Benchmark-Models-PEtab

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add visualization spec for Raimundez model

3

Figure 1C Figure 1D

plakrisenko

Visualize model fit with libpetab and deploy plots to GitHub pages. WIP :eyes: https://benchmarking-initiative.github.io/Benchmark-Models-PEtab/reports/index.html :eyes: https://benchmarking-initiative.github.io/Benchmark-Models-PEtab/reports/Alkan_SciSignal2018.html (currently only available if there were no pushes to master since the last update...

dweindl

Add a rough check for whether simulation tables are in the proper format (related to #278). (What *is* the proper format remains to be discussed - see also https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/issues/280)

dweindl

Validate simulation tables

1

Re: #276, #275, #277 Implement checks for simulation tables. Make sure that `petab.v1.calculate.calculate_llh` succeeds, and ideally, confirm that value with a simulator.

dweindl

I have the feeling the current simulation tables are less helpful than they could be. My understanding is that they are there to 1) facilitate assessing the goodness of fit...

dweindl

Comparing https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/f7af1eddbedee793a8eca113124d1a2f1e73d360/Benchmark-Models/Weber_BMC2015/measurementData_Weber_BMC2015.tsv and https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/f7af1eddbedee793a8eca113124d1a2f1e73d360/Benchmark-Models/Weber_BMC2015/simulatedData_Weber_BMC2015.tsv: `preequilibrationConditionId`, `observableParameters` and `noiseParameters` are missing in the simulations table

dweindl

Script for converting the current problems to PEtab v2.

dweindl

Bachmann_MSB2011

2

Users have reported that they are unable to reproduce paper figures with the current version in our collection. The problem should be updated to match the implementation in Data2Dynamics. https://github.com/Data2Dynamics/d2d/tree/master/arFramework3/Examples/Bachmann_MSB2011...

dilpath

Add Hoepfl_PLOSComputBiol2025

1

*Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor* https://doi.org/10.1371/journal.pcbi.1013076 PEtab files available online.

dweindl