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Need to adapt optimization to simulation parameter mapping (`core.get_optimization_to_simulation_parameter_mapping`). What else?
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Pass observable scale like lin, log, log10 as specified in measurement_file to amici (amici can do that, right? or do we have to apply the transformation manually beforehand?)
the way to go would p…
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When compiling an amici model in petab, the default location is currently ``./tmp/MODEL_NAME``. One might replace tmp by ``amici_models`` or something like that, since it is not really temporary files…
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Using at least one of the benchmark models. See test/test_petab_import.py.
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E.g.
- finalize column names
- rules for observable names
- rules for scaling parameter names in model and data files (`_offset_`, _scaling_`, `_sigma_`)
- specification of timepoints, inf, units…
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Currently only global SBML parameters are included. There should be an option to also include local ones. This is a bit tricky since there can be multiple local parameters with the same name in differ…
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Currently (see https://github.com/ICB-DCM/pyPESTO/blob/develop/pypesto/objective/petab_import.py#L201), if there are multiple replicates for an observable in a simulation condition, I guess only the l…
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File "/home/elba/PhD/PEtab/petab/core.py", line 314, in split_parameter_replacement_list
result = [x.strip() for x in list_string.split(';') if len(x.strip())]
AttributeError: 'int' object has n…
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LoosC updated
5 years ago
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In order to create the AMICI folder, PYPESTO needs some model name. This has been removed in the latest version of petab.
* Can a name be somehow extracted, or should the user be forced to create one…