{"id":29016335,"url":"https://github.com/karrlab/wc_lang","last_synced_at":"2025-08-18T15:09:57.476Z","repository":{"id":62588337,"uuid":"73089754","full_name":"KarrLab/wc_lang","owner":"KarrLab","description":"Language for describing whole-cell models as reaction networks","archived":false,"fork":false,"pushed_at":"2021-05-24T21:57:09.000Z","size":13686,"stargazers_count":9,"open_issues_count":30,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-06-25T22:07:59.783Z","etag":null,"topics":["cell-biology","computational-biology","modeling","simulation","systems-biology","whole-cell-modeling"],"latest_commit_sha":null,"homepage":"","language":"Python","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/KarrLab.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":"2016-11-07T15:03:21.000Z","updated_at":"2024-04-02T09:41:09.000Z","dependencies_parsed_at":"2022-11-03T17:01:38.891Z","dependency_job_id":null,"html_url":"https://github.com/KarrLab/wc_lang","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/KarrLab/wc_lang","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_lang","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_lang/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_lang/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_lang/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KarrLab","download_url":"https://codeload.github.com/KarrLab/wc_lang/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_lang/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271012549,"owners_count":24684565,"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","status":"online","status_checked_at":"2025-08-18T02:00:08.743Z","response_time":89,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["cell-biology","computational-biology","modeling","simulation","systems-biology","whole-cell-modeling"],"created_at":"2025-06-25T22:07:58.618Z","updated_at":"2025-08-18T15:09:57.450Z","avatar_url":"https://github.com/KarrLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![PyPI package](https://img.shields.io/pypi/v/wc_lang.svg)](https://pypi.python.org/pypi/wc_lang)\n[![Documentation](https://readthedocs.org/projects/wc-lang/badge/?version=latest)](https://docs.karrlab.org/wc_lang)\n[![Test results](https://circleci.com/gh/KarrLab/wc_lang.svg?style=shield)](https://circleci.com/gh/KarrLab/wc_lang)\n[![Test coverage](https://coveralls.io/repos/github/KarrLab/wc_lang/badge.svg)](https://coveralls.io/github/KarrLab/wc_lang)\n[![Code analysis](https://api.codeclimate.com/v1/badges/bd3cac02fd316d722216/maintainability)](https://codeclimate.com/github/KarrLab/wc_lang)\n[![License](https://img.shields.io/github/license/KarrLab/wc_lang.svg)](LICENSE)\n![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/wc_lang/README.md?pixel)\n\n# wc_lang\nLanguage for describing whole-cell models as reaction networks\n\n## Contents\n* [Overview](#overview)\n* [Installation](#installation)\n* [Documentation](#documentation)\n* [License](#license)\n* [Development team](#development-team)\n* [Questions and comments](#questions-and-comments)\n* [References](#references)\n\n## Overview\nWhole-cell (WC) models are comprehensive computational models of all of the biochemical activity inside individaul cells [Karr et al., 2015; Macklin et al., 2014]. WC models have great potential to enable bioengineers to rationally design microorganisms for industrial and medical applications and to enable physicians to personalize medical therapy [Carrera and Covert, 2015]. Please see [WholeCell.org](https://www.wholecell.org) for more information about WC modeling.\n\nThis package defines `wc_lang`, a language for describing WC models as reaction networks.\n\n## Installation\n\n* Install latest release from PyPI\n  ```\n  wc_lang\n  ```\n\n* Install latest revision from GitHub\n  ```\n  pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils\n  pip install git+https://github.com/KarrLab/obj_tables.git#egg=obj_tables\n  pip install git+https://github.com/KarrLab/wc_lang.git#egg=wc_lang\n  ```\n\n## Documentation\nPlease see the [documentation](https://docs.karrlab.org/wc_lang).\n\n## License\nThis package is released under the [MIT license](LICENSE).\n\n## Development team\nThis package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York.\n\n## Questions and comments\nPlease contact the [Karr Lab](https://www.karrlab.org) with any questions or comments.\n\n## References\n* Carrera J \u0026 Covert MW. (2015). Why Build Whole-Cell Models? *Trends in Cell Biology*, 25(12), 719-722. DOI: [10.1016/j.tcb.2015.09.004](https://doi.org/10.1016/j.tcb.2015.09.004)\n* Karr JR, Takahashi K \u0026 Funahashi A. (2015). The principles of whole-cell modeling. *Current Opinion in Microbiology*, 27, 18-24. DOI: [10.1016/j.mib.2015.06.004](https://doi.org/10.1016/j.mib.2015.06.004)\n* Macklin DN, Ruggero NA \u0026 Covert MW. (2014). The future of whole-cell modeling. *Current Opinion in Biotechnology*, 28, 111-115. DOI: [10.1016/j.copbio.2014.01.012](https://doi.org/10.1016/j.copbio.2014.01.012)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarrlab%2Fwc_lang","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkarrlab%2Fwc_lang","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarrlab%2Fwc_lang/lists"}