solved.
+
+# Example
+```
+solved_objective_value(flux_balance_analysis(model, ...))
+```
+"""
+solved_objective_value(opt_model)::Maybe{Float64} =
+    is_solved(opt_model) ? objective_value(opt_model) : nothing
+
+"""
+    flux_vector(opt_model)::Maybe{Vector{Float64}}
+
+Returns a vector of fluxes of the model, if solved.
+
+# Example
+```
+flux_vector(flux_balance_analysis(model, ...))
+```
+"""
+flux_vector(opt_model)::Maybe{Vector{Float64}} =
+    is_solved(opt_model) ? value.(opt_model[:x]) : nothing
+
+"""
+    flux_dict(model::MetabolicModel, opt_model)::Maybe{Dict{String, Float64}, Nothing}
+
+Returns the fluxes of the model as a reaction-keyed dictionary, if solved.
+
+# Example
+```
+flux_dict(model, flux_balance_analysis(model, ...))
+```
+"""
+flux_dict(model::MetabolicModel, opt_model)::Maybe{Dict{String,Float64}} =
+    is_solved(opt_model) ? Dict(reactions(model) .=> value.(opt_model[:x])) : nothing

src/base/types/CoreModel.jl

@@ -14,28 +14,27 @@ mutable struct CoreModel <: MetabolicModel
     S::SparseMat
     b::SparseVec
     c::SparseVec
-    xl::SparseVec
-    xu::SparseVec
+    xl::Vector{Float64}
+    xu::Vector{Float64}
     rxns::Vector{String}
     mets::Vector{String}
 
     function CoreModel(
-        S::M,
-        b::V,
-        c::V,
-        xl::V,
-        xu::V,
-        rxns::K,
-        mets::K,
-    ) where {V<:VecType,M<:MatType,K<:StringVecType}
-
+        S::MatType,
+        b::VecType,
+        c::VecType,
+        xl::VecType,
+        xu::VecType,
+        rxns::StringVecType,
+        mets::StringVecType,
+    )
         all([length(b), length(mets)] .== size(S, 1)) ||
             throw(DimensionMismatch("inconsistent number of metabolites"))
 
         all([length(c), length(xl), length(xu), length(rxns)] .== size(S, 2)) ||
             throw(DimensionMismatch("inconsistent number of reactions"))
 
-        new(sparse(S), sparse(b), sparse(c), sparse(xl), sparse(xu), rxns, mets)
+        new(sparse(S), sparse(b), sparse(c), collect(xl), collect(xu), rxns, mets)
     end
 end
 
@@ -61,11 +60,11 @@ metabolites(a::CoreModel)::Vector{String} = a.mets
 stoichiometry(a::CoreModel)::SparseMat = a.S
 
 """
-    bounds(a::CoreModel)::Tuple{SparseVec,SparseVec}
+    bounds(a::CoreModel)::Tuple{Vector{Float64},Vector{Float64}}
 
 `CoreModel` flux bounds.
 """
-bounds(a::CoreModel)::Tuple{SparseVec,SparseVec} = (a.xl, a.xu)
+bounds(a::CoreModel)::Tuple{Vector{Float64},Vector{Float64}} = (a.xl, a.xu)
 
 """
     balance(a::CoreModel)::SparseVec

src/base/types/CoreModelCoupled.jl

@@ -10,22 +10,16 @@ The linear model with additional coupling constraints in the form
 mutable struct CoreModelCoupled <: MetabolicModel
     lm::CoreModel
     C::SparseMat
-    cl::SparseVec
-    cu::SparseVec
-
-    function CoreModelCoupled(
-        lm::MetabolicModel,
-        C::M,
-        cl::V,
-        cu::V,
-    ) where {V<:VecType,M<:MatType}
+    cl::Vector{Float64}
+    cu::Vector{Float64}
 
+    function CoreModelCoupled(lm::MetabolicModel, C::MatType, cl::VecType, cu::VecType)
         length(cu) == length(cl) ||
             throw(DimensionMismatch("`cl` and `cu` need to have the same size"))
         size(C) == (length(cu), n_reactions(lm)) ||
             throw(DimensionMismatch("wrong dimensions of `C`"))
 
-        new(convert(CoreModel, lm), sparse(C), sparse(cl), sparse(cu))
+        new(convert(CoreModel, lm), sparse(C), collect(cl), collect(cu))
     end
 end
 
@@ -92,11 +86,11 @@ The number of coupling constraints in a `CoreModelCoupled`.
 n_coupling_constraints(a::CoreModelCoupled)::Int = size(a.C, 1)
 
