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Clarify steady state (#635)
An attempt to clarify what we consider steady state in the context of PEtab. --------- Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
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doc/v2/documentation_data_format.rst

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@@ -417,6 +417,23 @@ The experiment table has three mandatory columns ``experimentId``,
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unit specified in the model. ``-inf`` indicates that the respective
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condition will be simulated until a steady state is reached.
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.. note::
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In PEtab, the steady state definition is that *all* differential entities
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are at steady state, meaning that all differential entities have reached,
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and will remain at, a constant value.
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Determining whether differential entities are at steady state is left to
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the simulator and user. Reasonable numerical criteria should be used
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to determine whether a steady state is reached. Users should
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share their chosen numerical criteria when sharing their model, for
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reproducibility.
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It can be difficult to determine whether the differential entities are
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at steady state. For example, events and other discontinuities may
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occur after an apparent steady state is reached. It is left to the user to
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avoid situations where this issue is problematic.
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If the simulation of a condition with steady state fails to reach a steady state,
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and the condition is required for the evaluation of simulation at
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measurement points, the evaluation of the model is not well-defined.
@@ -512,7 +529,10 @@ Detailed field description
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Time point of the measurement in the time unit specified in the employed model,
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a finite numeric value, or ``inf`` (lower-case) for steady-state
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measurements.
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measurements (the same definition of steady state as in the
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:ref:`v2_experiment_table` applies here, with the additional
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sanity check that the steady state occurs during the final
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experiment period).
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This value must be greater than or equal to the first time point
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of the experiment referenced in the ``experimentId`` column
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that is not ``-inf``.

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