SBMLToolkit and Catalyst Warnings

Specific Domains Modelling & Simulations
, ,
1

I am importing an SBML file without a problem but I got the following warnings:

Warning: Stoichiometries of SpeciesReferences are not defined. Setting to 1.

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

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

Do you know why this is happening?

Here is the code. The warnings happen on the last line:

using DifferentialEquations
using SBMLToolkit
using ModelingToolkit

SBMLToolkit.checksupport_file("toy_model_sbml.xml");
mdl = readSBML("toy_model_sbml.xml");
rn = ReactionSystem(mdl);
2

The warnings are benign but we’ll get them fixed very soon.

3

@Nick1 you might want to open an issue on SBMLToolkit.jl about the warning you are getting with your code and the specific SBML file you are importing. It might be that a more descriptive warning could be created in this case. I have no idea what “Warning: Stoichiometries of SpeciesReferences are not defined. Setting to 1.” means, and the main SBMLToolkit developer doesn’t use Discourse (he is on Slack though and looks at the sciml-sysbio channel – user @Paul Lang there).

1 Like
4

Thanks @isaacsas! I will open a topic