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        "author": "Benjamin Jack",
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        "description": "![pinetree](https://github.com/benjaminjack/pinetree/blob/master/docs/pinetree-logo.png?raw=true)\n\n# pinetree \n[![Build Status](https://travis-ci.org/benjaminjack/pinetree.svg?branch=master)](https://travis-ci.org/benjaminjack/pinetree)\n[![Documentation Status](https://readthedocs.org/projects/pinetree/badge/?version=latest)](http://pinetree.readthedocs.io/en/latest/?badge=latest)\n\nA flexible gene expression simulator with codon-specific translation rates.\n\n## Requirements\n\nPinetree requires Python, CMake, and a modern C++ compiler. Python 3 is recommended.\n\n## Installation\n\nTo install the latest stable version of pinetree from PyPI, run the following:\n\n```\npip3 install cmake  # CMake must be installed before installing pinetree\npip3 install pinetree \n```\n\nThe latest development build may be installed from GitHub as follows:\n\n```\npip3 install cmake   \ngit clone https://github.com/benjaminjack/pinetree.git\ncd pinetree\npip3 install .\n```\n\n## Documentation\n\nFull documentation is available [here](http://pinetree.readthedocs.io/).\n\nYou may also build the documentation from the source code. Building the documentation requires sphinx.\n\n```\npinetree/setup.py build_sphinx\n```\n\n## Reproducing plots from manuscript\n\nThis 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:\n\n```\npython3 ./examples/three_genes.py\npython3 ./examples/three_genes_recoded.py\nRscript plots.R\n```\n\nTo simulate a bacteriophage T7 infection, run the following script.\n\n```\n# WARNING: This simulation takes approximately 2-3 hours to complete\npython3 ./examples/phage_model.py\n```",
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