Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Implement system functions (Hill and michaelis-menten) via Symbolics.jl #327

Merged
merged 11 commits into from
Apr 26, 2021
Merged

Implement system functions (Hill and michaelis-menten) via Symbolics.jl #327

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
f33b862
initial_upload
TorkelE Apr 20, 2021
56ada92
skip_problem_test
TorkelE Apr 20, 2021
deeaf7a
modify_tests
TorkelE Apr 20, 2021
46ea8da
add_hillAR_test
TorkelE Apr 20, 2021
4784520
swap out network which didn't make sense
TorkelE Apr 20, 2021
419a6ca
reduce_test_limit
TorkelE Apr 20, 2021
39882c5
requires_mtk_5_15
TorkelE Apr 20, 2021
8fa0d1d
enable latexify to read functions
TorkelE Apr 21, 2021
b3aae31
see_if_it_works_wothout_latexify_tests
TorkelE Apr 21, 2021
b7b78b2
re-generate latexify tests
TorkelE Apr 21, 2021
1a84043
additional_tests
TorkelE Apr 23, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions Project.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
Requires = "ae029012-a4dd-5104-9daa-d747884805df"
Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"

[compat]
DataStructures = "0.18"
Expand All @@ -21,6 +22,7 @@ ModelingToolkit = "5.14.0"
Parameters = "0.12"
Reexport = "0.2, 1.0"
Requires = "1.0"
Symbolics = "0.1.22"
julia = "1.5"

[extras]
Expand Down
4 changes: 4 additions & 0 deletions src/Catalyst.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ const DEFAULT_IV = (@parameters t)[1]
@reexport using ModelingToolkit
import MacroTools
import Base: (==), merge!, merge
using Symbolics
using Latexify, Requires

# as used in Catlab
Expand All @@ -33,6 +34,9 @@ include("reaction_network.jl")
# reaction network macro
export @reaction_network, @add_reactions

# registers CRN specific functions using Symbolics.jl
include("registered_functions.jl")

# functions to query network properties
include("networkapi.jl")
export species, params, reactions, speciesmap, paramsmap, numspecies, numreactions, numparams
Expand Down
16 changes: 0 additions & 16 deletions src/reaction_network.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -268,25 +268,9 @@ function recursive_expand_functions!(expr::ExprValues)
(typeof(expr)!=Expr) && (return expr)
foreach(i -> expr.args[i] = recursive_expand_functions!(expr.args[i]), 1:length(expr.args))
if expr.head == :call
in(expr.args[1],hill_name) && return hill(expr)
in(expr.args[1],hillR_name) && return hillR(expr)
in(expr.args[1],mm_name) && return mm(expr)
in(expr.args[1],mmR_name) && return mmR(expr)

!isdefined(Catalyst,expr.args[1]) && (expr.args[1] = esc(expr.args[1]))
end
return expr
end

#Hill function made avaiable (activation and repression).
hill_name = Set{Symbol}([:hill, :Hill, :h, :H, :HILL])
hill(expr::Expr) = :($(expr.args[3])*($(expr.args[2])^$(expr.args[5]))/($(expr.args[4])^$(expr.args[5])+$(expr.args[2])^$(expr.args[5])))
hillR_name = Set{Symbol}([:hill_repressor, :hillr, :hillR, :HillR, :hR, :hR, :Hr, :HR, :HILLR])
hillR(expr::Expr) = :($(expr.args[3])*($(expr.args[4])^$(expr.args[5]))/($(expr.args[4])^$(expr.args[5])+$(expr.args[2])^$(expr.args[5])))

#Michaelis-Menten function made available (activation and repression).
mm_name = Set{Symbol}([:MM, :mm, :Mm, :mM, :M, :m])
mm(expr::Expr) = :($(expr.args[3])*$(expr.args[2])/($(expr.args[4])+$(expr.args[2])))
mmR_name = Set{Symbol}([:mm_repressor, :MMR, :mmr, :mmR, :MmR, :mMr, :MR, :mr, :Mr, :mR])
mmR(expr::Expr) = :($(expr.args[3])*$(expr.args[4])/($(expr.args[4])+$(expr.args[2])))

