I am installing the gPKPDtoolbox as described in the reference below. I'm trying to run an example from the examples that download with the toolbox from the MathWorks site.
Hosseini, I., Gajjala, A., Yadav, D.B., Sukumaran, S., Ramanujan, S., Paxson, R., and Gadkar, K. (2018). gPKPDSim: a SimBiology®-based GUI application for PKPD modeling in drug development. J. Pharmacokinet. Pharmacodyn. 1–17.
The example case is called IDR-2compPK, and is included in an sbproj file. The example cannot be simulated as supplied, at least in my setup (2017b, ml, simbio, opt, global opt, stats, parallel).
1) The model uses a non-standard unit, "fraction". The workaround is to add the unit fraction, or to change this to "dimensionless".
2) The model throws an error regarding two reaction rates. The two errors are similar, so I'll list one: Reaction rate dimension for reaction '[CentralAmt(mcg/kg)] – [PeriAmt(mcg/kg)]' must be either concentration/time or substance/time. Dimension substance/time is assumed. As you can see, the modeler put the units in the title of the species block. The actual units in the model are blank! I suspect that this is because:
3) If you try to put the units used (microgram/kilogram, that is micrograms substance/kilogram of body weight), you get an error: Invalid InitialAmountsUnits for species. Valid quantity types are amount, mass, and concentration. Clearly, the actual units desired for the model (mcg/kg) can't be used. I view this as an unreasonable constraint in a modeling package. The user should be trusted to set units that make sense. Doubly important because
4) This also precludes things like AUC. I get the same error if I try to create a species with units microgram*day/milliliter.
5) The units conversion tab is not set. The tic boxes in simulation settings (for dimensional analysis and units conversion) are not set. The errors appear whether the default units dimension is amount or concentration.
6) Earlier units discussions in this forum reference deprecated GUI functions. The solutions that folks have proposed earlier can't work because the UI they reference don't exist in 2017b.
I'd appreciate knowing 1) what settings the original authors used to get this model to run, and 2) whether or not I can turn off this dimensional checking so that I can run mass specific (per kg) simulations.
Also, it would be nice to be able to create species with ANY dimensions (that is, it would be cool to be able to check a box in the species dialog box that says "ignore dimensions for this species" to turn off dimensional analysis.
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