Analyze SBML kinetics.
Project description
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. If you are using any of the code, please cite 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://modelengineering.github.io/kinetics_validator/ for details.
For developers
Setup environment
- Install spyder3
- Clone the
kinetics_validator
repository usinggit clone https://github.com/ModelEngineering/kinetics_validator
- Create a virtual environment for the project.
cd kinetics_validator
python -m venv kv
source kv/Scripts/activate
(Use "\" in windows.)pip install -r requirements.txt
deactivate
To verify the setup:
- Return to the
kinetics_evaluator
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 kinetics_validator
source kv/bin/activate
(Use "\" in windows.) When you're done, usedeactivate
.
Documentation
examples/tutorial.py
has code illustrating usageSBMLKinetics/common/*.py
has codes for the SmpleSBML (simple_sbml.py
), Reaction (reaction.py
), and KineticLaw (kinetic_law.py
).
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