106 changes: 106 additions & 0 deletions src/registered_functions.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,106 @@
using Symbolics

# Registers the Michaelis-Menten function.
mm(X,v,K) = v*X / (X + K)
Mm(X,v,K) = v*X / (X + K)
MM(X,v,K) = v*X / (X + K)

@register mm(X,v,K); @register Mm(X,v,K); @register MM(X,v,K);

Symbolics.derivative(::typeof(mm), args::NTuple{3,Any}, ::Val{1}) = (args[2]*args[3]) / (args[1]+args[3])^2
Symbolics.derivative(::typeof(mm), args::NTuple{3,Any}, ::Val{2}) = args[1]/(args[1]+args[3])
Symbolics.derivative(::typeof(mm), args::NTuple{3,Any}, ::Val{3}) = - args[2]*args[1]/(args[1]+args[3])^2

Symbolics.derivative(::typeof(Mm), args::NTuple{3,Any}, ::Val{1}) = (args[2]*args[3]) / (args[1]+args[3])^2
Symbolics.derivative(::typeof(Mm), args::NTuple{3,Any}, ::Val{2}) = args[1]/(args[1]+args[3])
Symbolics.derivative(::typeof(Mm), args::NTuple{3,Any}, ::Val{3}) = - args[2]*args[1]/(args[1]+args[3])^2

Symbolics.derivative(::typeof(MM), args::NTuple{3,Any}, ::Val{1}) = (args[2]*args[3]) / (args[1]+args[3])^2
Symbolics.derivative(::typeof(MM), args::NTuple{3,Any}, ::Val{2}) = args[1]/(args[1]+args[3])
Symbolics.derivative(::typeof(MM), args::NTuple{3,Any}, ::Val{3}) = - args[2]*args[1]/(args[1]+args[3])^2

# Registers the repressing Michaelis-Menten function.
mmR(X,v,K) = v*K / (X + K)
MmR(X,v,K) = v*K / (X + K)
MMR(X,v,K) = v*K / (X + K)

@register mmR(X,v,K); @register MmR(X,v,K); @register MMR(X,v,K);

Symbolics.derivative(::typeof(mmR), args::NTuple{3,Any}, ::Val{1}) = (args[2]*args[3]) / (args[1]+args[3])^2
Symbolics.derivative(::typeof(mmR), args::NTuple{3,Any}, ::Val{2}) = args[3]/(args[1]+args[3])
Symbolics.derivative(::typeof(mmR), args::NTuple{3,Any}, ::Val{3}) = - args[2]*args[1]/(args[1]+args[3])^2

Symbolics.derivative(::typeof(MmR), args::NTuple{3,Any}, ::Val{1}) = (args[2]*args[3]) / (args[1]+args[3])^2
Symbolics.derivative(::typeof(MmR), args::NTuple{3,Any}, ::Val{2}) = args[3]/(args[1]+args[3])
Symbolics.derivative(::typeof(MmR), args::NTuple{3,Any}, ::Val{3}) = - args[2]*args[1]/(args[1]+args[3])^2

Symbolics.derivative(::typeof(MMR), args::NTuple{3,Any}, ::Val{1}) = (args[2]*args[3]) / (args[1]+args[3])^2
Symbolics.derivative(::typeof(MMR), args::NTuple{3,Any}, ::Val{2}) = args[3]/(args[1]+args[3])
Symbolics.derivative(::typeof(MMR), args::NTuple{3,Any}, ::Val{3}) = - args[2]*args[1]/(args[1]+args[3])^2


# Registers the Hill function.
hill(X,v,K,n) = v*(X^n) / (X^n + K^n)
Hill(X,v,K,n) = v*(X^n) / (X^n + K^n)

@register hill(X,v,K,n); @register Hill(X,v,K,n);

