Metadata-Version: 1.1
Name: cameo
Version: 0.10.0b2
Summary: cameo - computer aided metabolic engineering & optimziation
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
        -----------------------------------------------------------
        
        |Join the chat at https://gitter.im/biosustain/cameo| |PyPI| |License|
        |Build Status| |Coverage Status| |DOI|
        
        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 methods, strain design methods, access
        to models, that targets developers that want custom analysis workflows.
        
        Computationally heavy methods have been parallelized and can be run on a
        clusters using the IPython parallelization framework (see example and
        documentation for more details). The default fallback is python's
        multiprocessing library.
        
        Furthermore, it exposes a high-level API to users that just want to
        compute promising strain designs.
        
        You got curious? Head over to `try.cameo.bio <http://try.cameo.bio>`__
        and give it a try.
        
        Installation
        ~~~~~~~~~~~~
        
        Use pip to install Cameo from
        `PyPI <https://pypi.python.org/pypi/cameo>`__ (we recommend doing this
        inside a `virtual
        environment <http://docs.python-guide.org/en/latest/dev/virtualenvs/>`__).
        
        ::
        
            pip install cameo
        
        We highly recommend updating ``pip`` beforehand
        (``pip install pip --upgrade``).
        
        In case you downloaded the source code, run
        
        ::
        
            pip install -e .  # recommended
        
        while you are in the top level directory. You might need to run these
        commands with administrative privileges if you're not using a virtual
        environment (using ``sudo`` for example).
        
        Examples
        ~~~~~~~~
        
        A number of examples are available as static
        (`nbviewer.ipython.org <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/tree/master/>`__)
        or executable Jupyter (née IPython) notebooks
        (`try.cameo.bio <http://try.cameo.bio>`__).
        
        High-level API (for users)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Compute strain engineering strategies for a desired product in a number
        of host organisms using the high-level interface.
        
        ::
        
            from cameo.api import design
            design(product='L-Serine')
        
        `Output <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/8-high-level-API.ipynb>`__
        
        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/6-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/7-predict-heterologous-pathways.ipynb>`__
        
        Dependencies
        ~~~~~~~~~~~~
        
        This library depends on:
        
        -  `cobrapy <https://github.com/opencobra/cobrapy>`__ for
           constraint-based modeling
        -  `optlang <https://github.com/biosustain/optlang>`__ for heuristic
           optimization and mathematical programming
        
        Furthermore, the following dependencies are needed:
        
        -  `numpy <http://www.numpy.org/>`__ and
           `scipy <http://www.scipy.org/>`__ for obvious reasons.
        -  `IPython <http://ipython.org/>`__ is needed for parallel computations
           and notebook interface.
        -  `bokeh <http://bokeh.pydata.org/>`__ is needed for reporting progress
           and plotting in the IPython notebook interface.
        -  `pandas <http://pandas.pydata.org/>`__ is needed because most
           functions returns results as pandas DataFrames.
        -  `inspyred <https://pypi.python.org/pypi/inspyred>`__ for evolutionary
           computations.
        
        Contributions
        ~~~~~~~~~~~~~
        
        ..are very welcome! Please read the `guideline <CONTRIBUTING.rst>`__ for instructions how to contribute.
        
        
        .. |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
        
        
Keywords: biology metabolism bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Utilities
Classifier: Programming Language :: Python :: 2.5
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: License :: OSI Approved :: Apache Software License
