{"id":16896236,"url":"https://github.com/clauswilke/pinetree","last_synced_at":"2025-03-22T09:31:44.403Z","repository":{"id":56151116,"uuid":"80039025","full_name":"clauswilke/pinetree","owner":"clauswilke","description":"🌲 a flexible gene expression simulator with codon-specific translation rates","archived":false,"fork":false,"pushed_at":"2025-03-06T04:42:41.000Z","size":3409,"stargazers_count":11,"open_issues_count":5,"forks_count":5,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-15T02:11:57.572Z","etag":null,"topics":["codons","gene-expression","gillespie-algorithm","stochastic-simulation","transcription","translation"],"latest_commit_sha":null,"homepage":"http://pinetree.readthedocs.io","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/clauswilke.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-01-25T17:36:36.000Z","updated_at":"2025-01-30T00:46:52.000Z","dependencies_parsed_at":"2023-01-30T01:45:39.257Z","dependency_job_id":null,"html_url":"https://github.com/clauswilke/pinetree","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/clauswilke%2Fpinetree","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/clauswilke%2Fpinetree/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/clauswilke%2Fpinetree/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/clauswilke%2Fpinetree/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/clauswilke","download_url":"https://codeload.github.com/clauswilke/pinetree/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244937751,"owners_count":20535124,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["codons","gene-expression","gillespie-algorithm","stochastic-simulation","transcription","translation"],"created_at":"2024-10-13T17:29:16.785Z","updated_at":"2025-03-22T09:31:43.242Z","avatar_url":"https://github.com/clauswilke.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"![pinetree](https://github.com/clauswilke/pinetree/blob/master/docs/pinetree-logo.png?raw=true)\n\n# pinetree \n[![Build Status](https://travis-ci.org/clauswilke/pinetree.svg?branch=master)](https://travis-ci.org/clauswilke/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```\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclauswilke%2Fpinetree","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fclauswilke%2Fpinetree","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclauswilke%2Fpinetree/lists"}