Benchmark-Models-PEtab

Benchmark-Models-PEtab copied to clipboard

Add missing visualization files

2

- [ ] Bachmann_MSB2011 - [ ] Beer_MolBioSystems2014 - [ ] Blasi_CellSystems2016 - [ ] Borghans_BiophysChem1997 - [ ] Brannmark_JBC2010 - [ ] Crauste_CellSystems2017 - [ ] Elowitz_Nature2000 - [...

dilpath

Currently varies, with values like `COPASI0`, `arFramework3`, or the model name. Seen in #153 Possible options: - the model name - `benchmark_models_petab` `metaid` and annotation attributes are described in the...

dilpath

Fix bounds and scales for some parameters in Isensee_JCB2018

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dilpath

Add Jafarnejad et al.

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Add model from https://www.nature.com/articles/s41540-019-0107-2

LeonardSchmiester

Additional Model: D’Alessandro LA, Samaga R, Maiwald T et al. PLoS CB 2015

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https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004192

MerktSimon

Add Miao et al. (2010)

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https://jvi.asm.org/content/84/13/6687.long SBML: https://www.ebi.ac.uk/biomodels/BIOMD0000000546 Estimate of complexity: low

JanHasenauer

Fix Hass model

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Simulations from AMICI differ to the simulations reported in the original Benchmark collection. Maybe due to negative timepoints? Needs to be checked

LeonardSchmiester

Add new model Dudziak et al. (2019)

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https://www.sciencedirect.com/science/article/pii/S0022519319301936

LeonardSchmiester

https://www.embopress.org/doi/full/10.15252/msb.20198947

LeonardSchmiester

**Publication details:** - Title: _Parameter estimation and identifiability in a neural population model for electro-cortical activity_ **Reference:** - https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006694 **Code and model availability:** - https://github.com/cds-swinburne/Hartoyo-et-al-2019-DATA-n-CODE - MATLAB - SBML files...

stephanmg