[SED-ML-discuss] Questions about repeated task

[Ilya K. <ax...@de...>]

Dear SedML community.

We are currently working on support of sed ml l1v2 in BioUML. So far we
have few questions about RepeatedTask construct.

In repeated task we can have multiple subTasks. It seems to me that it is
never stated that all subTasks should refer to the same model. However in
data generator variables may refer only to task and not to the model inside
the task. Then my questions are:

1. Is it true that all subTasks in repeatedTask must refer to the same
model?
2. Can several repeatedTasks use the same task as subTasks?
3. If task is used as a subtask then variable in data generator can not
refer to it directly and should refer to its "parent" RepeatedTask. Is that
correct?

Another question is regarding "resetModel" attribute. In Sed-ML
specification it is stated that "resetModel = false" means that model in
the task will not be reset to its normal state at the start of each
iteration.

Say we have subTask which refers to UniformTimeCourse simulation with
initialTime = 0 and outputEndTime = 100.

This means that next iteration will start from time = 0 but variables of
the model will be taken from the last time point of previous simulation
which is time = 100. This situation can lead to strange and nonsensical
results especially when time is explicitly involved in model equations.

For now it seems to me that "resetModel = false" makes sense only for
onestepper and steady state and "resetModel = true" for onestepper will be
also quite strange. Can anybody share showcases for such situations (I mean
"resetModel=false" for time course simulation and "resetModel = true" for
one step simulation)?

One showcase with time course simulation and resetModel = "false" I can
think of is not compatible with current Sed-ML specifications (but it is
doable in BioUML). It relies on changing of simulation parameters in
RepeatedTask iterations.
For example: perform timecourse simulation from 0 to 100 with step 0.1. At
the second iteration change initial time to 100 and completion time to 200,
do some other changes to model parameters and continue simulation.

Also, are there any tests for sedml? It will be very helpful for tool
developers. Currently we try to reproduce examples from specifications but
they lacks different constructions (e.g. multiple subtasks inside
repeatedTask or mentioned above situations).

-- 
Best regards, Ilya