{"id":13752457,"url":"https://github.com/biosustain/cameo","last_synced_at":"2025-04-06T13:11:02.894Z","repository":{"id":15402983,"uuid":"18134954","full_name":"biosustain/cameo","owner":"biosustain","description":"cameo - computer aided metabolic engineering \u0026 optimization","archived":false,"fork":false,"pushed_at":"2022-11-07T14:54:19.000Z","size":213073,"stargazers_count":115,"open_issues_count":43,"forks_count":45,"subscribers_count":24,"default_branch":"devel","last_synced_at":"2025-03-30T11:11:14.523Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://cameo.bio","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biosustain.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":"CONTRIBUTING.rst","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-03-26T10:50:33.000Z","updated_at":"2025-02-25T08:47:22.000Z","dependencies_parsed_at":"2023-01-11T20:23:17.211Z","dependency_job_id":null,"html_url":"https://github.com/biosustain/cameo","commit_stats":null,"previous_names":[],"tags_count":68,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fcameo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fcameo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fcameo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fcameo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biosustain","download_url":"https://codeload.github.com/biosustain/cameo/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247485287,"owners_count":20946398,"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":[],"created_at":"2024-08-03T09:01:06.162Z","updated_at":"2025-04-06T13:11:02.875Z","avatar_url":"https://github.com/biosustain.png","language":"Python","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"readme":"Cameo—Computer Aided Metabolic Engineering and Optimization\n-----------------------------------------------------------\n\n.. summary-start\n\n|Join the chat at https://gitter.im/biosustain/cameo| |PyPI| |License|\n|Build Status| |Coverage Status| |DOI| |zenhub| |binder|\n\nWhat is cameo?\n~~~~~~~~~~~~~~\n\n**Cameo** is a high-level python library developed to aid the strain\ndesign process in metabolic engineering projects. The library provides a\nmodular framework of simulation and strain design methods that targets\ndevelopers that want to develop new design algorithms and custom analysis workflows.\nFurthermore, it exposes a high-level API to users that just want to\ncompute promising strain designs.\n\nCurious? Head over to `try.cameo.bio \u003chttp://try.cameo.bio\u003e`__\nand give it a try.\n\nPlease cite https://doi.org/10.1021/acssynbio.7b00423 if you've used cameo in a scientific publication.\n\n.. summary-end\n\nInstallation\n~~~~~~~~~~~~\n\n.. installation-start\n\nUse pip to install cameo from `PyPI \u003chttps://pypi.python.org/pypi/cameo\u003e`__.\n\n::\n\n    $ pip install cameo\n\n\nIn case you downloaded or cloned the source code from `GitHub \u003chttps://github.com/biosustain/cameo\u003e`__\nor your own fork, you can run the following to install cameo for development.\n\n::\n\n    $ pip install -e \u003cpath-to-cameo-repo\u003e  # recommended\n\n\nYou might need to run these commands with administrative\nprivileges if you're not using a virtual environment (using ``sudo`` for example).\nPlease check the `documentation \u003chttp://cameo.bio/installation.html\u003e`__\nfor further details.\n\n.. installation-end\n\nDocumentation and Examples\n~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nDocumentation is available on `cameo.bio \u003chttp://cameo.bio\u003e`__. Numerous `Jupyter notebooks \u003chttp://nbviewer.ipython.org/github/biosustain/cameo-notebooks/tree/master/\u003e`__\nprovide examples and tutorials and also form part of the documentation. They are also availabe in executable form on (`try.cameo.bio \u003chttp://try.cameo.bio\u003e`__).\nFurthermore, course materials for a two day cell factory engineering course are available `here \u003chttps://biosustain.github.io/cell-factory-design-course/\u003e`__.\n\n.. showcase-start\n\nHigh-level API (for users)\n^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nCompute strain engineering strategies for a desired product in a number\nof host organisms using the high-level interface (runtime is on the order of hours).\n\n::\n\n    from cameo.api import design\n    design(product='L-Serine')\n\n`Output \u003chttp://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/08-high-level-API.ipynb\u003e`__\n\n\nThe high-level API can also be called from the command line.\n\n::\n\n    $ cameo design vanillin\n\nFor more information run\n\n::\n\n    $ cameo --help\n\nLow-level API (for developers)\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFind gene knockout targets using evolutionary computation.\n\n::\n\n    from cameo import models\n    from cameo.strain_design.heuristic import GeneKnockoutOptimization\n    from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield\n\n    model = models.bigg.e_coli_core\n    obj = biomass_product_coupled_yield(\n        model.reactions.Biomass_Ecoli_core_w_GAM,\n        model.reactions.EX_succ_e,\n        model.reactions.EX_glc_e)\n    ko = GeneKnockoutOptimization(model=model, objective_function=obj)\n    ko.run(max_evaluations=50000, n=1, mutation_rate=0.15, indel_rate=0.185)\n\n`Output \u003chttp://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/05-predict-gene-knockout-strategies.ipynb\u003e`__\n\nPredict heterologous pathways for a desired chemical.\n\n::\n\n    from cameo.strain_design import pathway_prediction\n    predictor = pathway_prediction.PathwayPredictor(model)\n    pathways = predictor.run(product=\"vanillin\")\n\n`Output \u003chttp://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/07-predict-heterologous-pathways.ipynb\u003e`__\n\n.. showcase-end\n\n\nContributions\n~~~~~~~~~~~~~\n\n... are very welcome! Please read the `guideline \u003cCONTRIBUTING.rst\u003e`__ for instructions how to contribute.\n\n\n.. url-marker\n\n.. |Join the chat at https://gitter.im/biosustain/cameo| image:: https://badges.gitter.im/biosustain/cameo.svg\n   :target: https://gitter.im/biosustain/cameo?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge\n.. |PyPI| image:: https://img.shields.io/pypi/v/cameo.svg\n   :target: https://pypi.python.org/pypi/cameo\n.. |License| image:: http://img.shields.io/badge/license-APACHE2-blue.svg\n   :target: http://img.shields.io/badge/license-APACHE2-blue.svg\n.. |Build Status| image:: https://travis-ci.org/biosustain/cameo.svg?branch=master\n   :target: https://travis-ci.org/biosustain/cameo\n.. |Coverage Status| image:: https://coveralls.io/repos/biosustain/cameo/badge.svg?branch=devel\n   :target: https://coveralls.io/r/biosustain/cameo?branch=devel\n.. |DOI| image:: https://zenodo.org/badge/5031/biosustain/cameo.svg\n   :target: https://zenodo.org/badge/latestdoi/5031/biosustain/cameo\n.. |zenhub| image:: https://img.shields.io/badge/Shipping_faster_with-ZenHub-5e60ba.svg?style=flat-square\n   :target: https://zenhub.com\n.. |binder| image:: https://mybinder.org/badge_logo.svg\n   :target: https://mybinder.org/v2/gh/biosustain/cameo-notebooks/master?urlpath=lab/tree/index.ipynb\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Fcameo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosustain%2Fcameo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Fcameo/lists"}