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sebapersson / PEtab.jl

Create parameter estimation problems for ODE models
https://sebapersson.github.io/PEtab.jl/stable/
MIT License
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Use Catalyst's `remove_conserved = true` option. #197

Open TorkelE opened 1 month ago

TorkelE commented 1 month ago

Catalyst have a feature for removing conservation laws from reaction systems (https://docs.sciml.ai/Catalyst/dev/model_creation/network_analysis/#network_analysis_conservation_laws) which could be useful to have as an option in PEtab to use. Currently, there are some MTK-induced problems (https://github.com/SciML/Catalyst.jl/issues/952) which should be considered so that they are avoided.

sebapersson commented 1 month ago

Thanks!

This would be a good option for PEtab to have, especially for models where we have to perform steady-state simulations as for these, it is easier to compute the steady-state if the ODE RHS has an invertible Jacobian. Moreover, we can also use more fun and efficient gradient methods with an invertible Jacobian.

I checked the attached issue, and as I understood it, in order to update everything correctly parameter updates must be applied via remake at the moment?

I also have some models we can test this one, once PEtab has updated to Catalyst v14.