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KinOpt Optimization Package

The kinopt package contains the kinase-phosphorylation optimization workflow.

Package Structure

kinopt/
├── __init__.py
├── fitanalysis/
│   ├── __init__.py
│   ├── __main__.py
│   └── helpers/
├── local/
│   ├── __init__.py
│   ├── __main__.py
│   ├── config/
│   ├── exporter/
│   ├── objfn/
│   ├── opt/
│   ├── optcon/
│   └── utils/
└── optimality/
    ├── __init__.py
    └── KKT.py

kinopt.local

kinopt.local runs constrained local optimization for kinase-phosphorylation time-series data. It contains:

  • Objective-function code in objfn.
  • Constraint and input construction helpers in optcon.
  • JAX/JAXopt-based local optimization routines in opt.
  • Export helpers in exporter.
  • Data and parameter utilities in utils.

Run it with:

pixi run kinopt-local

or:

PYTHONPATH=. python -m kinopt.local

kinopt.fitanalysis

kinopt.fitanalysis provides post-fit analysis helpers for reviewing optimization outputs.

Run it with:

pixi run kinopt-fitanalysis

or:

PYTHONPATH=. python -m kinopt.fitanalysis

kinopt.optimality

kinopt.optimality contains KKT and feasibility diagnostics used to inspect optimization results after a run.