Jan Hasenauer

uniform vs. logUniform prior

30

so far we only allow for uniform, however, we should in my opinion distinguish between uniform and logUniform. in most cases we use actually log-uniform as we consider a uniform...

fixed parameters

4

In the branch feature_new_optimizers, we offer the possibility of fixing some parameters. Currently, this "option" is provided by PestoOptions. As PestoOptions is however not provided to routines such as getParameterConfidenceIntervals,...

Generation of report

3

It would be nice to have a routine which summarises the available results of the fitting in a report, e.g., slides generated using latex beamer. This could improve the workflow...

improvement of sampling pipeline

4

Sampling currently requires quite a bit of manual work, e.g. shortening of chains, ... . I think it would be great to have a routine which performs multiple sampling runs,...

Add Heldt et al. (2012)

2

https://www.ncbi.nlm.nih.gov/pubmed/22593159 SBML: https://www.ebi.ac.uk/biomodels/BIOMD0000000463 Estimated complexity of implementation: low

Add Miao et al. (2010)

2

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

https://www.embopress.org/doi/full/10.1038/msb.2013.19 SBML model: https://www.ebi.ac.uk/biomodels/BIOMD0000000482 Complexity: medium

Write function to generate benchmark_model_characteristics.xlsx automatically

4

Most of the fields are very easy to fill. We simply need the bibtex files for the models in the respective folders and (optional) also a remark file (in case...

Additional Model: Jignesh H. Parmar & Pedro Mendes, PLoS CB, 2019

6

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006680 The model is also available in BioModels

Add Fribourg et al. (2014)

5

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012420/ SBML: https://www.ebi.ac.uk/biomodels/BIOMD0000000529#Overview Estimated complexity of implementation: low