SBMLKinetics

SBMLKinetics is a Python package to evaluate and classify kinetics in SBML models. There are many possible kinetics like the zeroth order, mass action, Michaelis-Menten, Hill kinetics and others. This work characterizes the kinetics in the BioModels Database as an example to improve modeling best practices. Our tool can analyze any data sets with SBML files as input. Users can also use this tool to compare different data sets. For instance, we compare the distribution of kinetics for the signaling and metabolic networks and find the substantial differences between two types of networks.

Citing

If you are using any of the code, please cite the article (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05380-3) and the PYPI web page (https://pypi.org/project/SBMLKinetics/).

For users

Installation

pip install SBMLKinetics

A Classification Example

Here is a classification example generated by SBMLKinetics:

Please see more examples in the documentation.

Documentation

Please see the documentation at https://sunnyxu.github.io/SBMLKinetics/ for details.

For developers

Setup environment

• Install spyder3
• Clone the SBMLKinetics repository using git clone https://github.com/SunnyXu/SBMLKinetics
• Create a virtual environment for the project.
  • cd SBMLKinetics
  • python -m venv kv
  • source kv/Scripts/activate (Use "\" in windows.)
  • pip install -r requirements.txt
  • deactivate

To verify the setup:

• Return to the SBMLKinetics directory.
• source kv/Scripts/activate (Use "\" in windows.)
• export PYTHONPATH=`pwd`
• python tests/test_simple_sbml.py. The tests should run without error. (Use "\" in windows.)

Running Codes

• cd SBMLKinetics
• source kv/bin/activate (Use "\" in windows.) When you're done, use deactivate.

Documentation

• examples/tutorial.py has code illustrating usage
• SBMLKinetics/common/*.py has codes for the SmpleSBML (simple_sbml.py), Reaction (reaction.py), and KineticLaw (kinetic_law.py).