Benchmark-Models-PEtab icon indicating copy to clipboard operation
Benchmark-Models-PEtab copied to clipboard
verified publisher icon Benchmarking-Initiative

Bachmann_MSB2011

Open dilpath opened this issue 7 months ago • 2 comments

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

For now, we should remove it from our collection.

dilpath avatar Jun 24 '25 08:06 dilpath

In https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010322#sec023 I did an exhaustive comparison to data2dynamics and found that our implementation matches what they have. If the paper figures don't match, I suspect there might be an issue with the d2d implementation.

FFroehlich avatar Jun 24 '25 08:06 FFroehlich

For us a very poor fit was reached, and that manifested in the visualizations (without using a PEtab visualization specification file).

I will dig again into the issue, and provide more details here then.

stephanmg avatar Jul 04 '25 17:07 stephanmg