Metadata-Version: 1.1
Name: corda
Version: 0.1
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](https://travis-ci.org/cdiener/corda.svg?branch=master)](https://travis-ci.org/cdiener/corda)
        [![codecov.io](https://codecov.io/github/cdiener/corda/coverage.svg?branch=master)](https://codecov.io/github/cdiener/corda?branch=master)
        [![Code Health](https://landscape.io/github/cdiener/corda/master/landscape.svg?style=flat)](https://landscape.io/github/cdiener/corda/master)
        
        # 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. We recommend
        installation via the [anaconda or miniconda](https://www.continuum.io/downloads)
        distribution. After installing anaconda or miniconda you can install cobrapy
        from the bioconda repository
        
        ```bash
        conda install -c bioconda cobra
        ```
        After that you can install CORDA using the pip from conda
        
        ```bash
        pip install https://github.com/cdiener/corda/archive/master.zip
        ```
        
        After CORDA for Python comes out of its infancy I will prepare a conda package
        as well. For now the master branch is usually working and tested whereas all
        new stuff is kept in the devel branch.
        
        ## 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.com/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.
        
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
