Metadata-Version: 2.1
Name: cameo
Version: 0.12.0
Summary: cameo - computer aided metabolic engineering & optimization
Home-page: http://cameo.bio
Author: Nikolaus Sonnenschein, Joao Cardoso, Emre Özdemir, Kristian Jensen
Author-email: niko.sonnenschein@gmail.com
License: Apache License Version 2.0
Description: Cameo—Computer Aided Metabolic Engineering and Optimization
        -----------------------------------------------------------
        
        .. summary-start
        
        |Join the chat at https://gitter.im/biosustain/cameo| |PyPI| |License|
        |Build Status| |Coverage Status| |DOI| |zenhub|
        
        What is cameo?
        ~~~~~~~~~~~~~~
        
        **Cameo** is a high-level python library developed to aid the strain
        design process in metabolic engineering projects. The library provides a
        modular framework of simulation and strain design methods that targets
        developers that want to develop new design algorithms and custom analysis workflows.
        Furthermore, it exposes a high-level API to users that just want to
        compute promising strain designs.
        
        Curious? Head over to `try.cameo.bio <http://try.cameo.bio>`__
        and give it a try.
        
        Please cite https://doi.org/10.1021/acssynbio.7b00423 if you've used cameo in a scientific publication.
        
        .. summary-end
        
        Installation
        ~~~~~~~~~~~~
        
        .. installation-start
        
        Use pip to install cameo from `PyPI <https://pypi.python.org/pypi/cameo>`__.
        
        ::
        
            $ pip install cameo
        
        
        In case you downloaded or cloned the source code from `GitHub <https://github.com/biosustain/cameo>`__
        or your own fork, you can run the following to install cameo for development.
        
        ::
        
            $ pip install -e <path-to-cameo-repo>  # recommended
        
        
        You might need to run these commands with administrative
        privileges if you're not using a virtual environment (using ``sudo`` for example).
        Please check the `documentation <http://cameo.bio/installation.html>`__
        for further details.
        
        .. installation-end
        
        Documentation and Examples
        ~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Documentation is available on `cameo.bio <http://cameo.bio>`__. Numerous `Jupyter notebooks <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/tree/master/>`__
        provide 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>`__).
        Furthermore, course materials for a two day cell factory engineering course are available `here <https://biosustain.github.io/cell-factory-design-course/>`__.
        
        .. showcase-start
        
        High-level API (for users)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Compute strain engineering strategies for a desired product in a number
        of host organisms using the high-level interface (runtime is on the order of hours).
        
        ::
        
            from cameo.api import design
            design(product='L-Serine')
        
        `Output <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/08-high-level-API.ipynb>`__
        
        
        The high-level API can also be called from the command line.
        
        ::
        
            $ cameo design vanillin
        
        For more information run
        
        ::
        
            $ cameo --help
        
        Low-level API (for developers)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Find gene knockout targets using evolutionary computation.
        
        ::
        
            from cameo import models
            from cameo.strain_design.heuristic import GeneKnockoutOptimization
            from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield
        
            model = models.bigg.e_coli_core
            obj = biomass_product_coupled_yield(
                model.reactions.Biomass_Ecoli_core_w_GAM,
                model.reactions.EX_succ_e,
                model.reactions.EX_glc_e)
            ko = GeneKnockoutOptimization(model=model, objective_function=obj)
            ko.run(max_evaluations=50000, n=1, mutation_rate=0.15, indel_rate=0.185)
        
        `Output <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/05-predict-gene-knockout-strategies.ipynb>`__
        
        Predict heterologous pathways for a desired chemical.
        
        ::
        
            from cameo.strain_design import pathway_prediction
            predictor = pathway_prediction.PathwayPredictor(model)
            pathways = predictor.run(product="vanillin")
        
        `Output <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/07-predict-heterologous-pathways.ipynb>`__
        
        .. showcase-end
        
        
        Contributions
        ~~~~~~~~~~~~~
        
        ... are very welcome! Please read the `guideline <CONTRIBUTING.rst>`__ for instructions how to contribute.
        
        
        .. url-marker
        
        .. |Join the chat at https://gitter.im/biosustain/cameo| image:: https://badges.gitter.im/biosustain/cameo.svg
           :target: https://gitter.im/biosustain/cameo?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
        .. |PyPI| image:: https://img.shields.io/pypi/v/cameo.svg
           :target: https://pypi.python.org/pypi/cameo
        .. |License| image:: http://img.shields.io/badge/license-APACHE2-blue.svg
           :target: http://img.shields.io/badge/license-APACHE2-blue.svg
        .. |Build Status| image:: https://travis-ci.org/biosustain/cameo.svg?branch=master
           :target: https://travis-ci.org/biosustain/cameo
        .. |Coverage Status| image:: https://coveralls.io/repos/biosustain/cameo/badge.svg?branch=devel
           :target: https://coveralls.io/r/biosustain/cameo?branch=devel
        .. |DOI| image:: https://zenodo.org/badge/5031/biosustain/cameo.svg
           :target: https://zenodo.org/badge/latestdoi/5031/biosustain/cameo
        .. |zenhub| image:: https://img.shields.io/badge/Shipping_faster_with-ZenHub-5e60ba.svg?style=flat-square
           :target: https://zenhub.com
        
Keywords: biology metabolism bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Utilities
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: Apache Software License
Provides-Extra: docs
Provides-Extra: plotly
Provides-Extra: bokeh
Provides-Extra: jupyter
Provides-Extra: test
Provides-Extra: parallel
Provides-Extra: sbml
Provides-Extra: all
