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AnabelSMRuggiero / sbmltoodepy

A tool for creating Python implementations of SBML models.
BSD 3-Clause "New" or "Revised" License
13 stars 4 forks source link

JOSS reviewer 2 comment 1 #2

Closed marouenbg closed 5 years ago

marouenbg commented 5 years ago

Review openjournals/joss-reviews#1643 sbmltoode is a great tool for fast conversion and simulation of ode models, the conversion to json strings is a great feature to have.

The software installs correctly on python 3.7, tests correctly with COPASI results, tutorials are clear. If possible, it would be nice to clarify how sbmltoode preserves model components potentially through applying standards like sed-ml and kisao. From a user perspective, the main goal of a converter would be to maintain the original model specification. Also, if possible, a sentence in the text to compare COPASI and sbmltoode.

ashleefv commented 5 years ago

Since we expect users to take and modify or use the code generated by SBMLtoODEpy in ways we can't predict, the burden of applying SED-ML or KiSAO will have to be on the user. Additionally most SBML components are stored as entries in dictionaries that are members of the class implementing the model. Currently rules and initial assignments are not implemented this way and annotations stored in the SBML model are not retained. We plan to address these in a future update.

We updated the paper to expand on the comparison to COPASI. My comment to reviewer #1 addresses the comparison to COPASI and Systems Biology Format Converter in more depth.