SBMLKinetics 0.1.0

Analyze SBML kinetics.

SBMLKinetics

SBMLKinetics is a package of tests to analyze kinetics expressions in SBML models. 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

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 using git 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, 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).