8000 specify column name for simulation data for optional simulation.tsv · Issue #628 · PEtab-dev/PEtab · GitHub
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specify column name for simulation data for optional simulation.tsv #628

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fbergmann opened this issue May 13, 2025 · 2 comments · May be fixed by #632
Open

specify column name for simulation data for optional simulation.tsv #628

fbergmann opened this issue May 13, 2025 · 2 comments · May be fixed by #632

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@fbergmann
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Which problem would you like to address? Please describe.
Specs for v1 and v2 mention that we can have an optional simulation data file "in the same format as the measurement" file, however whenever they are used the measurement column has a different name. That name has not been consistent in the past it was either 'simulatedDataorsimulation`.

Describe the solution you would like
Add a clarification that the format has to be the same as the measurement file, with measurement replaced by simulation
@dweindl
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dweindl commented May 13, 2025

Agreed that this should be specified somewhere. I am not sure it should be in the PEtab specs, though. As long as there is no clear interaction with the rest of PEtab, I would rather remove any mention of that file.

We should (1) keep the simulation file in the specs and describe it properly, or (2) remove it from there completely. Either works for me, but I'd prefer (2).

@matthiaskoenig
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+1 for proper description and keeping it

dweindl added a commit that referenced this issue May 21, 2025
@dweindl
v2: Clarify simulation file
a35c3b1 
* Remove the simulation from the list of PEtab files, because it is not part of the parameter estimation problem.
* Add a section under *measurement table* stating the expected column name.

Closes #628.
@dweindl dweindl linked a pull request May 21, 2025 that will close this issue
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v2: Clarify simulation file PEtab-dev/PEtab
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@matthiaskoenig @fbergmann @dweindl
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