Hello,
I have built several models of protein dynamics with ModelingToolkit.jl (using @mtkmodel and @mtkbuild) and I would like to perform a parameter identifiability assessement with StructuralIdentifiability.jl.
But apparently I’m unable to pass the ODE system built with @mtkbuilt to StructuralIdentifiability.assess_local_identifiability(). It cannot find the output functions although they have been specified. It works if I define the ODE system with @ODEmodel as explained on the tutorial: ODE Tools · StructuralIdentifiability.jl, but if possible, I’d like to avoid having to redefine all models.
As an example, here is the error message I get when I copy-paste the code provided on ModelingToolkit tutorial: Parameter Identifiability in ODE Models · ModelingToolkit.jl
using StructuralIdentifiability, ModelingToolkit
using ModelingToolkit: t_nounits as t, D_nounits as D
@mtkmodel Biohydrogenation begin
@variables begin
x4(t)
x5(t)
x6(t)
x7(t)
y1(t), [output = true]
y2(t), [output = true]
end
@parameters begin
k5
k6
k7
k8
k9
k10
end
# define equations
@equations begin
D(x4) ~ -k5 * x4 / (k6 + x4)
D(x5) ~ k5 * x4 / (k6 + x4) - k7 * x5 / (k8 + x5 + x6)
D(x6) ~ k7 * x5 / (k8 + x5 + x6) - k9 * x6 * (k10 - x6) / k10
D(x7) ~ k9 * x6 * (k10 - x6) / k10
y1 ~ x4
y2 ~ x5
end
end
# define the system
@mtkbuild de = Biohydrogenation()
# query local identifiability
# we pass the ode-system
local_id_all = assess_local_identifiability(de, prob_threshold = 0.99)
ERROR: LoadError: Measured quantities (output functions) were not provided and no outputs were found.
I get the same error message with my MTK models. Does anyone know how to fix this?