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PYPI_README.md

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PhosKinTime is a modular Python package for modeling phosphorylation kinetics using ODEs. It supports multiple mechanistic hypotheses—distributive, successive, and random models—and offers tools for parameter estimation, steady-state computation, sensitivity analysis, and visualization. Designed for systems biology and phosphoproteomics research, the package enables robust, time-resolved analysis of kinase-substrate dynamics.

Features

  • Mechanistic modeling with ODEs (distributive, successive, random)
  • Parameter estimation (sequential or global)
  • Steady-state condition solvers
  • Morris sensitivity analysis
  • Publication-ready plots (fits, PCA, t-SNE, sensitivity indices)
  • CLI for preprocessing, optimization, and simulation
  • HTML reports for complete analysis output

Installation

Install via pip (recommended inside a virtualenv):

pip install phoskintime

Or clone from GitHub for full access:

git clone https://github.com/bibymaths/phoskintime.git
cd phoskintime
pip install -r requirements.txt

Usage

Run all stages of the workflow:

python phoskintime all

Run kinase optimization:

python phoskintime kinopt --mode evol

For complete usage, see the GitHub repository.

License

BSD 3-Clause License