Catalyst.jl compositions with parameters as stoichiometric constants

Specific Domains Modelling & Simulations
, ,
1

I am trying to build a set of reaction models that I can compose together using Catalyst.jl, but running into a small problem.

Say I want to model a system and include stoichiometric terms as parameters. For instance, the A → B reaction parameterized such that A can produce n number of B’s:

using Catalyst
rn_simple = @reaction_network simple begin
    k1, A --> n*B
    k2, B --> C
end k1  k2 n

This evaluates and works just fine with all downstream tools.

However, lets say now I want to decouple the A->B step from the B->C reaction and compose them later:

rn_AB = @reaction_network AB begin
    k1, A --> n*B
end k1 n

rn_BC = @reaction_network BC begin
    k2, B --> C
end k2

This fails:

@variables t
@named rs = ReactionSystem(t; systems = [rn_AB, rn_BC])

MethodError: no method matching Reaction(::Sym{Real, Base.ImmutableDict{DataType, Any}}, ::Vector{Term{Real, Base.ImmutableDict{DataType, Any}}}, ::Vector{Term{Real, Base.ImmutableDict{DataType, Any}}}, ::Vector{Any}, ::Vector{Any}, ::Vector{Pair{Term{Real, Base.ImmutableDict{DataType, Any}}}}, ::Bool)
Closest candidates are:
  Reaction(::Any, ::Vector, ::Vector, ::Vector{T}, ::Vector{T}, ::Array{Pair{S, T}, 1}, ::Bool) where {S, T} at ~/.julia/packages/Catalyst/48igp/src/reactionsystem.jl:74
  Reaction(::Any, ::Any, ::Any, ::Any, ::Any; netstoich, only_use_rate, kwargs...) at ~/.julia/packages/Catalyst/48igp/src/reactionsystem.jl:100
  Reaction(::Any, ::Any, ::Any; kwargs...) at ~/.julia/packages/Catalyst/48igp/src/reactionsystem.jl:155

Stacktrace:
  [1] namespace_equation(rx::Reaction{Any, Any}, name::ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}})
    @ Catalyst ~/.julia/packages/Catalyst/48igp/src/reactionsystem.jl:195
  [2] (::ModelingToolkit.var"#79#80"{ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}}})(eq::Reaction{Any, Any})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/fWNRg/src/systems/abstractsystem.jl:390
  [3] iterate
    @ ./generator.jl:47 [inlined]
  [4] _collect(c::Vector{Reaction}, itr::Base.Generator{Vector{Reaction}, ModelingToolkit.var"#79#80"{ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}}}}, #unused#::Base.EltypeUnknown, isz::Base.HasShape{1})
    @ Base ./array.jl:744
  [5] collect_similar(cont::Vector{Reaction}, itr::Base.Generator{Vector{Reaction}, ModelingToolkit.var"#79#80"{ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}}}})
    @ Base ./array.jl:653
  [6] map(f::Function, A::Vector{Reaction})
    @ Base ./abstractarray.jl:2867
  [7] namespace_equations(sys::ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/fWNRg/src/systems/abstractsystem.jl:390
  [8] _broadcast_getindex_evalf
    @ ./broadcast.jl:670 [inlined]
  [9] _broadcast_getindex
    @ ./broadcast.jl:643 [inlined]
 [10] getindex
    @ ./broadcast.jl:597 [inlined]
 [11] copy
    @ ./broadcast.jl:899 [inlined]
 [12] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, typeof(ModelingToolkit.namespace_equations), Tuple{Vector{ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}}}}})
    @ Base.Broadcast ./broadcast.jl:860
 [13] equations(sys::ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}})
    @ Catalyst ~/.julia/packages/Catalyst/48igp/src/reactionsystem.jl:650
 [14] show(io::IOContext{IOBuffer}, mime::MIME{Symbol("text/plain")}, sys::ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/fWNRg/src/systems/abstractsystem.jl:715
 [15] limitstringmime(mime::MIME{Symbol("text/plain")}, x::ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}})
    @ IJulia ~/.julia/packages/IJulia/AQu2H/src/inline.jl:43
 [16] display_mimestring
    @ ~/.julia/packages/IJulia/AQu2H/src/display.jl:71 [inlined]
 [17] display_dict(x::ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}})
    @ IJulia ~/.julia/packages/IJulia/AQu2H/src/display.jl:102
 [18] #invokelatest#2
    @ ./essentials.jl:716 [inlined]
 [19] invokelatest
    @ ./essentials.jl:714 [inlined]
 [20] execute_request(socket::ZMQ.Socket, msg::IJulia.Msg)
    @ IJulia ~/.julia/packages/IJulia/AQu2H/src/execute_request.jl:112
 [21] #invokelatest#2
    @ ./essentials.jl:716 [inlined]
 [22] invokelatest
    @ ./essentials.jl:714 [inlined]
 [23] eventloop(socket::ZMQ.Socket)
    @ IJulia ~/.julia/packages/IJulia/AQu2H/src/eventloop.jl:8
 [24] (::IJulia.var"#15#18")()
    @ IJulia ./task.jl:429

WARNING: both Symbolics and ModelingToolkit export "infimum"; uses of it in module Catalyst must be qualified
WARNING: both Symbolics and ModelingToolkit export "supremum"; uses of it in module Catalyst must be qualified

However if I drop the n parameter, it composes just fine:

rn_AB_no_n = @reaction_network AB begin
    k1, A --> B
end k1

@named rs_no_n = ReactionSystem(t; systems = [rn_AB_no_n, rn_BC])

Am I doing something dumb here, or is this a bug?

2

It looks like when we added parametric stoichiometry we forgot to update the function that handles renaming subsystems for parameters in the stoichiometry. Sorry about that! I’ll put through a fix shortly.

1 Like
3

Thanks for the confirmation! Looking forward to the fix.

4

Version 12.2.1 should be out now with the fix. Feel free to let us know if you have further issues – the parametric stoichiometry is relatively new, and probably hasn’t been used with all the compositional features real thoroughly (they’ve been around longer).

5

Thanks so much for the super fast turnaround and all your great work on Catalyst!

1 Like