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?
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Arthur Goldsipe
2020-7-7
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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