stochastic simulation of gene expression with site-specific translation rates
A flexible gene expression simulator with codon-specific translation rates.
Pinetree requires Python, CMake, and a modern C++ compiler. Python 3 is recommended.
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 .
Full documentation is available here.
You may also build the documentation from the source code. Building the documentation requires 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
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
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