PEtab
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PEtab-dev
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
* https://gitlab.com/fitmulticell/libpetab-python-MS * https://petab-select.readthedocs.io/en/latest/
Consider adding the Poisson and negative binomial distributions for parameter priors and noise models for PEtab v2.
Add a short tutorial for PEtab v2 based on the Boehm model (as done for PEtab v1). Closes #627. :eyes: https://petab--652.org.readthedocs.build/en/652/v2/tutorial/tutorial.html
Move the current [PEtab tutorial](https://petab.readthedocs.io/en/latest/tutorial.html) to a PEtab v1 section and add an updated version for PEtab v2. (After the v2 yaml file format is finalized -> #609)
Use `myst-parser` instead of `m2r2`. Fixes the following warning when building docs: ``` lib/python3.13/site-packages/m2r2.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal...
In PEtab v2 events are to be handled during pre-equilibration. I think it should be stated explicitly what the initial value is after pre-equilibration. My current interpretation of the specs...
I think it would be helpful to have some how-tos for addressing common application problems in PEtab (in additional to the basic tutorial). Some cases that come to mind: *...
We should add a clarification sentence about what are the start time and end time for simulations. This is important for time triggered events and be more explicit. - simulations...
