Closed rwmcintosh closed 1 year ago
These parameters are all excluded for being not species specific
Parameter name |
---|
SA proportionality factor |
Specific clearance (endosome) |
Surface area scaling exponent |
Weight |
Weight of blood organs |
Weight of tissue organs |
pH (blood cells) |
pH (interstitial) |
pH (intracellular) |
pH (plasma) |
Scaling exponent for fluid recirculation flow rate |
Thickness (endothelium) |
Fraction endosomal (global) |
Protein ratio (interstial/plasma) |
Vf (lipid, blood cells) |
Vf (lipid, plasma) |
Vf (neutral lipid, blood cells)-WS |
Vf (neutral lipid, plasma)-RR |
Vf (protein,blood cells) |
Vf (protein,plasma) |
Vf (water,blood cells) |
Vf (water,interstitial) |
Vf (water,plasma) |
Surface/Volume ratio (blood cells) |
Vf (neutral lipid, plasma)-PT |
Vf (neutral phospholipid, blood cells)-WS |
Vf (neutral phospholipid, plasma)-RR |
Fraction of endosomal uptake from plasma (global) |
Ontogeny factor (albumin) |
Ontogeny factor (alpha1-acid glycoprotein) |
Plasma protein scale factor |
Vf (acidic phospholipids, blood cells)-WS |
Vf (neutral lipid, blood cells)-RR |
Vf (phospholipid, plasma)-PT |
Vf (neutral phospholipid, blood cells)-RR |
Vf (water,plasma)-PT |
Fraction recycled to plasma (global) |
Acidic phospholipids (blood cells) [mg/g] - RR |
Vf (intracellular water, blood cells)-RR |
Rate constant for endosomal uptake (global) |
Rate constant for recycling from endosomal space (global) |
Hematocrit |
MeanBW |
Percentile |
Mean |
Deviation |
Weight (tissue) |
Density (tissue) |
Allometric scale factor |
Fraction vascular |
Volume |
Initial concentration |
Peripheral blood flow fraction |
Fraction endosomal |
Blood flow rate |
Fluid recirculation flow rate |
Lymph flow rate |
Volume (endothelium) |
Fraction intracellular |
Fluid recirculation flow proportionality factor |
Lymph flow proportionality factor |
Organ volume mouse |
Fraction of blood for sampling |
Flow fraction via large pores |
Hydraulic conductivity |
Radius (large pores) |
Radius (small pores) |
Vf (lipid) |
Vf (neutral lipid)-PT |
Vf (phospholipid)-PT |
Vf (protein) |
Fraction interstitial |
Albumin ratio (tissue/plasma) |
Albumin ratio (tissue/plasma)-PT |
Lipoprotein ratio (tissue/plasma) |
Vf (water) |
Vf (water)-PT |
Vf (neutral lipid)-RR |
Vf (neutral lipid)-WS |
Vf (neutral phospholipid)-RR |
Vf (neutral phospholipid, plasma)-WS |
Vf (extracellular water)-RR |
Vf (protein)-WS |
Vf (intracellular water)-RR |
Vf (water)-WS |
Acidic phospholipids [mg/g] - RR |
Vf (acidic phospholipids)-WS |
Specific blood flow rate |
pH |
Fraction expressed basolateral |
Relative expression |
Fraction expressed at blood brain barrier |
Fraction expressed brain tissue |
GeometricDeviation |
GFR (specific) |
Renal aging scaling factor |
fGFRpremat |
Fraction expressed apical |
Effective surface area variability factor |
Geometric surface area |
Volume (gut wall) |
Fractional steady state fill level |
pH in fed state |
Thickness of gut wall |
Inverse rate of inflow of liquid into stomach |
pH in fasted state |
Distal radius |
Gastric emptying time |
GET_alpha (Weibull function) variability factor |
GET_beta (Weibull function) variability factor |
Length |
Proximal radius |
Effective surface area |
Intestinal transit rate |
Microvilli factor |
Effective surface area enhancement factor |
Small intestinal transit time factor |
Fluid recirculation flow rate (incl. mucosa) |
Lymph flow rate (incl. mucosa) |
Volume (mucosa) |
Mucosa blood flow fraction |
Small intestinal transit time factor intercept |
Small intestinal transit time factor slope |
Small intestinal transit time |
Fraction mucosa |
Fraction of regional blood flow rate |
Large intestinal transit time factor |
Large intestinal transit time factor intercept |
Large intestinal transit time factor slope |
Large intestinal transit time |
Is liver zonated |
Fraction of periportal zone |
EHC continuous fraction |
Microsomal protein mass/g tissue |
Number of cells/g tissue |
Kd (FcRn, endogenous IgG) in plasma/interstitial |
kass (FcRn, endogenous IgG) |
Kd (FcRn, endogenous IgG) in endosomal space |
Radius (endogeneous IgG) |
Start concentration of free endogenous IgG (plasma) |
Start concentration of free FcRn (endosome) |
Surface area (blood cells/plasma) |
Surface area (interstitial/intracellular) |
Surface area (plasma/interstitial) |
Reference concentration |
t1/2 (liver) |
t1/2 (intestine) |
Ontogeny factor GI |
Ontogeny factor |
Relative expression in blood cells |
Relative expression in vascular endothelium |
Integration tests are showing that if we exclude all these from an Individual Core building block then there's issues creating the simulation
OneTimeSetUp: PKSim.Core.Services.CannotCreateSimulationException
