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extending spatial structures in MoBi #704

Closed csungeun closed 3 years ago

csungeun commented 3 years ago

I want to expand the lung model. I referenced the paper(Applied Concepts in PBPK Modeling: How to Extend an Open Systems Pharmacology Model to the Special Population of Pregnant Women(2018)) but failed.

help me...... lung model.zip

AndreDlm commented 3 years ago

Dear @csungeun,

the errors tell you what went wrong - you can display them by displaying the Notification panel: image

The first error tells you that one input variable needed for the the reaction via the unknown liver enzyme is missing (namely the Partition coefficient (water/container) in the compartment ELF in the lung). In the current implementation, this reaction occurs in all compartments where the unknown liver enzyme is present. This is defined in the MSV building block: image

When setting up a new simulation, this enzyme is per default also present in the new lung compartment. So to solve this you would either need to add the parameter Partition coefficient (water/container) in all sub-compartments of the new the lung or you define in the MSV building blocks that the unknown liver enzyme is not present in these compartments. To do so, you need to switch to the MSV building block, click on Extend in the ribbon bar menu and deselect the unknown liver enzyme in all compartments of nLung:

image

image

The second error in the model is that the transport equation PassiveDiffusionInt2Cell refers to a parameter that cannot be found, namely the Partition coefficient (interstitial/water) under the path Neighborhoods|nLung_int_nLung_cell|Digoxin|Partition coefficient (interstitial/water). To solve this, you just have to navigating there and correct the typos, then it should work: image

I hope this helps

csungeun commented 3 years ago

나는 당신의 대답에 감동했습니다. 대단히 감사합니다.