Metadata-Version: 2.1
Name: corda
Version: 0.5.1
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: |actions| |codecov.io|
        
        CORDA for Python
        ================
        
        This is a Python implementation based on the papers of Schultz et. al. with
        some added optimizations. It is based on the following two publiactions:
        
        - `Reconstruction of Tissue-Specific Metabolic Networks Using
          CORDA <http://journals.plos.org/ploscompbiol/article/authors?id=10.1371%2Fjournal.pcbi.1004808>`_
        - `IDENTIFYING CANCER SPECIFIC METABOLIC SIGNATURES USING CONSTRAINT-BASED MODELS
          <http://dx.doi.org/10.1142/9789813207813_0045>`_
        
        This Python package is developed in the
        `Human Systems Biology Group <https://resendislab.github.io>`_ of
        Prof. Osbaldo Resendis Antonio at the `National Institute of Genomic
        Medicine Mexico <https://inmegen.gob.mx>`_ and includes recent updates to
        the method (*CORDA 2*).
        
        
        How to cite?
        ------------
        
        This particular implementation of CORDA has not been published so far. In the
        meantime you should if you cite the respective publications for the method
        mentioned above and provide a link to this GitHub repository.
        
        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/resendislab/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?
        ----------------
        
        You can follow the [introduction](docs/index.ipynb).
        
        What's the advantage over other reconstruction algorithms?
        ----------------------------------------------------------
        
        No commercial solver needed
        ***************************
        
        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 glpk version is a bout 3 times
        faster than the fastest tested commercial solver (cplex).
        
        Fast reconstructions
        ********************
        
        CORDA for Python uses a strategy similar to FastFVA, where
        a previous solution basis is recycled repeatedly.
        
        Some reference times for reconstructing the minimal growing models for
        iJO1366 (*E. coli*) and Recon3:
        
        .. code::
        
            Python 3.10.8 (main, Oct 24 2022, 10:07:16) [GCC 12.2.0]
            Type 'copyright', 'credits' or 'license' for more information
            IPython 8.4.0 -- An enhanced Interactive Python. Type '?' for help.
        
            In [1]: from cobra.io import load_model
        
            In [2]: from corda import benchmark
        
            In [3]: ecoli = load_model("iJO1366")
            Restricted license - for non-production use only - expires 2023-10-25
        
            In [4]: opt = benchmark(ecoli)
            Running setup for model `iJO1366`.
            Running CORDA setup... ✔ [0.479 s]
            Running CORDA build... ✔ [7.44 s]
            Running validation on reduced model... ✔ [0.448 s]
        
            In [5]: print(opt)
            build status: reconstruction complete
            Inc. reactions: 447/2583
            - unclear: 0/0
            - exclude: 446/2582
            - low and medium: 0/0
            - high: 1/1
        
        
            In [6]: recon3 = load_model("Recon3D")
        
            In [7]: opt = benchmark(recon3)
            Running setup for model `Recon3D`.
            Running CORDA setup... ✔ [2 s]
            Running CORDA build... ✔ [13.7 s]
            Running validation on reduced model... ✔ [1.68 s]
        
            In [8]: print(opt)
            build status: reconstruction complete
            Inc. reactions: 114/10600
            - unclear: 0/0
            - exclude: 113/10599
            - low and medium: 0/0
            - high: 1/1
        
        .. |actions| image:: https://github.com/resendislab/corda/actions/workflows/pythonpackage.yml/badge.svg
           :target: https://github.com/resendislab/corda/actions/workflows/pythonpackage.yml
        .. |codecov.io| image:: https://codecov.io/github/resendislab/corda/coverage.svg?branch=main
           :target: https://codecov.io/github/resendislab/corda?branch=main
        
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
Provides-Extra: dev
Provides-Extra: test
