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Petab tutorial #695

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Petab tutorial #695

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TorkelE
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@TorkelE TorkelE commented Sep 27, 2023

Creates a tutorial on how to use PEtab (https://github.com/sebapersson/PEtab.jl/) to fit the parameters of ODE CRNs to data (adapted from that documentation to provide a shorter summary to get someone started).

What is currently missing:

  1. Plots to evaluate optimisation runs are not complete yet (Add plot recipes for PEtabOptimisationResult sebapersson/PEtab.jl#83). When that is done, I will complete that tutorial.
  2. The get_best_ps function is not yet implemented in PEtab (but hopefully will be soon Function for retrieving a full parameter set from a calibration output sebapersson/PEtab.jl#85).
  3. PEtab does not currently support events, so that section will be empty until it does.
  4. It is possible to have different parameters for different experimental/simulation conditions. I started a tutorial for this, but haven't completed it yet (still figuring out the best way to do this).

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TorkelE commented Sep 28, 2023

This includes some new stuff, so the documentary will fail until PEtab 2.0 is released.

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TorkelE commented Oct 7, 2023

I am not sure if that did things any better, but now ti should be on the master at lesat.

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isaacsas commented Oct 7, 2023

It is still showing a ton of merged and existing code as part of this PR.

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TorkelE commented Oct 7, 2023

When I try rebasing this on master it all shows up OK. I think Git have just gone bananas between this and other PRs, and most of these changes are just basically synching this with older stuff. I think the only work around would be to create a new PR.

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TorkelE commented Oct 7, 2023

Closed by #701

@TorkelE TorkelE closed this Oct 7, 2023
@TorkelE TorkelE deleted the PEtab_tutorial branch June 8, 2024 18:32
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4 participants