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https://github.com/ICB-DCM/PEtab/blob/367a0d1d893b30ec6d16d91122a148c96034d782/petab/visualize/helper_functions.py#L168
In the PEtab format the column "conditionName" is optional. If one chooses t…
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According to the documentation[1] it seems that the noiseParameters column is optional, however `petablint` and pypesto import fail in this scenario with:
```
Traceback (most recent call last):
…
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AttributeError: module 'petab.core' has no attribute 'get_optimization_to_simulation_parameter_mapping'
in: https://travis-ci.com/ICB-DCM/pyPESTO/builds/123856510
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If you chose log or log10 in the field `yScale` in the visualization file it has no effect on the plot.
Example Isensee:
![Figure_2](https://user-images.githubusercontent.com/49190262/70948304-711c1…
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Right now there is no really good way to handle visu files with a very large amount of plotIds.
The only option is to split it up in several files.
So two options solving this would be
- allowing…
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petab.core is getting quite large. organize functions a bit better. smaller files will also improve browsabiity of documentation.
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- 1 column for observation parameters (observableParameter1;observableParameter2), 1 column for noise parameters (noiseParameter1;noiseParameter2,...), parameters separated by semicolon
- add noise m…
LoosC updated
4 years ago
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At the moment all parameters in the SBML model need to be present in the parameters sheet (also the fixed parameters that are not subject to optimization). Might be more convenient to make it optional…
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Continuation of #17, see also #131, #206.
Currently, there are {priorX}, {initializationPriorX}, {objectivePriorX}, with X = {Type|Parameters}. The sole prior is supposed to simplify the setting wh…