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Benchmarking-Initiative / Benchmark-Models-PEtab

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
BSD 3-Clause "New" or "Revised" License
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new format for swameye #23

Open LoosC opened 6 years ago

dweindl commented 5 years ago

Model parameter 'spline_t_0' neither present in condition table nor in parameter table.

LoosC commented 5 years ago

aaah the spline, need to think about how to treat this one...

paulstapor commented 4 years ago

Just saw this... An assignment rule might do the trick, maybe? Dunno if SBML knows something like a spline-function however... Guess almost that "no", as zillions of splines are possible and just defining "some" spline is not well-defined then...

LeonardSchmiester commented 4 years ago

In the original version of the model from the old repository, it is done via an assignment rule and events. I guess we could just use that one as soon as events are implemented?! ;-)

paulstapor commented 3 years ago

We can use this one, but I'd actually be happy to use the new spline implementation as soon as this one is finished. That will change the model to some degree (as now Amici will get cubic Hermite splines and originally the model had cubic C2 splines), but also using events instead of splines does so, so I think it's overall fine...

dweindl commented 1 year ago

https://github.com/AMICI-dev/AMICI/pull/1515 contains this model. the spline is added there as piecewise. should be easy now to include that in the benchmark collection