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bioRxiv · 10.1101/030312

SimpleSBML: A Python package for creating and editing SBML models

Caroline Cannistra·Kyle Medley·Herbert Sauro
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Abstract

SummaryIn this technical report we describe a simple extension to python-libSBML that allows users of Python to more easily construct SBML based models. The most commonly used package for constructing SBML models in Python is python-libSBML based on the C/C++ library libSBML. python-libSBML supports a comprehensive set of model types, but is difficult for new users to learn and requires long scripts to create even the simplest models. We present SimpleSBML, a package that allows users to add species, parameters, reactions, events, and rules to a libSBML model with only one command for each. Models can be exported to SBML format, and SBML files can be imported and converted to SimpleSBML commands that creates each element in a new model. This allows users to create new models and edit existing models for use with other software. Accessibility and ImplementationSimpleSBML is publicly available and licensed under the liberal Apache 2.0 open source license. It supports SBML levels 2 and 3. Its only dependency is libSBML. It is supported on Windows and Mac OS X. All code has been deposited at the GitHub site https://github.com/sys-bio/simplesbml Contactcarolc24@u.washington.edu or hsauro@u.washington.edu

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Caroline Cannistra, Kyle Medley, Herbert Sauro. 2015-10-30. SimpleSBML: A Python package for creating and editing SBML models. https://doi.org/10.1101/030312

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