 """
-    coupling_bounds(a::CoreModelCoupled)::Tuple{SparseVec,SparseVec}
+    coupling_bounds(a::CoreModelCoupled)::Tuple{Vector{Float64},Vector{Float64}}
 
 Coupling bounds for a `CoreModelCoupled`.
 """
-coupling_bounds(a::CoreModelCoupled)::Tuple{SparseVec,SparseVec} = (a.cl, a.cu)
+coupling_bounds(a::CoreModelCoupled)::Tuple{Vector{Float64},Vector{Float64}} = (a.cl, a.cu)
 
 """
     reaction_stoichiometry(model::CoreModelCoupled, rid::String)::Dict{String, Float64}

src/base/types/FluxSummary.jl

@@ -47,7 +47,7 @@ larger than `large_flux_bound` are only stored if `keep_unbounded` is `true`.
 
 # Example
 ```
-julia> sol = flux_balance_analysis_dict(model, Tulip.Optimizer)
+julia> sol = flux_dict(flux_balance_analysis(model, Tulip.Optimizer))
 julia> fr = flux_summary(sol)
 Biomass:
   BIOMASS_Ecoli_core_w_GAM: 0.8739

src/base/types/JSONModel.jl

@@ -146,12 +146,8 @@ Get the bounds for reactions, assuming the information is stored in
 `.lower_bound` and `.upper_bound`.
 """
 bounds(model::JSONModel) = (
-    sparse([
-        get(rxn, "lower_bound", -_constants.default_reaction_bound) for rxn in model.rxns
-    ]),
-    sparse([
-        get(rxn, "upper_bound", _constants.default_reaction_bound) for rxn in model.rxns
-    ]),
+    [get(rxn, "lower_bound", -_constants.default_reaction_bound) for rxn in model.rxns],
+    [get(rxn, "upper_bound", _constants.default_reaction_bound) for rxn in model.rxns],
 )
 
 """

src/base/types/MATModel.jl

@@ -59,8 +59,8 @@ stoichiometry(m::MATModel) = sparse(m.mat["S"])
 Extracts bounds from the MAT file, saved under `lb` and `ub`.
 """
 bounds(m::MATModel) = (
-    sparse(reshape(get(m.mat, "lb", fill(-Inf, n_reactions(m), 1)), n_reactions(m))),
-    sparse(reshape(get(m.mat, "ub", fill(Inf, n_reactions(m), 1)), n_reactions(m))),
+    reshape(get(m.mat, "lb", fill(-Inf, n_reactions(m), 1)), n_reactions(m)),
+    reshape(get(m.mat, "ub", fill(Inf, n_reactions(m), 1)), n_reactions(m)),
 )
 
 """

src/base/types/SBMLModel.jl

@@ -47,12 +47,12 @@ function stoichiometry(model::SBMLModel)::SparseMat
 end
 
 """
-    bounds(model::SBMLModel)::Tuple{SparseVec,SparseVec}
+    bounds(model::SBMLModel)::Tuple{Vector{Float64},Vector{Float64}}
 
 Get the lower and upper flux bounds of model [`SBMLModel`](@ref). Throws `DomainError` in
 case if the SBML contains mismatching units.
 """
-function bounds(model::SBMLModel)::Tuple{SparseVec,SparseVec}
+function bounds(model::SBMLModel)::Tuple{Vector{Float64},Vector{Float64}}
     lbu, ubu = SBML.flux_bounds(model.sbml)
 
     unit = lbu[1][2]
@@ -67,7 +67,7 @@ function bounds(model::SBMLModel)::Tuple{SparseVec,SparseVec}
         ),
     )
 
-    return sparse.((getvalue.(lbu), getvalue.(ubu)))
+    return (getvalue.(lbu), getvalue.(ubu))
 end
 
 """

src/base/types/StandardModel.jl

@@ -144,29 +144,29 @@ function stoichiometry(model::StandardModel)::SparseMat
 end
 
 """
-    lower_bounds(model::StandardModel)
+    lower_bounds(model::StandardModel)::Vector{Float64}
 
 Return the lower bounds for all reactions in `model` in sparse format.
 """
-lower_bounds(model::StandardModel)::SparseVec =
+lower_bounds(model::StandardModel)::Vector{Float64} =
     sparse([model.reactions[rxn].lb for rxn in reactions(model)])
 
 """
-    upper_bounds(model::StandardModel)
+    upper_bounds(model::StandardModel)::Vector{Float64}
 
 Return the upper bounds for all reactions in `model` in sparse format.
 Order matches that of the reaction ids returned in `reactions()`.
 """
-upper_bounds(model::StandardModel)::SparseVec =
+upper_bounds(model::StandardModel)::Vector{Float64} =
     sparse([model.reactions[rxn].ub for rxn in reactions(model)])
 
