Partition coefficient (water/container) cannot be found

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Partition coefficient (water/container) cannot be found #948

Closed tztz117 closed 3 years ago

tztz117 commented 3 years ago

I am adding a spatical structrure of breast using kidney as the container template. Followed Dallmann 2018 paper and when trying to run simulation this error message showed, could someone help to take a look?

path cant find Clarithromycin lactation.zip

tztz117 commented 3 years ago

path cant find Anyone help to take a look at this? thanks very much!

msevestre commented 3 years ago

You will need to add this parameter specifically in the spatial structure. It is probably outlined in the paper. If not, search the forum for the section "how do define a tumor model" or sthg like this. Let me know if this helps

tztz117 commented 3 years ago

thank you very much, Michael! I have followed the steps in that tumor model and the paper of adding spatial structure,

The interstitial/water partition was added under neighborhood as below:

I found this path under reactions, but can't find it in the spatial structure:

issue path error 2

tztz117 commented 3 years ago

in front of this path, it has "..|", when I trying to add one by myself for testing, it don't have "..|", what it means?

msevestre commented 3 years ago

..| is a way to specify where to find the parameter. So it will be in the parent container in this case ".." can be read as "parent" Maybe check some of the documentation https://docs.open-systems-pharmacology.org/working-with-mobi/mobi-documentation/first-steps

tztz117 commented 3 years ago

Hi Michael,

I checked discussion "Define partition coefficient (int/water) when adding a new compartment Open-Systems-Pharmacology/MoBi#302". I have added partition cofficient (interstitial/water) as guided by the paper and those discussions. but the error message here is "partition coefficient (water/container) can not be found. how to find this? I can't find it in other tissues either.

path cant find

msevestre commented 3 years ago

Can you attach your project? I'll check it out tomorrow

tztz117 commented 3 years ago

Clarithromycin lactation.zip

Yes, Michael. Thank you very much!

I am also wondering whehter it has something to do with the model, which has both parent and metabolite.

msevestre commented 3 years ago

@tztz117 Ok I looked at your model and there are quite a few things that are wrong I believe. I do not think that you followed the steps described in the tutorial

I would suggest looking at the step by step instructions again
In your milk compartment, the parameter Partition coefficient (water/container) is missing (spatial structure). This is clearly what the message in MoBi is telling you.
In fact, the milk compartment should have the same structure as any other compartment probably.
What tutorial did you follow?

Last but not least. If you need help, you need to create an issue in the Forum. MoBi issues are only to report bugs or feature requests.

I will move the issue for you