pinetree 0.5.0

stochastic simulation of gene expression with site-specific translation rates

pinetree

A flexible gene expression simulator with codon-specific translation rates.

Requirements

Pinetree requires Python, CMake, and a modern C++ compiler. Python 3 is recommended.

Installation

To install the latest stable version of pinetree from PyPI, run the following:

pip3 install cmake  # CMake must be installed before installing pinetree
pip3 install pinetree 

The latest development build may be installed from GitHub as follows:

pip3 install cmake   
git clone https://github.com/benjaminjack/pinetree.git
cd pinetree
pip3 install .

Documentation

Full documentation is available here.

You may also build the documentation from the source code. Building the documentation requires sphinx.

pinetree/setup.py build_sphinx

Reproducing plots from manuscript

This repository contains scripts to reproduce the simulations and plots from the manuscript that describes Pinetree. R and the R packages cowplot, readr, dplyr, and stringr are required to generate plots. Run the following to reproduce the plots from the manuscript:

python3 ./examples/three_genes.py
python3 ./examples/three_genes_recoded.py
Rscript plots.R

To simulate a bacteriophage T7 infection, run the following script.

# WARNING: This simulation takes approximately 2-3 hours to complete
python3 ./examples/phage_model.py