PEtab
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PEtab-dev
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Regarding the visualization specification in PEtab1.0: I was wondering whether the tsv format was really a good choice there. Currently each line in the visualization table corresponds to one data...
Currently different data series are combined into one single plot based on `plotId` in the visualization table. What about extending that to allow grouping different plots into figures? I.e. introducing...
Related to https://github.com/AMICI-dev/AMICI/issues/1319, i was wondering about the following: In case of preequilibration, should the occurrence in the condition table of any parameter that somehow impacts the initial state trigger...
Often models are parameterized in terms of rate constants `k_f` and `k_r` for which it's hard to provide a prior as opposed to equilibrium constants `K = k_f / k_r`....
Would be great to have. Maybe in an additional qualitative observation TSV file.
In the observable table one can introduce new output parameters (not specified in the SBML model) in observableFormula and noiseFormula. Is it allowed to use those parameters in the condition...
specifying 'noiseFormula' as 'lambda reg' will make https://github.com/ICB-DCM/AMICI/blob/16e3d762a94a35d21825f904d9d4381f82d117ab/python/amici/petab_import.py#L502 fail since `sp.sympify('lambda reg')`. I assume this will be a general issue and is not related to amici and that amici does...
Draft. Previously, the math expression syntax wasn't specified. This was very problematic, because different libraries and programming languages have different names for the same functions, and more importantly, differ in...
Here is a first draft of the petab result format. There are some open questions to it: - [ ] Which of the three versions should be keep? Personally I...
