Help with Units of species and simulation run error messages

Hi all,

Here I am again with a more specific question about a model I am trying to work on (please see attached). So, this is a published model bya group which I wanted to use as an exercise & example to familiarize myself with SimBiology. While I can follow most of the different sections including parameters, compartments and species, it seems that there is a discrepancy with the units "nmolar". While the default units of the model which were used to run the simulation was indeed "nmolar", the program shows error messages when I am trying to re-run the simulation using EXACTLY the same input values, parameters and units that were used initially by the authors. In other words, the units of the species are shown as "nmolar" in the compartments and species section, but this concentration term is not included as an option in the Property Editor section. I do not know how the authors were able to run the simulations without getting error messages.

Am I missing something here? Any help and insights are greatly appreciated!

Many thanks,

Best,

Christos

Answer 1

[Florian Augustin]

Hi Christos,

the SimBiology model uses a custom unit "nmolar". Custom units are currently (R2022b) not bundled with SimBiology models and need to be defined separately.

Here is the reference page for how to add custom units to your installation of SimBiology from the the MATLAB Command Window. You can also add custom units from within the SimBiology Model Builder app. To do this, open the SimBiology Library dialog, either by clicking on the Libraries button in the app's toolstrip (select Custom Libraries -> Units), or by clicking on "Fix" in the Property Editor of any model component that has a unit error:

You can then add the unit in the SimBiology Libraries dialog:

The example above defines the custom unit "nmolar" as "molarity", a builtin unit in SimBiologyu, with a multiplier of 1e-9, i.e. "nmolar" is mapped to "nanomolarity".

I hope this helps.

Florian

[emjey]

hi Florian, are you planing to bundle custom units with sbproj any time soon? I think it would be very useful. It is often nearly impossible to find out what the definition should be and it is a source of errors which could be easily prevented.

[Florian Augustin]

Hi emjey,

we have plans to bundle units with SimBiology models. However, I cannot give a timeline for this feature unfortunately.

Best,

-Florian

[Christos]

Hi Florian,

Thank you so much for your response! This is really helpful. I will try to do what you suggested and let you know if I have more questions.

Best regards,

Christos