 """
-    bounds(model::StandardModel)
+    bounds(model::StandardModel)::Tuple{Vector{Float64},Vector{Float64}}
 
 Return the lower and upper bounds, respectively, for reactions in `model`.
 Order matches that of the reaction ids returned in `reactions()`.
 """
-bounds(model::StandardModel)::Tuple{SparseVec,SparseVec} =
+bounds(model::StandardModel)::Tuple{Vector{Float64},Vector{Float64}} =
     (lower_bounds(model), upper_bounds(model))
 
 """

src/base/types/abstract/MetabolicModel.jl

@@ -105,11 +105,11 @@ function stoichiometry(a::MetabolicModel)::SparseMat
 end
 
 """
-    bounds(a::MetabolicModel)::Tuple{SparseVec,SparseVec}
+    bounds(a::MetabolicModel)::Tuple{Vector{Float64},Vector{Float64}}
 
 Get the lower and upper flux bounds of a model.
 """
-function bounds(a::MetabolicModel)::Tuple{SparseVec,SparseVec}
+function bounds(a::MetabolicModel)::Tuple{Vector{Float64},Vector{Float64}}
     _missing_impl_error(bounds, (a,))
 end
 
@@ -151,12 +151,12 @@ function n_coupling_constraints(a::MetabolicModel)::Int
 end
 
 """
-    coupling_bounds(a::MetabolicModel)::Tuple{SparseVec,SparseVec}
+    coupling_bounds(a::MetabolicModel)::Tuple{Vector{Float64},Vector{Float64}}
 
 Get the lower and upper bounds for each coupling bound in a model, as specified
 by `coupling`. By default, the model does not have any coupling bounds.
 """
-function coupling_bounds(a::MetabolicModel)::Tuple{SparseVec,SparseVec}
+function coupling_bounds(a::MetabolicModel)::Tuple{Vector{Float64},Vector{Float64}}
     return (spzeros(0), spzeros(0))
 end
 

src/reconstruction/CoreModel.jl

@@ -26,8 +26,8 @@ function add_reactions!(model::CoreModel, rxns::Vector{Reaction})
     Sadd = sparse(I, J, V, n_metabolites(model), length(rxns))
     model.S = [model.S Sadd]
     model.c = dropzeros([model.c; cs])
-    model.xu = sparse(ubs)
-    model.xl = sparse(lbs)
+    model.xu = ubs
+    model.xl = lbs
     return nothing
 end
 
@@ -42,25 +42,25 @@ add_reaction!(model::CoreModel, rxn::Reaction) = add_reactions!(model, [rxn])
 """
     add_reactions(
         m::CoreModel,
-        s::V1,
-        b::V2,
+        s::VecType,
+        b::VecType,
         c::AbstractFloat,
         xl::AbstractFloat,
         xu::AbstractFloat;
         check_consistency = false,
-    ) where {V1<:VecType,V2<:VecType}
+    )
 
 Add reaction(s) to a `CoreModel` model `m`.
 """
 function add_reactions(
     m::CoreModel,
-    s::V1,
-    b::V2,
+    s::VecType,
+    b::VecType,
     c::AbstractFloat,
     xl::AbstractFloat,
     xu::AbstractFloat;
     check_consistency = false,
-) where {V1<:VecType,V2<:VecType}
+)
     return add_reactions(
         m,
         sparse(reshape(s, (length(s), 1))),
@@ -75,27 +75,27 @@ end
 """
     add_reactions(
         m::CoreModel,
-        s::V1,
-        b::V2,
+        s::VecType,
+        b::VecType,
         c::AbstractFloat,
         xl::AbstractFloat,
         xu::AbstractFloat,
         rxn::String,
         mets::K;
         check_consistency = false,
-    ) where {V1<:VecType,V2<:VecType,K<:StringVecType}
+    )
 """
 function add_reactions(
     m::CoreModel,
-    s::V1,
-    b::V2,
+    s::VecType,
+    b::VecType,
     c::AbstractFloat,
     xl::AbstractFloat,
     xu::AbstractFloat,
     rxn::String,
-    mets::K;
+    mets::StringVecType;
     check_consistency = false,
-) where {V1<:VecType,V2<:VecType,K<:StringVecType}
+)
     return add_reactions(
         m,
         sparse(reshape(s, (length(s), 1))),
@@ -112,23 +112,23 @@ end
 """
     add_reactions(
         m::CoreModel,
-        Sp::M,
-        b::V,
-        c::V,
-        xl::V,