Intestinal Permeability: Two parameters with almost identical names=> Hard to know which one to optimize

[AndreDlm]

When conducting a parameter identification for intestinal permeability (transcellular), I can transfer the result to the simulation but there's no way to commit it to the molecule building block, which is the ultimate source where I want to have it changed.

The manual step for this parameter (copy/paste it from simulation to molecule BB) is not only inconvenient, I think it can also be misleading for less experienced users, in case multiple molecule values are fitted (e.g. lipophilicity, fu, and intestinal permeability) and transferred to the simulation. When committing these changes to the molecule BB through the context menu, it may not be obvious that the intestinal permeability is in fact not committed.

I would appreciate if the intestinal permeability is more strictly linked to the molecule BB.

[UlrichSi]

I believe the permeability is a simulation parameter, i.e., it is calculated both from Molecule and Organism BBs and cannot be assigned to one BB only. Maybe the PSV BB could be used for storing fitted parameter values, since there are discussions in reworking it completely.

[msevestre]

You need to use an alternative for permeability that is not the calculated one (e.g. not a model but an actual value). In that case, you will be able to commit to the building block

[AndreDlm]

Well, actually I did use a manually created alternative to the calculated P_int in the simulation and PI, but I could not find a way to commit to BB. Can you explain how that is possible @msevestre?

An example file where the commit seems to be not possible is attached. Thank you :)

Caffeine_Test.zip

[msevestre]

Going to rename to reflect the fact that the issue was that it is hard to distinguish between simulaiton parameter and compound parameter

[msevestre]

@Yuri05 I think we should display in the paraemter selection some kind of color coded stuff or even maybe icon to see what TYPE the parmaeter is: e.g. is this a compound parmaeter or a simlation parameter. Both parameters in that case where under the SAME molecule node. Unless you really know how the internals are built, it can be hard to understand why you should choose one or the other

[AndreDlm]

@msevestre Thanks for helping to identify the actual issue! I fully agree with your suggestion

[Yuri05]

I think we should display in the paraemter selection some kind of color coded stuff or even maybe icon to see what TYPE the parmaeter is

Yep, good idea