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SciML / CellMLToolkit.jl

CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.
https://docs.sciml.ai/CellMLToolkit/stable/
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Component model #39

Open anandijain opened 3 years ago

anandijain commented 3 years ago

Also a test on component model will be great to have

shahriariravanian commented 3 years ago

Look at https://libcellml.org/ . This is the official C++ library from the CellML folks. It is still a work in progress, but has many interesting test scenarios (components included). Let's take a look and see if we can adapt the tests.

anandijain commented 3 years ago

https://github.com/cellml/libcellml/issues/838

We should team up with these guys to come up with the DAE library

ChrisRackauckas commented 3 years ago

Note that you can use ODAEProblem and DAEProblem, instead of just ODEProblem, to handle alternative lowering behaviors like having D(x) on the RHS.

shahriariravanian commented 3 years ago

I agree. I've been going through the files that give an error and try to find the reason, especially for "value of X is not found" errors. Some CellML files are just defective (missing the initial_value), but some are caused by the circular definition of algebraic variables, which need DAE to solve.

anandijain commented 3 years ago

Feto is an example of the circular definition, right?

What's a model missing u0?

shahriariravanian commented 3 years ago

Probably, but it is such a large model that I haven't got to it. I'm starting with smaller models. One example is "saucerman_mcculloch_2004/saucerman_mcculloch_2004.cellml" (variable PKACII_RyR). Another example is "siebert_rode_herzog_till_blickhan_2008/siebert_CC_2008.cellml" (variables f_v and v_cc).