Define VolumePlasma as SumFormula

[msevestre]

see Open-Systems-Pharmacology/Forum#1174 (comment)

@Yuri05 Do you know why it's still a hard coded formula?
How could we defined it dynamically? Using Plasma as a tag I guess? Thoughts?

[msevestre]

/cc @PavelBal

[PavelBal]

Yes, I was surprised that it is still a hard-coded sum.

I have implemented this in my models with the following criteria:

[msevestre]

and what about the rest of the formula ?

[PavelBal]

The default:

[Yuri05]

I wonder why the condition is "In Container" Plasma and not "Tagged with" Plasma?

[StephanSchaller]

I thought we implemented this a long time ago (last year) based on our specifications.. I remember marco albrecht sending a document specifying all left-over hard-coded sums as a sum formula... anyway...

[msevestre]

Better late than never

[PavelBal]

I wonder why the condition is "In Container" Plasma and not "Tagged with" Plasma?

Could you explain the main differences between "Tagged" and "In Container" and why you think "Tagged with" would be more appropriate here?

[Yuri05]

"Tagged" = container itself.
"In container" = container itself or any direct or indirect parent container

Now imagine you define in Mobi a new subcontainer of e.g. Bone/Plasma and reduce the Bone/Plasma/Volume by the volume of this new subcontainer.
"Tagged with 'Plasma'" will return for Bone Bone/Plasma/Volume - as expected
"In container 'Plasma'" will return for Bone Bone/Plasma/Volume + Bone/Plasma/Subcontainer/Volume - wrong

[PavelBal]

Oh, you are right then. Didn't think about the children of the container.

@msevestre Must be "Tagget with: Plasma" then.

[msevestre]

So it does not work with Taged with "Plasma"
We are looking for Parameter Volume. If we tag them with "Plasma", we need to add the Tag "Plasma" to all parameters.
This is what we do with TissueOrgan (WHY?!? @Yuri05 )

Do we add the tag of the parent container to all parameters?

[msevestre]

@Yuri05
yes
https://github.com/Open-Systems-Pharmacology/PK-Sim/blob/develop/src/PKSim.Core/Model/PKSimSpatialStructureFactory.cs#L90

We are adding the tag of the parent container to all children. that's why the "TAGGED TissueOrgan" works. I don't think this is a good way of doing things. But of course, example above would create a problem (that's why we have to remove Periportal and Pericentral)

[PavelBal]

I don't think this is a good way of doing things.

I agree, I do not like this at all. I actually think that "In Container: Plasma" is a better solution. For Yuris use case - well the user would have to take care of manually excluding the sub-compartment.

[Yuri05]

We are adding the tag of the parent container to all children. that's why the "TAGGED TissueOrgan" works. I don't think this is a good way of doing things. But of course, example above would create a problem (that's why we have to remove Periportal and Pericentral)

Yep. I think all this comes from the time before (NOT) In Container criteria were introduced. That's why we have this for parameters and also for containers:

Ideally we should go through all our formulas and replace (NOT) Match condition with (NOT) In Container condition where possible (=where it refers to any parent container in the hierarchy of the object); and when done for all formulas - remove all those unnecessary "parent containers" tags.
But would take some time and not high prio for me.