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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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Add Armistead_CellDeathDis2024 #248

Open m-philipps opened 2 days ago

m-philipps commented 2 days ago

replaces #247 to match the model ID.

The model describes the synthesis of Sphinganine and successive conversion to Ceramide, Sphingosine and Sphingosine-1-phosphate (S1P); and the inhibition through hai1a. There are measurements for all 4 species from antibody stainings of zebrafish epidermal cells, in wildtype animals and hai1a deletion mutants. Spinganine, Ceramide and Sphingosine were measured at two time points (2 and 4 days after fertilization) in quadruplicates, S1P was measured only at 2 days after fertilization, in five replicates.

According to the publication:

Parameter estimation was done with the hybrid Hessian approximation algorithm Fides with 100 starts.

The scripts that were published alongside the manuscript used 200 starts for the Fides optimizer, AMICI for simulation, forward sensitivities, absolute = relative tolerances = 1e-7. Calibration was very fast to reproduce, the fit is very good and 85/200 optimization results converge to the same parameters:

parameters

model_fit_legend

The nominal parameters were taken from the original publication.

https://doi.org/10.1038/s41419-024-07134-2

m-philipps commented 19 hours ago

The information from the publication's Figure 4 k) can be reproduced using the visualization table, but the PEtab visualization specification is not flexible enough to reproduce the Figure visually.

dilpath commented 16 hours ago

The information from the publication's Figure 4 k) can be reproduced using the visualization table, but the PEtab visualization specification is not flexible enough to reproduce the Figure visually.

When working on this, I noticed the model timepoints 0 and 2 appear to correspond to 2 and 4 (respectively) days past fertilization in Fig 4k.