PEtab-dev / PEtab-dev/PEtab

v2: add clarification sentence about simulation start time and end times

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Description

We should add a clarification sentence about what are the start time and end time for simulations. This is important for time triggered events and be more explicit.

  • simulations should start from the first time given in the experiments table or time of the first measurement for that experiment in the measurements table (i.e. what is earlier)
  • and run until the last time given in the experiments table or the time of the last measurement for that experiment in the measurements table (i.e. what is later)
  • If no experiment is specified, the model simulation is assumed to start at time 0, unless the model specifies a different initial time and runs until the last measurement for that experiment.

Personally I would prefer that we enforce that the first time given in the experiments table must be <= the time of the first measurement and the last time must be >= the time of the last measurement. Than the start and end time of the simulation would be clearly defined.

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Research direction

No file or test is named; start by locating the specification section that defines simulation times and review its treatment of experiments and measurements. Resolve whether the proposed enforcement is required, then add the agreed clarification covering start time, end time, and the no-experiment case.

Written by the indexing model from the issue text.

Assessment

Domain
documentation
Issue type
Documentation
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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