Suggested change to SBML multi-compartment model example

[sbmlsecretary]

We should update the example of multicompartmental model use in the SBML specification (example 7.8 on p. 130 of SBML Level 3 Version 2 Core Release 2 of 29 March 2019 as the current definition is problematic, being both ambiguous and incorrectly scaled.

Submitted on behalf of Prof J.-H.S. Hofmeyr who suggests the following:

""" I suggest the following changes to the SBML compartment model so that it can serve as an example of correct scaling. Replace

v_T = k_T (y_1n - y_1c) V_c

with

v_T = k_T (y_1n - y_1c) A

and provide new values for A (in dm^2) and k_T (in dm/s) that still give A.k_T = 25000 dm^3/s (the value that V_c.k_T currently gives). In fact, just make A = 1 dm^2. This means that the model will still give identical numerical output.

This also means that they can just write "The reaction between the compartments called cytosol and nucleus is a transport reaction whose detailed mechanism is not modeled here; it is regarded simply as a reversible process that spans the two three-dimensional compartments." """

Reported by: bgoli

Original Ticket: sbml/sbml-specifications//366

[sbmlsecretary]

I agree with this suggestion.

Original comment by: fbergmann

[sbmlsecretary]

Nice catch by Dr. Hofmeyr. Thank you for bringing this up.

Original comment by: mhucka

[sbmlsecretary]

• labels: --> Level 2 Version 5 Core, Level 3 Version 1 Core, Level 3 Version 2 Core

Original comment by: luciansmith