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fix #525
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doc/documentation_data_format.rst

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@@ -212,7 +212,7 @@ Detailed field description
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- ``observableId`` [STRING, NOT NULL, REFERENCES(observables.observableID)]
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Observable ID as defined in the observables table described below.
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Observable ID as defined in the observable table described below.
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- ``preequilibrationConditionId`` [STRING OR NULL, REFERENCES(conditionsTable.conditionID), OPTIONAL]
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@@ -277,8 +277,8 @@ Detailed field description
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``datasetId``, which is helpful for plotting e.g. error bars.
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Observables table
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-----------------
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Observable table
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----------------
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Parameter estimation requires linking experimental observations to the model
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of interest. Therefore, one needs to define observables (model outputs) and

doc/tutorial.rst

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@@ -130,7 +130,7 @@ functions. Additionally, a noise model can be introduced to account for
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the measurement errors. In PEtab, this can be encoded in the observable
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file:
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.. list-table:: Observables table ``observables.tsv``.
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.. list-table:: Observable table ``observables.tsv``.
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:header-rows: 1
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* - observableId
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- Rel. STAT5A abundance [%]
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- ...
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.. list-table:: Observables table ``observables.tsv`` (continued).
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.. list-table:: Observable table ``observables.tsv`` (continued).
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:header-rows: 1
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* - ...
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- 100*(STAT5A + pApB + 2*pApA) / (2 \* pApB + 2\* pApA + STAT5A + STAT5B + 2*pBpB)
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- ...
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.. list-table:: Observables table ``observables.tsv`` (continued).
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.. list-table:: Observable table ``observables.tsv`` (continued).
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:header-rows: 1
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* - ...
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brevity, only the first and last time point of the example are shown
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here (the omitted measurements are indicated by “...” in the example).
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* *noiseParameters* relates to the *noiseParameters* in the observables
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file. In our example, the measurement noise is unknown. Therefore we
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* *noiseParameters* relates to the *noiseParameters* in the observable table.
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In our example, the measurement noise is unknown. Therefore we
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define parameters here which have to be estimated (see parameters sheet
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below). If the noise is known, e.g. from multiple replicates, numeric
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values can be used in this column.

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