BoolODE

Overview

The BoolODE package converts a Boolean model to an ODE model and carries out stochastic simulations. It reads a model definition file, and outputs the simulated expression data for a given model.

python src/BoolODE.py --path=data/test_vars.txt --max-time=5 --num-cells 10

BoolODE Guide

• Defining an input model
• Running BoolODE
• Working with BoolODE output
• Generating inputs for BEELINE
• Compute Pseudotime using Slingshot
• Generate dropouts from expression data

Command Line Options

For a full list of available command line options, run:

python src/BoolODE.py --help

API Reference

Note

BoolODE is an external package. The following pages document its module structure; docstring content will only appear if the src/ package is present on the Python path at build time.

• src package
  • Submodules
  • src.BoolODE module
  • src.simulator module
  • src.utils module