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JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.

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Uncorrect units of Species with initialConcentration

mephenor opened this issue · comments

commented

In the Hynne2001_Glycolysis model ( 61 in the currated biomodels database, level="2" version="1") the species have set initialConcentration.
So when reading this model, the units should be mol and liter^-1 due to initialConcentration and the overall units in the kinetic laws.
But it seems that the units of the model's species is just mol as if initialAmount is set instead of initialConcentration.

Reported by: a-doerr

commented
  • labels: 1231700 -->
  • assigned_to: nobody --> alexander-doerr

Original comment by: niko-rodrigue

commented

This seems more a bug in the way we create the unit for the species than a problem in the reading of the XML. The XML reading is good and very well tested now. The way we get the DerivedUnit might be more the problem.

How do you obtain the unit ? Using which method ?

Original comment by: niko-rodrigue

commented
  • assigned_to: alexander-doerr --> andreas-draeger
  • status: open --> closed-fixed

Original comment by: niko-rodrigue