Ontogeny factor in Expression Profile?

[rwmcintosh]

Should this parameter be part of Expression Profile Building Block

[PavelBal]

The parameter Ontogeny factor is currently not exported in the Expression Profile BB, and basically gets "lost" during export process.

This can be solved by defining the parameter as a table parameter or even an equation depending on age. Combination of expression profiles and individuals in MoBi would then create correct ontogenies.

@msevestre @Yuri05 thoughts?

[Yuri05]

2 parameters are required: Ontogeny factor and Ontogeny factor GI

[msevestre]

There is no parameter in the expression profile building block? is this the reason?

Now I think it's a great idea to have the parameter as a table formula. I am not sure how this will be used later on because it will be function of AGE and not of Time..... but at least the info is here

[Yuri05]

Will probably need to create Table formula with argument in the individual/simulation (similar to the pH-Solubility table)

[PavelBal]

How is the ontogeny stored in the DB? Not as an equation?

[Yuri05]

table (supporting points { $Mean_i \ ; (geo)SD_i$ })

[PavelBal]

@Yuri05 Could you help us out specifying what has to be done?

[msevestre]

After discussion today, here is the initial plan

IndividualMoleculeFactory => CreateMolecule

• We will add two new parameters with a constant value of 1:
  • Ontogeny factor GI Table
  • Ontogeny factor Table

If we are dealing with an individual, then add 2 parameters (See AddAgeDependentOntogenyParametersTo)

• Same parameters as before
• Formula is now a TableFormulaWithxArgument
  • x=>Age
  • Formula = > Ontogeny Factor XX Table

MoleculeOntogenyVariabilityUpdater => void UpdateMoleculeOntogeny(IndividualMolecule molecule, Ontogeny ontogeny, ISimulationSubject simulationSubject);

This method is called when an ontogeny is selected in the Expression Profile (OR When updating an Expression Profile in an Individual)

molecule is the molecule (either in the expr profile or the individual)
simulationSubject is either the parameterless individual in the expression profile (just for the container structure) or the individual where the expression profile will be applied

If we are using an expression profile

• we create the table (DistributedTableFormula object maybe) from the ontogenyRepository (todo find code in PKSim doing this already...TBD)

• If we are using a real individual

• Maybe we have to do nothing

Check that

• expressionProfileUpdater.SynchronizeAllSimulationSubjectsWithExpressionProfile(_simulationSubject); is synchronizing also TableParameters
• Mapping from EP to EP building block works with Formula
• Mapping from Ind to Ind Building block works with Formula and FormulaWithXArgument

NOTE:
Goal is not to change if possible

• public class ParameterUpdater : IParameterUpdater
• DistributedParameterToTableParameterConverter

[msevestre]

ok this is a duplicate of #2626

[msevestre]

starting on this

[msevestre]

@PavelBal @Yuri05
This is proving to be VERY challenging. I have spent two full days on this and I am nowhere done. We need to discuss what we want exactly and why because right now, I am opening a massive can of worms

The main problem that I have is about reusability and consistency.
At the moment, I have the table in the expression profile. This works. But in the individual, we need to have a parameter as a function of PMA and this table in the expression. This works also but when we want to export to mobi, we have this weird mismatch: We do not want the ontogeny factor in the expression profile because it references age of the individual. But we do not want the parameter in the individual either because it references a specific expression profile.

Not sure how to deal with this best

[msevestre]

For now, I have added the paramter to the expression profile....To be continued

[msevestre]

@Yuri05 @PavelBal
What about ontogeny factor albumin and glycoprotein. Those two could also be implemented the same way (and exported as table + arg, but this time in the individual. Thoughts?)

[PavelBal]

What about ontogeny factor albumin and glycoprotein. Those two could also be implemented the same way (and exported as table + arg, but this time in the individual. Thoughts?)

I think this also makes sense.

[Yuri05]

What about ontogeny factor albumin and glycoprotein. Those two could also be implemented the same way (and exported as table + arg, but this time in the individual. Thoughts?)

makes sense :)