Dilan Pathirana

Some background in this thesis "Mathematical Modeling to Connect Bone Responses to Systemic Mechanisms" https://www.proquest.com/docview/3068633067?pq-origsite=gscholar&fromopenview=true&sourcetype=Dissertations+&+Theses= The paper is: https://aiche.onlinelibrary.wiley.com/doi/full/10.1002/aic.17809 SBML model and code here: https://github.com/ashleefv/Wnt10bBoneCompartment

Long formats for conditions and experiments (timecourses)

3

Follow-up to https://github.com/PEtab-dev/PEtab/issues/585 (no need to read that). Here are specs for long formats of the conditions and experiments (timecourses) tables. Additional feedback is very welcome! # Conditions table |...

Use somewhat normalized "experiments" table instead of conditions/timecourses

16

@matthiaskoenig and others have suggested we make our tables more [normalized](https://en.wikipedia.org/wiki/Database_normalization). Instead of a timecourses table (#581), I would suggest an experiments table, which merges the conditions and timecourses tables...

Since it's generally recommended, it would be good to have it in the examples. e.g. https://github.com/ICB-DCM/pyPESTO/blob/ead29b36db80d2eeee91b5d29bfbf4430137f8aa/pypesto/objective/base.py#L431

Support `sensi_orders` in gradient checks

1

While debugging another model, the issue arose again that sometimes `Objective(x, sensi_orders=(0,))` provides a different `fval` than `Objective(x, sensi_orders=(0,1))`. Tolerances etc. can be adjusted until these two are similar; however,...

Continuing on #1461 / #1473 It looks like there is unnecessary computation in the evidence tests. There are `optimize.minimize` and `sample.sample` calls there. These could be done once locally and...

Isensee_JCB2018: fix SBML parameter values

2

In #132, this problem was changed to remove model selection parameters (if they were not selected). All model selection parameters in the SBML model were also set to 0. This...

v2: Add log10-uniform distribution to support conversion from v1

1

**Which problem would you like to address? Please describe.** v1 problems support `parameterScale=log10`. There is no way to convert this into a v2 problem currently. `parameterScale=log` is not an issue...

Bachmann_MSB2011

2

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...

Select: postprocessor to save models to YAML intermediately

1

Useful to save models as they are calibrated, rather than at the end of model selection. This means model selection can be restarted without needing to recalibrate models, if e.g....