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https://github.com/biosustain/cameo

cameo - computer aided metabolic engineering & optimization
https://github.com/biosustain/cameo

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cameo - computer aided metabolic engineering & optimization

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README 

        
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| |binder|



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 `__

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 `__.



::



    $ pip install cameo



In case you downloaded or cloned the source code from `GitHub `__

or your own fork, you can run the following to install cameo for development.



::



    $ pip install -e   # 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 `__

for further details.



.. installation-end



Documentation and Examples

~~~~~~~~~~~~~~~~~~~~~~~~~~



Documentation is available on `cameo.bio `__. Numerous `Jupyter notebooks `__

provide examples and tutorials and also form part of the documentation. They are also availabe in executable form on (`try.cameo.bio `__).

Furthermore, course materials for a two day cell factory engineering course are available `here `__.



.. 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 `__



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 `__



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 `__



.. showcase-end



Contributions

~~~~~~~~~~~~~



... are very welcome! Please read the `guideline `__ 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

.. |binder| image:: https://mybinder.org/badge_logo.svg

   :target: https://mybinder.org/v2/gh/biosustain/cameo-notebooks/master?urlpath=lab/tree/index.ipynb