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dkaschek / dMod

Dynamic modeling and parameter estimation in R
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PEtab (SBML) import to dMod #61

Open ivborissov opened 2 years ago

ivborissov commented 2 years ago

Hi, could you,please, clarify what is the current way to import PEtab models to dMod (in particular SBML files) ? I have tried PEtab2dmod library with libSBML 5.19 but I have a number of issues with SBML import. Namely, initialAssignments (formulas in my case) are not imported and some reactions are not fully imported too. Are there any restrictions on SBML features in PEtab2dmod ? I believe I can provide MWE if needed.

dlill commented 2 years ago

Dear Ivan,

the current support of SBML models is still very poor, even though a lot of progress on PEtab has been made recently in another package which uses dMod as backend: https://github.com/dlill/petab However, the import basically didn't change much in the new package compared to the PEtab2dmod function. If you could provide an example we could try to fix it (timescale >~1month, as we're all busy with other things). Formulas for initialAssignments have been on the list for quite a while, so it's good to have a use case for our implementation. Would this help you or is the proposed month too long?

Best Daniel

ivborissov commented 2 years ago

Hi Daniel,

thank you for your quick response! I will try to rewrite this model directly in dMod (it is not big). Does dMod support formulas for initial Assignments ? Also this model includes events and I haven't found similar examples in dMod documentation. In case the model I am testing may improve dMod - Petab (SBML) compatibility I am attaching SBML file model_1.zip .

dlill commented 2 years ago

Okay, thanks for the model. Initial assignments are handled via parameter transformations in dMod. A good start is for example the steadyStates vignette from Marcus https://dlill.github.io/html/steadyStates.html

ivborissov commented 2 years ago

Thanks for the link!