Closed a2mahara closed 4 years ago
Hi Anil,
For #4, the intervals on which the anatomy and physiology are updated can be seen if you export the simulation to Mobi with 'allow aging' checked and then go to the parameter path in the Spatial Structure (e.g. Organism|Kidney|Volume). The parameter is specified as a table as a function of discrete ages.
Paul
Thanks, Paul.
I noted these tables, which define changes in parameters by simulation time, are accessible in PK-Sim as well. I was wondering how often are these parameters updated during the actual simulation run....i.e., does the kidney volume (which is interpolated using the table) update every 24 hours? OR is the kidney volume being continuously being updated during the simulation?
Thanks, I didn't realize that interpolation was applied.
I ran an observer for kidney volume in a male european default subject from 1 day old to 2 years and it looks like kidney volume updates at every simulation step. Here is the output of the observer KVupdate.xlsx : Also, turns out its linear interpolation with a few sparse points. The premature pop updates a lot more frequently from my experience.
@a2mahara PK-Sim stores information about all model parameters (particularly about anatomical and physiological parameters) in one of 3 ways. Each parameter is described by one of the following alternatives:
I. Analytical formula (equation depending on other model quantities) II. Constant (age independent) non-formula III. Age-dependent non-formula
Parameters of the first two kinds are handled in the same way both in simulations with and without aging. Where it comes to differences are parameters of the type III (and the explanation below is for these parameters).
An individual in PK-Sim is given in the first place by the combination of covariates {Population, Gender, [Gestational Age], Age, Weight, Height}
(Gestational Age applies only for the Preterms population).
For every parameter of the type III and every combination of the covariates {Population, Gender, [Gestational Age]}
the information is stored in PK-Sim on the predefined grid of ages (supporting points) based on literature data. For each supporting point information is stored in form of probability distribution {Distribution type; Mean; STD}
.
When creating an individual of age which is not on the predefined age grid, the probability distribution for a given parameter is linearly interpolated based on the information in the supporting points.
Further, the probability distributions like in example above, are stored for the Mean body weight and Mean Height of a combination {Population, Gender, [Gestational Age]}
. If the required weight and/or height differs from the mean value: probability distributions of some parameters are scaled as described in detail in the Create Individual Algorithm.
Finally, after an individual was created, user can optionally modify some of the individual parameters. Based on the probability distribution of a parameter and its current value, a percentile for this parameter can be calculated (which is also shown in PK-Sim).
Now the short answer to your questions 1. and 2.: the percentile of each distributed parameter is kept constant during the whole simulation duration.
In more detail: when a simulation with the aging option is created, for each distributed parameter the following is done:
{Population, Gender, [Gestational Age]}
of the individual is taken from the PK-Sim database For example, if you create a 80 years old European_ICRP MALE individual with mean body weight and mean height and then create a simulation with aging based on this individual, then the table for the heart volume would look like this: Which is the original table shifted by 80 years. (and if you change body weight/height when creating the individual or change the heart volume manually, the values in the table will change according to the new percentile of the heart volume)
Now during the simulation with aging, table values are used all the time to retrieve the values of anatomical and physiological parameters. So the answer to your question 4: parameters are updated continuously.
Regarding the last question:
- Does each subject's anatomy and physiology change based on their own growth curve for population simulations?
For a population it's exactly the same principle. Each individual in a population has corresponding probability distributions for age-dependent (non-formula) parameters and corresponding percentiles. So for each individual of a population lookup-tables for distributed parameters are created as described above and used during the simulation for continuous updating of parameter values.
P.S. Age grids of the supporting points differ between populations and are not equidistant.
Like @Yuri05 said
Great!!! Thanks @prvmalik. Also Thanks @Yuri05 for the comprehensive explanation. That pretty much covers everything I asked from #1-4
However, one last follow-up. I noted that models edited in MoBi and exported back to PK-Sim to conduct population simulations will NOT permit for aging during the simulation (even if the original simulation that was first exported to MoBi from PK-Sim included the 'allow aging' option). Is this something that is being considered for future releases?
Is this something that is being considered for future releases?
You might give a like here: https://github.com/Open-Systems-Pharmacology/PK-Sim/issues/1458 😉
Thanks again for the info, @Yuri05!!
Hello Everyone,
I was looking to find information about how the 'allow aging' module works for simulations. Specifically, what is the time-dependence of how a subject's anatomy and physiology changes with aging (in PK-Sim)?
If the subject is the an 'average individual' (i.e at the 50th percentile of body weight and height for age), does the subject's anatomy of physiology represent an 'average subject' as they age?
If the subject is NOT an 'average subject' (i.e., body weight and height NOT at the 50th percentile for age), how does anatomy and physiology change with aging?
Does each subject's anatomy and physiology change based on their own growth curve for population simulations?
How often is anatomy and physiology updated in the simulations (every 24 hours?)
If anyone can point me in right direction to answer these questions, that would be much appreciated.
Thanks!