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Where can I find parameters in NEIGHBORHOOD|MOLECULE ? #395

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wangwei1619 opened this issue Oct 8, 2019 · 3 comments

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@wangwei1619
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commented Oct 8, 2019

Hi, all

Does anyone know how to find parameters like absorption rate in NEIGHBORHOOD|MOLECULE in
MoBi?
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commented Oct 8, 2019

There is not a part named by drug name in Neighbrhoods

@msevestre msevestre added the question label Oct 10, 2019
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commented Oct 11, 2019

@wangwei1619

NEIGHBORHOOD or MOLECULE are reserved keywords.
These keywords will be replaced automatically in the simulation by real instances of a neighborhood or a molecule. (e.g. everywhere, where your transport will take place and with the name of the molecule being transported)

Example:

If your transporter takes place between Muscle|int and Muscle|cell, you would have a neighborhood defined in your spatial structure, called for example Muscle_int_Muscle_cell.

When an instance of the transporter is created in the simulation, the keyword NEIGHBORHOOD will be replaced with Muscle_int_Muscle_cell.
On their other hand, the keyword MOLECULE will be replaced by the name of the molecule being transported. Meaning that in the simulation, you have a full valid path

This technic allows you to define your transporter only once and apply them everywhere in a very generic way.

Now looking specifically at the DrugAbsorption_para passive transport, you can see that the transport will be from all compartments tagged with the tag Lumen to compartments tagged with the tag Mucosa AND Plasma AND SmallIntestineSegment

image

To see where instances of the transport are created, I usually advise to create simulation report (right click on simulation and press Create Simulation Report
image.

There you can search for DrugAbsorption_para and see where it has been created.

In my example, it has been created 5 times

Transport: DrugAbsorption_para
	Source: S1|Organism|Lumen|UpperJejunum|Caffeine
	Target: S1|Organism|SmallIntestine|Mucosa|UpperJejunum|Plasma|Caffeine
	Formula: DrugAbsorptionLumenToMucosaRate
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_uje_UpperJejunum_pls|Caffeine|Drug absorption rate (lumen to mucosa)(0 [µmol/min])
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_uje_UpperJejunum_pls|Caffeine|Drug absorption rate (lumen to mucosa)
	Description: Drug absorption paracellular

Transport: DrugAbsorption_para
	Source: S1|Organism|Lumen|LowerJejunum|Caffeine
	Target: S1|Organism|SmallIntestine|Mucosa|LowerJejunum|Plasma|Caffeine
	Formula: DrugAbsorptionLumenToMucosaRate
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_lje_LowerJejunum_pls|Caffeine|Drug absorption rate (lumen to mucosa)(0 [µmol/min])
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_lje_LowerJejunum_pls|Caffeine|Drug absorption rate (lumen to mucosa)
	Description: Drug absorption paracellular

Transport: DrugAbsorption_para
	Source: S1|Organism|Lumen|UpperIleum|Caffeine
	Target: S1|Organism|SmallIntestine|Mucosa|UpperIleum|Plasma|Caffeine
	Formula: DrugAbsorptionLumenToMucosaRate
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_uil_UpperIleum_pls|Caffeine|Drug absorption rate (lumen to mucosa)(0 [µmol/min])
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_uil_UpperIleum_pls|Caffeine|Drug absorption rate (lumen to mucosa)
	Description: Drug absorption paracellular

Transport: DrugAbsorption_para
	Source: S1|Organism|Lumen|LowerIleum|Caffeine
	Target: S1|Organism|SmallIntestine|Mucosa|LowerIleum|Plasma|Caffeine
	Formula: DrugAbsorptionLumenToMucosaRate
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_lil_LowerIleum_pls|Caffeine|Drug absorption rate (lumen to mucosa)(0 [µmol/min])
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_lil_LowerIleum_pls|Caffeine|Drug absorption rate (lumen to mucosa)
	Description: Drug absorption paracellular

Transport: DrugAbsorption_para
	Source: S1|Organism|Lumen|Duodenum|Caffeine
	Target: S1|Organism|SmallIntestine|Mucosa|Duodenum|Plasma|Caffeine
	Formula: DrugAbsorptionLumenToMucosaRate
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_duo_Duodenum_pls|Caffeine|Drug absorption rate (lumen to mucosa)(0 [µmol/min])
		DrugAbsorptionLumenToMucosaRate: S1|Neighborhoods|Lumen_duo_Duodenum_pls|Caffeine|Drug absorption rate (lumen to mucosa)
	Description: Drug absorption paracellular

As you can see NEIGHBORHOOD|MOLECULE|Drug absorption rate (lumen to mucosa) has been replaced everytime wih a concreate instance of a neighborhood and molecule, for example
S1|Neighborhoods|Lumen_uje_UpperJejunum_pls|Caffeine|Drug absorption rate (lumen to mucosa)

Hope that helps,

Cheers,
Michael

@msevestre msevestre added the answer label Oct 11, 2019
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commented Oct 13, 2019

@msevestre,
Thanks for your specific explanation. I find the parameter by following your illustration, thank you!
Best regards,
Wang Wei

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