Metadata-Version: 1.1
Name: geckopy
Version: 1.1.1
Summary: Methods for using the GECKO model with cobrapy
Home-page: https://github.com/SysBioChalmers/GECKO/tree/master/geckopy
Author: Bejamin Sanchez
Author-email: bensan@chalmers.se
License: MIT License
Description-Content-Type: UNKNOWN
Description: .. image:: GECKO.png
        
        The **GECKO** toolbox is a Matlab/Python package for enhancing a
        **G**\ enome-scale model to account for **E**\ nzyme **C**\ onstraints,
        using **K**\ inetics and **O**\ mics. It is the companion software to
        the publication:
        
        Benjamin J. Sanchez, Cheng Zhang, Avlant Nilsson, Petri-Jaan Lahtvee,
        Eduard J. Kerkhoven, Jens Nielsen (2017). *Improving the phenotype
        predictions of a yeast genome-scale metabolic model by incorporating
        enzymatic constraints.* `Molecular Systems Biology, 13(8):
        935 <http://www.dx.doi.org/10.15252/msb.20167411>`__
        
        The software comes in two flavors, Python and Matlab scripts to fetch
        online data and build the published ecYeast7 GECKO models, and a Python
        package which can be used with
        `cobrapy <https://opencobra.github.io/cobrapy/>`__ to obtain a ecYeast7
        model object, optionally adjusted for provided proteomics data.
        
        Last update: 2017-12-08
        
        This repository is administered by Benjamin J. Sanchez (`@BenjaSanchez <https://github.com/benjasanchez>`__), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
        
        Building a GECKO model
        ----------------------------------
        
        
        Required software - Python module
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  `Python 2.7 <https://www.python.org/>`__
        -  `setuptools for python 2.7 <http://www.lfd.uci.edu/~gohlke/pythonlibs/#setuptools>`__
        -  SOAPpy: for this, open command prompt as admin, and then do:
        
        ::
        
            cd C:\Python27\Scripts
            easy_install-2.7 SOAPpy
        
        
        Required software - Matlab module
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  `MATLAB <http://www.mathworks.com/>`__ (7.5 or higher) + Optimization
           Toolbox.
        -  The `COBRA toolbox for
           MATLAB <https://github.com/opencobra/cobratoolbox>`__. Note that
           `libSBML <http://sbml.org/Software/libSBML>`__ and the `SBML
           toolbox <http://sbml.org/Software/SBMLToolbox>`__ should both be
           installed. Both of them are free of charge for academic users.
           Aditionally, you should add the cobra folder to your MATLAB search
           path.
        
        
        Usage
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        See the supporting information of `Sanchez et al.
        (2017) <https://dx.doi.org/10.15252/msb.20167411>`__
        
        
        Integrating proteomic data to the yeast model
        -----------------------------------------------------------------------------
        
        If all you need is the ecYeast7 model to use together with cobrapy you
        can use the ``geckopy`` Python package.
        
        
        Required software
        ~~~~~~~~~~~~~~~~~
        
        -  Python 2.7, 3.4, 3.5 or 3.6
        -  cobrapy
        
        
        Installation
        ~~~~~~~~~~~~
        
        ::
        
            pip install geckopy
        
        
        Usage
        ~~~~~
        
        .. code:: python
        
            from geckopy import GeckoModel
            import pandas
            some_measurements = pandas.Series({'P00549': 0.1, 'P31373': 0.1, 'P31382': 0.1})
            model = GeckoModel('multi-pool')
            model.limit_proteins(some_measurements)
            model.optimize()
        
        Contributors
        -----------------------------------------------------------------------------
        
        * Moritz Emanuel Beber (`@Midnighter <https://github.com/Midnighter>`__), Danish Technical University, Lyngby Denmark
        * Henning Redestig (`@hredestig <https://github.com/hredestig>`__), Danish Technical University, Lyngby Denmark
        * `Benjamin J. Sanchez <https://www.chalmers.se/en/staff/Pages/bensan.aspx>`__ (`@BenjaSanchez <https://github.com/benjasanchez>`__), Chalmers University of Technology, Gothenburg Sweden
        * Cheng Zhang, Science for Life Laboratory, KTH - Royal Institute of Technology
        
        
        =======
        History
        =======
        
        0.0.1 (2017-09-07)
        ------------------
        
        * First release on PyPI.
        
Keywords: geckopy
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
