Benchmark-Models-PEtab

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cleanup empty annotations

matthiaskoenig

Roadmap for the next PEtab version

1

- [ ] move repo to `PEtab-dev` org - [ ] rename repo `benchmark-problems` (i.e. `PEtab-dev/benchmark-problems`) - [ ] rename `Benchmark-Models` directory to `problem` (i.e. `PEtab-dev/benchmark-problems/problems`) - [ ] add...

dilpath

> Visualization table references datasetId(s) {'model1_data1_IRsum'}, but no such dataset(s) exist in the measurement table Surfaced while testing https://github.com/PEtab-dev/libpetab-python/pull/255

dweindl

Add models with oscillations

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We discussed that it would be interesting to have some oscillatory models in the collection. Anyone have ideas for models including real experimental data?

LeonardSchmiester

The model of hepatocyte growth factor (HGF) signal transduction combined with global proteomics, captures HGF-induced signal transduction via the MAPK cascade, the PI3K pathway and mTOR signaling. https://doi.org/10.1038/s44320-023-00007-4 https://www.ebi.ac.uk/biomodels/MODEL2306280002 Available...

plakrisenko

Add Mishra_MetabEng2023

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A kinetic metabolic model of lipid metabolism in Saccharomyces cerevisiae that integrates fatty acid biosynthesis, glycerophospholipid metabolism, sphingolipid metabolism, storage lipids, lumped sterol synthesis, and the synthesis and transport of...

plakrisenko

Dynamic modeling of Nrf2 pathway activation in liver cells after toxicant exposure. https://doi.org/10.1038/s41598-022-10857-x The model is available in PEtab: https://github.com/JetiLab/Nrf2-signaling.

plakrisenko

Finish Raia model

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Cannot validate the model with AMICI as the noise model is not supported yet.

LeonardSchmiester

Add new model Leonhardt et al. (2014)

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https://www.sciencedirect.com/science/article/pii/S1549963413006734?via%3Dihub https://www.nature.com/articles/s41540-018-0079-7 PESTO Example: https://github.com/ICB-DCM/PESTO/tree/master/examples/mRNA_transfection

LeonardSchmiester

Adding suggestion of optimizers for benchmark models.

3

stephanmg