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Enable model simulations from within petabvis #16

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dweindl opened this issue Mar 4, 2021 · 2 comments
Open

Enable model simulations from within petabvis #16

dweindl opened this issue Mar 4, 2021 · 2 comments

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@dweindl
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dweindl commented Mar 4, 2021

It would be convenient if one could generate the simulation data from within the tool in addition to providing an externally generated file. One option would be using https://github.com/SMRuggiero/sbmltoodepy.
@dilpath
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dilpath commented Mar 8, 2021

Might be nice to use the output of a petab.simulate.Simulator.simulate call. If so, then simulators could be automatically detected and used via a common interface. The output of a PEtab Simulator is a PEtab simulation df, so it should be possible to implement this functionality in petabvis with just a few lines of codes.

If the PEtab Simulator is used, then currently anyone with a working AMICI installation should be able to use it easily (example in pyPESTO). Anyone with python-copasi installed could also use it soon hopefully (still working on it), and I guess python-copasi is as convenient to install as sbmltoodepy.

@dweindl
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dweindl commented Mar 8, 2021

Sounds good.

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@dweindl @dilpath