PEtab
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PEtab-dev
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Conditions should be calculable based on the model variables and parameters. E.g. I want to change S1 to 2*S1 in a condition. I.e. formulas should be allowed in the condition...
This draft PR adds the descriptions from the [Time course specification](https://docs.google.com/document/d/1Uo0mtU8Tb6m0yZc-A-NprDXeS-9ZDYPA8U3Y_aChqEM/edit) to the `release/2.0.0` branch. preview site is:
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 |...
@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...
Initially, `initializationPriorType` and `initializationPriorParameters` were introduced to provide prior distributions for sampling initial points in a multi-start optimization setting. For other global optimization schemes it is less clear how this...
Currently, noise and observable parameter placeholders require `_${observableId}` as suffix. This suffix appears to be redundant and superfluous to me, as they need to be specified in the measurements table...
**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...
See https://github.com/PEtab-dev/PEtab/issues/609 One could also think about adding the option to specify models for individual conditions, but that definitely sounds like extension territory.
There have been different interpretations of how parameter bounds and parameter priors interact. The current specifications don't address that explicitly. My interpretation would be that if a prior distribution exceeds...
So far, the [spec says](https://petab.readthedocs.io/en/latest/v1/documentation_data_format.html#parameter-estimation-problems-combining-multiple-models): > Parameter estimation problems can comprise multiple models. For now, PEtab allows to specify multiple SBML models with corresponding condition and measurement tables, and one...