I won't list the whole message, but a few issues where the parameter appears to be excluded from both the Individual and Spatial Structure
Observer 'Whole Blood' with path 'Whole Blood' references an entity with path '..|..|Plasma|Inhibitor|Concentration' that cannot be found
Observer 'Whole Blood' with path 'Whole Blood' references an entity with path 'simulation|Organism|Hematocrit' that cannot be found
Observer 'Interstitial Unbound' with path 'Interstitial Unbound' references an entity with path '..|..|Interstitial|Inhibitor|Partition coefficient (water/container)' that cannot be found
Observer 'Tissue' with path 'simulation|Organism|Bone|Specific blood flow rate|Drug|Tissue' references an entity with path '..|..|Fraction interstitial' that cannot be found
Distributed Parameter 'Age of aging onset' with path 'simulation|Organism|Kidney|Age of aging onset' references an entity with path 'Mean' that cannot be found
Distributed Parameter 'Aging half-time' with path 'simulation|Organism|Kidney|Aging half-time' references an entity with path 'Mean' that cannot be found
Distributed Parameter 'Hill coefficient for aging GFR' with path 'simulation|Organism|Kidney|Hill coefficient for aging GFR' references an entity with path 'Mean' that cannot be found
Distributed Parameter 'Maximal decreasing rate factor' with path 'simulation|Organism|Kidney|Maximal decreasing rate factor' references an entity with path 'Mean' that cannot be found
Distributed Parameter 'GFRmat' with path 'simulation|Organism|Kidney|GFRmat' references an entity with path 'Mean' that cannot be found
Distributed Parameter 'GFRmat' with path 'simulation|Organism|Kidney|GFRmat' references an entity with path 'Deviation' that cannot be found
Observer 'Whole Blood' with path 'Whole Blood' references an entity with path 'simulation|Organism|Hematocrit' that cannot be found
Looks for hematocrit and it should be there. It's in the list of not being species specific. Too many parameter are filtered out
@Yuri05 The implementation of the common parameters is wrong, or at least not complete
"Common parameters" are those which are present for every species, not necessarily with the same value or the same formula. That was the idea.
Then this concept is missing something because how do we decide where to export ? Right now, we duplicate a lot of stuff
The mean parameter however is still a bug I think
Something like this, no?
Regarding the Mean/STD parameters: they are not part of the PK-Sim DB and are created on the fly. They should always get the same "common" state as their "parent" parameter?
Ok so this repository returns true where it should return false or vice versa for parameters that it does not know. Probably the logic for unknown parameter should be it's NOT common
Common parameters should be created both in the spatial structure and in the individual-BB In the spatial structure with NaN value In the Individual-BB: with their value or formula
I don't know. Do we want to create the formula for BW = Sum of all organs weight as sum formula in ALL individuals? I thought this would be defined in the SP structure. Then it's ok but the individual really is huge and the spatial structure has only NaNs lol
Ok so this repository returns true where it should return false or vice versa for parameters that it does not know. Probably the logic for unknown parameter should be it's NOT common
hmm, need to check this...
Do we want to create the formula for BW = Sum of all organs weight as sum formula in ALL individuals?
yes!
I thought this would be defined in the SP structure.
yes! BW is common parameter, right?
Then I don't understand what we are trying to do lol What's the point of defining BW in the individual with a formula that is the same for all species?
And why adding parameters with NAN in your structure?
And why adding parameters with NAN in your structure?
That's something we have discussed some time ago... But I also don't see a problem, if we export individual parameters with their current value/formula to the spatial structure instead of NaN. @PavelBal
I understand when there is a parameter with different formulas. But with the same formulas, I am just highly confused about what we are trying to do
21.06.2023: Proposal to put all parameters that are defined by a formula AND the formula is identical for all species - put the parameter into the spatial structure.
Is this clear by now, or do we need additional discussion?
I have created another issue for the DB query which is required for this one: https://github.com/Open-Systems-Pharmacology/PK-Sim/issues/2699 Once the PR for that issue is merged - this one can be fixed (not by me then 😉 )
There are too many parameters added to individual building blocks when converting to a core building block.
Individual building block should only include species specific parameters.