SimpleSBML: A Python package for creating, editing, and interrogating SBML models: Version 2.0

TL;DR

SimpleSBML 2.0 is a user-friendly Python package that simplifies creating, editing, and inspecting SBML models, making model manipulation more accessible especially for new users.

Contribution

The paper introduces SimpleSBML 2.0, enhancing ease of use with new inspection methods and simplified commands for SBML model manipulation in Python.

Findings

Simplifies SBML model creation and editing in Python

Provides new 'get' methods for model inspection

Enables easy import and export of SBML models

Abstract

In this technical report, we describe a new version of SimpleSBML which provides an easier to use interface to python-libSBML allowing users of Python to more easily construct, edit, and inspect 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 is a comprehensive library with a large range of options but can be difficult for new users to learn and requires long scripts to create even the simplest models. Inspecting existing SBML models can also be difficult due to the complexity of the underlying object model. Instead, we present SimpleSBML, a package that allows users to add and inspect 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 making it very easy to edit the original SBML model. In the new version, a range of `get' methods is provided that allows users to inspect existing SBML models without having to understand the underlying object model used by libSBML.