Symbolics.derivative(::typeof(hill), args::NTuple{4,Any}, ::Val{1}) = args[2] * args[4] * (args[3]^args[4]) * (args[1]^(args[4]-1)) / (args[1]^args[4] + args[3]^args[4])^2
Symbolics.derivative(::typeof(hill), args::NTuple{4,Any}, ::Val{2}) = (args[1]^args[4]) / (args[1]^args[4] + args[3]^args[4])
Symbolics.derivative(::typeof(hill), args::NTuple{4,Any}, ::Val{3}) = - args[2] * args[4] * (args[1]^args[4]) * (args[3]^(args[4]-1)) / (args[1]^args[4] + args[3]^args[4])^2
Symbolics.derivative(::typeof(hill), args::NTuple{4,Any}, ::Val{4}) = args[2] * (args[1]^args[4]) * (args[3]^args[4]) * (log(args[1])-log(args[3])) / (args[1]^args[4] + args[3]^args[4])^2

Symbolics.derivative(::typeof(Hill), args::NTuple{4,Any}, ::Val{1}) = args[2] * args[4] * (args[3]^args[4]) * (args[1]^(args[4]-1)) / (args[1]^args[4] + args[3]^args[4])^2
Symbolics.derivative(::typeof(Hill), args::NTuple{4,Any}, ::Val{2}) = (args[1]^args[4]) / (args[1]^args[4] + args[3]^args[4])
Symbolics.derivative(::typeof(Hill), args::NTuple{4,Any}, ::Val{3}) = - args[2] * args[4] * (args[1]^args[4]) * (args[3]^(args[4]-1)) / (args[1]^args[4] + args[3]^args[4])^2
Symbolics.derivative(::typeof(Hill), args::NTuple{4,Any}, ::Val{4}) = args[2] * (args[1]^args[4]) * (args[3]^args[4]) * (log(args[1])-log(args[3])) / (args[1]^args[4] + args[3]^args[4])^2


# Registers the repressing hill function (alterantive to negative n).
hillR(X,v,K,n) = v*(K^n) / (X^n + K^n)
HillR(X,v,K,n) = v*(K^n) / (X^n + K^n)

@register hillR(X,v,K,n); @register HillR(X,v,K,n);

Symbolics.derivative(::typeof(hillR), args::NTuple{4,Any}, ::Val{1}) = - args[2] * args[4] * (args[3]^args[4]) * (args[1]^(args[4]-1)) / (args[1]^args[4] + args[3]^args[4])^2
Symbolics.derivative(::typeof(hillR), args::NTuple{4,Any}, ::Val{2}) = (args[3]^args[4]) / (args[1]^args[4] + args[3]^args[4])
Symbolics.derivative(::typeof(hillR), args::NTuple{4,Any}, ::Val{3}) = args[2] * args[4] * (args[1]^args[4]) * (args[3]^(args[4]-1)) / (args[1]^args[4] + args[3]^args[4])^2
Symbolics.derivative(::typeof(hillR), args::NTuple{4,Any}, ::Val{4}) = args[2] * (args[1]^args[4]) * (args[3]^args[4]) * (log(args[3])-log(args[1])) / (args[1]^args[4] + args[3]^args[4])^2

Symbolics.derivative(::typeof(HillR), args::NTuple{4,Any}, ::Val{1}) = - args[2] * args[4] * (args[3]^args[4]) * (args[1]^(args[4]-1)) / (args[1]^args[4] + args[3]^args[4])^2
Symbolics.derivative(::typeof(HillR), args::NTuple{4,Any}, ::Val{2}) = (args[3]^args[4]) / (args[1]^args[4] + args[3]^args[4])
Symbolics.derivative(::typeof(HillR), args::NTuple{4,Any}, ::Val{3}) = args[2] * args[4] * (args[1]^args[4]) * (args[3]^(args[4]-1)) / (args[1]^args[4] + args[3]^args[4])^2
Symbolics.derivative(::typeof(HillR), args::NTuple{4,Any}, ::Val{4}) = args[2] * (args[1]^args[4]) * (args[3]^args[4]) * (log(args[3])-log(args[1])) / (args[1]^args[4] + args[3]^args[4])^2


# Registers the activation/repressing hill function.
hillC(X,Y,v,K,n) = v*(X^n) / (X^n + Y^n + K^n)
hillAR(X,Y,v,K,n) = v*(X^n) / (X^n + Y^n + K^n)
HillC(X,Y,v,K,n) = v*(X^n) / (X^n + Y^n + K^n)
HillAR(X,Y,v,K,n) = v*(X^n) / (X^n + Y^n + K^n)

