-
Notifications
You must be signed in to change notification settings - Fork 12
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Condition table not specified for parameters governed by rate rules #539
Comments
I just saw, this is probably also related to #513 |
Hi @matthiaskoenig, thanks for reporting. Fully agreed that there is some clarification required. We were just discussing that topic during yesterday's PEtab editor meeting. We'll follow up shortly. |
Yes that's correct. PEtab currently doesn't specify how to handle such situations in sufficient detail. We are working on updating the specification in #538, but it looks like the specific condition you mentioned isn't addressed yet, so thanks for bringing that up! |
Which problem would you like to address? Please describe.
Parameters in SBML can be either
constant=True
orconstant=False
. In case ofconstant=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 areconstant=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 AMICI-dev/AMICI#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
instead of
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.
The text was updated successfully, but these errors were encountered: