Metadata-Version: 1.1
Name: corda
Version: 0.2.0
Summary: Genome-scale model construction with CORDA
Home-page: https://github.com/cdiener/corda
Author: Christian Diener
Author-email: mail@cdiener.com
License: MIT
Description: |Build Status| |codecov.io| |Code Health|
        
        CORDA for Python
        ================
        
        This is a Python implementation based on the paper of Schultz et. al.
        
        `Reconstruction of Tissue-Specific Metabolic Networks Using
        CORDA <http://journals.plos.org/ploscompbiol/article/authors?id=10.1371%2Fjournal.pcbi.1004808>`__
        
        What does it do?
        ----------------
        
        CORDA, short for Cost Optimization Reaction Dependency Assessment is a
        method for the reconstruction of metabolic networks from a given
        reference model (a database of all known reactions) and a confidence
        mapping for reactions. It allows you to reconstruct metabolic models for
        tissues, patients or specific experimental conditions from a set of
        transcription or proteome measurements.
        
        How do I install it
        -------------------
        
        CORDA for Python works only for Python 3.4+ and requires
        `cobrapy <http://github.com/opencobra/cobrapy>`__ to work. After having
        a working Python installation with pip (Anaconda or Miniconda works fine
        here as well) you can install corda with pip
        
        .. code:: bash
        
            pip install corda
        
        This will download and install cobrapy as well. I recommend using a
        version of pip that supports manylinux builds for faster installation
        (pip>=8.1).
        
        For now the master branch is usually working and tested whereas all new
        features are kept in its own branch. To install from the master branch
        directly use
        
        .. code:: bash
        
            pip install https://github.com/cdiener/corda/archive/master.zip
        
        What do I need to run it?
        -------------------------
        
        CORDA requires a base model including all reactions that could possibly
        included such as Recon 1/2 or HMR. You will also need gene expression or
        proteome data for our tissue/patient/experimental setting. This data has
        to be translated into 5 distinct classes: unknown (0), not
        expressed/present (-1), low confidence (1), medium confidence (2) and
        high confidence (3). CORDA will then ensure to include as many high
        confidence reactions as possible while minimizing the inclusion of
        absent (-1) reactions while maintaining a set of metabolic requirements.
        
        How do I use it?
        ----------------
        
        A small tutorial is found at https://cdiener.github.io/corda.
        
        What's the advantage over other reconstruction algorithms
        ---------------------------------------------------------
        
        I would say there are two major advantages:
        
        1. It does not require any commercial solvers, in fact it works fastest
           with the free glpk solver that already comes together with cobrapy.
           For instance for the small central metabolism model (101 irreversible
           reactions) included together with CORDA the reconstruction uses the
           following times:
        
           cglpk: 0.02 s
           cplex: 0.30 s
           gurobi: 0.12 s
           mosek: 0.23 s
        
        2. It's fast. CORDA for Python uses a strategy similar to FastFVA, where
           a previous solution basis is recycled repeatedly (speed-up of ~4-10
           times). A normal reconstruction for Recon 1 with mCADRE can take
           several hours. With the original Matlab implementation of CORDA this
           takes about 40 minutes and with CORDA for Python it takes less than 5
           minutes. A Recon 2 reconstruction can be achieved in less than 30
           minutes.
        
        .. |Build Status| image:: https://travis-ci.org/cdiener/corda.svg?branch=master
           :target: https://travis-ci.org/cdiener/corda
        .. |codecov.io| image:: https://codecov.io/github/cdiener/corda/coverage.svg?branch=master
           :target: https://codecov.io/github/cdiener/corda?branch=master
        .. |Code Health| image:: https://landscape.io/github/cdiener/corda/master/landscape.svg?style=flat
           :target: https://landscape.io/github/cdiener/corda/master
        
Keywords: biology metabolism reconstruction cobra
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
