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Invalid Reaction Value error for SBML transfer from COPASI to Matlab

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I am trying to transfer a model from COPASI to Matlab Simbiology by exporting it as an SBML (.xml) file. When I try to import this file into Matlab through either the command window or Simbiology Load Model function I get the following 'Invalid Reaction' error (after renaming the species to fit the naming convention):
Invalid Reaction value. Spaces are required before and after species names and
stoichiometric values, for example, 2 A + B -> 2 C. Stoichiometric values must
be greater than zero. Type 'help SimBiology.Model.addreaction' for more
information.
Error in privatesbmlio
How do I resolve this issue and is there a better way to go about this transfer?

  2 Comments

Darke Hull
Darke Hull on 7 Jul 2020
Here is the file, a liver iron simulation written by Simon Mitchell in his PHD thesis "A Computational Model of Human Iron Metabolism". It has been modified for the species names to fit the compartment.species convention.

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Accepted Answer

Arthur Goldsipe
Arthur Goldsipe on 7 Jul 2020
Hi Darke,
This is a bug in how SimBiology imports reaction modifiers. The model is imported incorrectly if either the name of a species modifier is not a valid MATLAB identifier or the model has multiple compartments (or both). I will work on fixing this bug.
In the meatime, the best workaround is probably to replace the modifiers in the SBML file by instead adding each modifier species as both a reactant and a product. I am attached an updated version of the SBML file that does this.
Also, I noticed that this SBML file makes use of piecewise. This is not a function that ships with SimBiology. However, there is a version available on the File Exchange. For your convenience, I am also attaching that file here. If you download both files, you should be able to import and simulate the model using SimBiology.
-Arthur

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