Any progress on relaxing the constraints on species units?

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In SimBiology, there is a limited set of units one case use. Amount, or concentration.
This is often inconvenient, as (for example) I might want to use timers (units of time), or surrogates for concentration (like MFI for nanomoles/milliliter). Too, many sbml models use units that aren't in the set of acceptable ones.
One can use user-defined units, but these generally link with defined units and this means that one could have unit conversions that have no bearing on reality.
What is the recommended work-around for this?
What progress has been made with respect to allowing species units that are neither amounts nor concentrations?
Thanks!

Accepted Answer

Arthur Goldsipe
Arthur Goldsipe on 28 Jan 2022
I'd love to pick your brain about exactly what you need and expect from such functionality!
Which is to say that today species in SimBiology are still constrained to have units of amount/mass or concentration. The two most common workarounds I can think of are to use parameters and rate rules instead of species and reactions or to reformulate your problem so that species can be written with units of amount or concentration. For example, I've seen models where species amounts are scaled by body mass (with units of mg/kg). In such cases, I've recommended writing the model (namely, species and reactions) on the basis of 1 kg of body mass, and then rescaling the results as needed either via post-processing or via repeated assignment rules and/or observables.
And let me give you some insight into why this is such a challenge. Today, SimBiology needs to be able to perform mass balances for all species. We need to know whether the units of a species are in extensive (amount) or intensive (concentration) units, and how to convert between the two. For example, we know we can a species concentration by the corresponding compartment volume to determine the amount. We also need to know how to convert all reaction rates to amount/time. Or in the case of most reactions that span multiple compartments, we need to ensure that the user-specified reaction rate is explicitly in amount/time (unless it's clear which compartment volume we need to multiply by). And this is related to why we don't allow one species in a reaction to use mass units (like kilogram or kilogram/liter) while another uses amount (mole, molecule, molar, etc.), since we don't yet have a way to explicitly specify the molecular weight of a species.
Anyway, here are some of the things I'd like know from you: What is MFI? What does the larger modeling approach look like in cases where you want more flexible units? Will you have one or multiple compartments? Will you mix extensive and intensive units for species? For reaction rates? Any concrete examples you can share would be extremely helpful. Feel free to reach out to me via email to follow up on this.
Thanks,
Arthur
  9 Comments
Jim Bosley
Jim Bosley on 20 Jul 2023
Arthur,
This issue came up again. I'm looking at Miyano et al. 2021 "A Mathematical Model to Identify Optimal Combinations of Drug Targets..." In the model, concentrations of endogenous compounds are given in "fold" over the original concentration. One reason to like this is that all initial conditions are 1, and the variables scaling is inherent in the model!
One can write the model in Matlab or Python with these units, or one can just ignore the units and not enter anything, which kind of defeats the purpose of having units.
Is no one else finding this a barrier to using SimBiology?
Thanks,
Jim
Arthur Goldsipe
Arthur Goldsipe on 20 Jul 2023
Thanks for sharing this reference. I'll add a note to our enhancement database. I hope you and other SimBiology users continue to share what's making it harder for you to use SimBiology. That feedback makes it much easier for us to figure out what we should be working on next. And in particular, it would be helpful to know how common a problem the unit limitations are for our users.

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