Condition table not specified for parameters governed by rate rules
還沒有人認領這個 Issue。
評估
- 難度
- 1/5
- 預估耗時
- 1 小時以內
- 新手友好度
- 45/100
- Issue 類型
- 文件
- 描述清晰度
- 描述清楚
- 活躍度
- 停滯
研究方向
Start at the condition-table section of documentation_data_format.html and review the current condition table description against the issue's proposed wording. Update the documentation to mention initial values of parameters governed by RateRules, then check the rendered page for clarity and formatting.
由索引模型根據 Issue 內容生成。
描述
Which problem would you like to address? Please describe.
Parameters in SBML can be either constant=True or constant=False. In case of constant=False the parameter can be either governed by an AssignmentRule or a RateRule. In case of a RateRule the parameter becomes a state variable in the ODE (analoque to species and compartments which are constant=False and governed by a RateRule or in case of species by reactions).
For such parameters which are governed by RateRules a typical condition is to set the initial value of the state variable, but this is currently not mentioned in the condition table.
See also https://github.com/AMICI-dev/AMICI/issues/1750 for an example PETab problem.
Describe the solution you would like
I propose to clarify the description of the condition table, i.e.,
I.e. the more correct way for the condition table description in
https://petab.readthedocs.io/en/latest/documentation_data_format.html#condition-table
should be
The condition table specifies constant parameters, or initial values of species, compartments or parameters for specific simulation conditions (generally corresponding to different experimental conditions).
instead of
The condition table specifies parameters, or initial values of species and compartments for specific simulation conditions (generally corresponding to different experimental conditions).
Describe alternatives you have considered
An alternative is to encode the parameter as a species or compartment governed by a RateRule. While this would be supported, the semantics would be incorrect and also the units would create problems.
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