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SBML subsystem interaction modeling toolbox in Python

Project description


Sub-SBML is a Python based toolbox


Python toolbox to to create, edit, combine, and model interactions among multiple Systems Biology Markup Language (SBML) models.

Build Status codecov PyPI version

Sub-SBML works with a "subsystem" architecture of modeling where a single SBML model can be contained within a subsystem. Three major functionalities are developed in Sub-SBML that take advantage of this subsystem framework of modeling –
creating subsystems, combining multiple subsystems, and modeling interactions such as transport of molecules and input-output relationships among multiple subsystems.

Refer to the Wiki for more information.

To run - Go through tutorial files inside tutorials folder then check out some common examples in the examples folder. To check if different tools are working properly, run tests.

Contact : Ayush Pandey (apandet at caltech dot edu) for any feedback or suggestions.

Simple example


Install the latest version of AutoReduce::

$ pip install subsbml 

Install with all optional dependencies::

$ pip install subsbml[all]


Report any bugs that you find here. You can also fork the repository on GitHub, and the create a pull request (PR) with any changes. We welcome all changes, big or small, and we will help you make the PR if you are new to git (just create a new issue)


Sub-SBML versions:

  • 1.0.0 (beta release): To install run pip install subsbml==1.0.0


Released under the BSD 3-Clause License (see LICENSE)

Copyright (c) 2020, Ayush Pandey. All rights reserved.

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