PEtab
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PEtab-dev
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
To be discussed at a later point
It would be good to be able to include constraints on functions of parameters. e.g ```par1 = par2 + par3``` where only ```par2``` and ```par3``` are to be estimated but...
Currently there is no means of specifying a t_0 different from 0.0. Would be helpful to allow for that. If not, at least t < 0.0 should be reported as...
Documentation is inconsistent in using "observables table" and "observable table" https://petab.readthedocs.io/en/latest/documentation_data_format.html#observables-table Code seems to be pretty consistent with "observable_df", so maybe we should stick with that?
The format documentation often refers to "optimization", while "estimation" would probably be more general. PEtab is designed to also work with non-optimization based methods such as sampling, right?
**Which problem would you like to address? Please describe.** An elaborate, monolithic format would make it difficult to understand and implement support for PEtab, leading to a steep learning curve...
**Which problem would you like to address? Please describe.** Lack of specification of the format for formulae (e.g. observable/noise formulae) in PEtab tables. **Describe the solution you would like** A...
**Which problem would you like to address? Please describe.** It would be convenient if there was an option to scale data before plotting. E.g. the time unit in the model...
**Which problem would you like to address? Please describe.** Mapping of phospho-peptides to protein phospho sites can be ambiguous, leading to correlations in the measured data. This could be captured...
**Which problem would you like to address? Please describe.** It would be great if one could specify units for measurements (and potentially parameters) in PEtab in a systematic way. This...