SBML Support
In order to use SBML files, please see the final example in the examples notebook. This example reads in an SBML file and simulates it using bioscrape. Additionally, please note that SBML compatibility has the following limitations.
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Cannot support delays or events when reading in SBML files. Events will be ignored and a warning will be printed out.
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SBML reaction rates must be in a format such that when the reaction rates are converted to a string formula, sympy must be able to parse the formula. This will work fine for usual PEMDAS rates. This will fail for complex function definitions and things like that.
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Species will be initialized to their initialAmount field when it is nonzero. If the initialAmount is zero, then the initialConcentration will be used instead.
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Any information about compartments will be ignored. Bioscrape will only parse in information about reactions, species, and rates. If your model has more than one compartment or the compartment changes in volume, these facts will be ignored.
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Assignment rules are supported, but any other type of rule will be ignored and an associated warning will be printed out.
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Parameter names must start with a letter and be alphanumeric, same for species names. Furthermore, log, exp, abs, heaviside, and other associated keywords for functions are not allowed to be variable names. When in doubt, just pick something else.