Visualization files for all models (list)

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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Visualization files for all models (list) #28

Open MerktSimon opened 5 years ago

MerktSimon commented 5 years ago

This issue serves as an overview of which models already have the visualization file. During the work on each model this model's issue should be re-opened. Once all models have one this can be closed.

Models which already have a visualization file:

Isensee
Chen
Fujita
Swameye_PNAS2003
Boehm
Bruno_JExpBio2016
Raia_CancerResearch2011

MerktSimon commented 5 years ago

Since a lacking visualization file is not a PEtab error, reopening LeonardSchmiester/Benchmark-Models#53 didn't seem to fit. But of course this can be discussed. Also re-opening all models' issues could work but seems a bit confusing

MerktSimon commented 4 years ago

Fujita does not actually have a file yet. It only serves as example for no-file visualization in PEtab. Hence I removed it from the list. Thanks @erikadudki for pointing it out.

erikadudki commented 4 years ago

I just added a visualization file for the Chen model.

erikadudki commented 4 years ago

I will work now on the visualization file for the Fujita model. Fujita visualization file finished!

erikadudki commented 4 years ago

working now on Boehm

LaraFuhrmann commented 4 years ago

Added visualization file for Swameye_PNAS2003. Plots fit with the plots in the publication.

LaraFuhrmann commented 4 years ago

Added visualization file for Bruno_JExpBio2016. Measurements of model1_data3 and model1_data6 seem a bit odd to me, since some measurements are in the range of [0,3] and others in the range of [1000,2500] Edit: change to log10-scale for those measurement values

erikadudki commented 4 years ago

added visualization file for Raia_CancerResearch2011

dweindl commented 4 years ago

Would be great if you could also update the YAML files when adding new vis tables (see Bruno for example).