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        "author": "Nikolaus Sonnenschein, Joao Cardoso, Emre \u00d6zdemir, Kristian Jensen",
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            "License :: OSI Approved :: Apache Software License",
            "Programming Language :: Python :: 2.5",
            "Programming Language :: Python :: 2.6",
            "Programming Language :: Python :: 2.7",
            "Topic :: Utilities"
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Head over to `try.cameo.bio <http://try.cameo.bio>`__\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 <https://pypi.python.org/pypi/cameo>`__.\n\n::\n\n    $ pip install cameo\n\n\nIn case you downloaded or cloned the source code from `GitHub <https://github.com/biosustain/cameo>`__\nor your own fork, you can run the following to install cameo for development.\n\n::\n\n    $ pip install -e <path-to-cameo-repo>  # 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 <http://cameo.bio/installation.html>`__\nfor further details.\n\n.. installation-end\n\nDocumentation and Examples\n~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nDocumentation is available on `cameo.bio <http://cameo.bio>`__. Numerous `Jupyter notebooks <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/tree/master/>`__\nprovide examples and tutorials and also form part of the documentation. They are also availabe in executable form on (`try.cameo.bio <http://try.cameo.bio>`__).\nFurthermore, course materials for a two day cell factory engineering course are available `here <https://biosustain.github.io/cell-factory-design-course/>`__.\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 <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/08-high-level-API.ipynb>`__\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 <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/05-predict-gene-knockout-strategies.ipynb>`__\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 <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/07-predict-heterologous-pathways.ipynb>`__\n\n.. showcase-end\n\n\nContributions\n~~~~~~~~~~~~~\n\n... are very welcome! Please read the `guideline <CONTRIBUTING.rst>`__ 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&utm_medium=badge&utm_campaign=pr-badge&utm_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\n\n",
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