@register hillC(X,Y,v,K,n); @register hillAR(X,Y,v,K,n); @register HillC(X,Y,v,K,n); @register HillAR(X,Y,v,K,n);

Symbolics.derivative(::typeof(hillC), args::NTuple{5,Any}, ::Val{1}) = args[3] * args[5] * (args[1]^(args[5]-1)) * (args[2]^args[5]+args[4]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(hillC), args::NTuple{5,Any}, ::Val{2}) = - args[3] * args[5] * (args[2]^(args[5]-1)) * (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(hillC), args::NTuple{5,Any}, ::Val{3}) = (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])
Symbolics.derivative(::typeof(hillC), args::NTuple{5,Any}, ::Val{4}) = - args[3] * args[5] * (args[3]^(args[5]-1)) * (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(hillC), args::NTuple{5,Any}, ::Val{5}) = args[3] * (args[1]^args[5]) * (log(args[1])*(args[2]^args[5] + args[4]^args[5]) - (args[2]^args[5])*log(args[2]) - (args[4]^args[5])*log(args[4])) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2

Symbolics.derivative(::typeof(hillAR), args::NTuple{5,Any}, ::Val{1}) = args[3] * args[5] * (args[1]^(args[5]-1)) * (args[2]^args[5]+args[4]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(hillAR), args::NTuple{5,Any}, ::Val{2}) = - args[3] * args[5] * (args[2]^(args[5]-1)) * (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(hillAR), args::NTuple{5,Any}, ::Val{3}) = (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])
Symbolics.derivative(::typeof(hillAR), args::NTuple{5,Any}, ::Val{4}) = - args[3] * args[5] * (args[3]^(args[5]-1)) * (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(hillAR), args::NTuple{5,Any}, ::Val{5}) = args[3] * (args[1]^args[5]) * (log(args[1])*(args[2]^args[5] + args[4]^args[5]) - (args[2]^args[5])*log(args[2]) - (args[4]^args[5])*log(args[4])) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2

Symbolics.derivative(::typeof(HillC), args::NTuple{5,Any}, ::Val{1}) = args[3] * args[5] * (args[1]^(args[5]-1)) * (args[2]^args[5]+args[4]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(HillC), args::NTuple{5,Any}, ::Val{2}) = - args[3] * args[5] * (args[2]^(args[5]-1)) * (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(HillC), args::NTuple{5,Any}, ::Val{3}) = (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])
Symbolics.derivative(::typeof(HillC), args::NTuple{5,Any}, ::Val{4}) = - args[3] * args[5] * (args[3]^(args[5]-1)) * (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(HillC), args::NTuple{5,Any}, ::Val{5}) = args[3] * (args[1]^args[5]) * (log(args[1])*(args[2]^args[5] + args[4]^args[5]) - (args[2]^args[5])*log(args[2]) - (args[4]^args[5])*log(args[4])) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2

Symbolics.derivative(::typeof(HillAR), args::NTuple{5,Any}, ::Val{1}) = args[3] * args[5] * (args[1]^(args[5]-1)) * (args[2]^args[5]+args[4]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(HillAR), args::NTuple{5,Any}, ::Val{2}) = - args[3] * args[5] * (args[2]^(args[5]-1)) * (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(HillAR), args::NTuple{5,Any}, ::Val{3}) = (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])
Symbolics.derivative(::typeof(HillAR), args::NTuple{5,Any}, ::Val{4}) = - args[3] * args[5] * (args[3]^(args[5]-1)) * (args[1]^args[5]) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2
Symbolics.derivative(::typeof(HillAR), args::NTuple{5,Any}, ::Val{5}) = args[3] * (args[1]^args[5]) * (log(args[1])*(args[2]^args[5] + args[4]^args[5]) - (args[2]^args[5])*log(args[2]) - (args[4]^args[5])*log(args[4])) / (args[1]^args[5] + args[2]^args[5] + args[4]^args[5])^2