Metadata-Version: 1.1
Name: geckopy
Version: 0.0.1
Summary: Methods for using the GECKO model with cobrapy
Home-page: https://github.com/Biosustain/geckopy
Author: Bejamin Sanchez
Author-email: bensan@chalmers.se
License: custom..
Description-Content-Type: UNKNOWN
Description: <img src="https://github.com/SysBioChalmers/GECKO/blob/master/GECKO.png" alt="GECKO logo" width="300">
        
        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 following 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)_
        
        GECKO was written by Benjamin J. Sanchez (@BenjaSanchez), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, and Cheng Zhang, Science for Life Laboratory, KTH - Royal Institute of Technology.
        
        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.
        
        ## Scripts for building a GECKO model
        
        Only tested on Windows, probably works on other platforms as well with adjusted installation procedure.
        
        ### Required software for running the Python scripts
        
        * [Python](https://www.python.org/) 2.7
        * setuptools for python 2.7, accessible [here](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 for using the Matlab scripts
        
        * [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 [Sánchez et al. (2017)]([citation](https://dx.doi.org/10.15252/msb.20167411))
        
        ## Using the geckopy Python package for obtaining an adjusted GECKO model object
        
        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
        
        ```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()
        ```
        
        
        =======
        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 :: Apache Software 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
