https://github.com/clauswilke/pinetree

🌲 a flexible gene expression simulator with codon-specific translation rates
https://github.com/clauswilke/pinetree

codons gene-expression gillespie-algorithm stochastic-simulation transcription translation

Last synced: 2 months ago
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🌲 a flexible gene expression simulator with codon-specific translation rates

• Host: GitHub
• URL: https://github.com/clauswilke/pinetree
• Owner: clauswilke
• License: mit
• Created: 2017-01-25T17:36:36.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2022-12-20T19:09:00.000Z (about 2 years ago)
• Last Synced: 2024-10-14T17:28:55.499Z (3 months ago)
• Topics: codons, gene-expression, gillespie-algorithm, stochastic-simulation, transcription, translation
• Language: C++
• Homepage: http://pinetree.readthedocs.io
• Size: 2.56 MB
• Stars: 11
• Watchers: 6
• Forks: 5
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
![pinetree](https://github.com/clauswilke/pinetree/blob/master/docs/pinetree-logo.png?raw=true)

# pinetree 

[![Build Status](https://travis-ci.org/clauswilke/pinetree.svg?branch=master)](https://travis-ci.org/clauswilke/pinetree)

[![Documentation Status](https://readthedocs.org/projects/pinetree/badge/?version=latest)](http://pinetree.readthedocs.io/en/latest/?badge=latest)

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](http://pinetree.readthedocs.io/).

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

```