Metadata-Version: 2.1
Name: multitfa
Version: 0.1.2
Summary: Multivariate thermodynamics-based metabolic flux analysis in Python.
Home-page: https://github.com/biosustain/multitfa
Author: Vishnuvardhan Mahamkali
Author-email: v.mahamkali@uq.edu.au
License: Apache-2.0
Download-URL: https://pypi.org/project/multitfa/
Project-URL: Source Code, https://github.com/biosustain/multitfa
Project-URL: Documentation, https://multitfa.readthedocs.io
Project-URL: Bug Tracker, https://github.com/biosustain/multitfa/issues
Description: ========
        multiTFA
        ========
        
        .. image:: https://img.shields.io/pypi/v/multitfa.svg
           :target: https://pypi.org/project/multitfa/
           :alt: Current PyPI Version
        
        .. image:: https://img.shields.io/pypi/pyversions/multitfa.svg
           :target: https://pypi.org/project/multitfa/
           :alt: Supported Python Versions
        
        .. image:: https://img.shields.io/pypi/l/multitfa.svg
           :target: https://www.apache.org/licenses/LICENSE-2.0
           :alt: Apache Software License Version 2.0
        
        .. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
           :target: .github/CODE_OF_CONDUCT.md
           :alt: Code of Conduct
        
        .. image:: https://github.com/biosustain/multitfa/workflows/CI-CD/badge.svg
           :target: https://github.com/biosustain/multitfa/workflows/CI-CD
           :alt: GitHub Actions
        
        .. image:: https://codecov.io/gh/biosustain/multitfa/branch/main/graph/badge.svg
           :target: https://codecov.io/gh/biosustain/multitfa
           :alt: Codecov
        
        .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
           :target: https://github.com/ambv/black
           :alt: Code Style Black
        
        .. image:: https://readthedocs.org/projects/multitfa/badge/?version=latest
           :target: https://multitfa.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        
        .. summary-start
        
        We present multiTFA, a multivariate thermodynamics-based metabolic flux analysis
        package for Python. The framework takes advantage of the reactions' Gibbs free
        energy covariance matrix to tightly constrain metabolic models using
        thermodynamic constraints. It represents an improvement over a previous
        thermodynamic metabolic flux analysis (tMFA) method described in [1]_.
        
        This implementation requires a COBRA model as input, as well as additional
        compartment conditions and metabolite concentrations. It allows user to perform
        various thermodynamic analyses on COBRA models, such as thermodynamic metabolic
        flux analysis, variability analysis, or flux sampling.  Please see below for
        further details.
        
        
        Install
        =======
        
        To install multitfa from PyPI is as simple as: (We recommend using a `virtual environment <https://docs.python-guide.org/dev/virtualenvs/>`_).
        
        .. code-block:: console
        
            pip install multitfa
        
        To install from source,
        
        .. code-block:: console
        
           git clone https://github.com/biosustain/multitfa.git
           cd multitfa
           pip install .
        
        
        
        We highly recommend the installing `CPLEX <https://www.ibm.com/analytics/cplex-optimizer>`_. Although we support `GUROBI <https://www.gurobi.com/>`_ solver, we noticed that it is slower and often stuck when solving quadratic constraint problems.
        
        Please note, Installation takes upto 3 GB. This is to accomodate `equilibrator-api <https://gitlab.com/equilibrator/equilibrator-api>`_ database files.
        
        Install Requirements
        ====================
        
        Installation requires
        
        - cobra
        - depinfo
        - optlang<1.4.6
        - numpy
        - scipy
        - pandas
        - equilibrator-api==0.3.2b7
        - component-contribution==0.3.2b4
        - equilibrator-cache==0.3.2b2
        
        Usage
        =====
        
        The documentation is available online at `readthedocs <https://multitfa.readthedocs.io/en/latest/>`_.
        
        Copyright
        =========
        
        * Copyright © 2018, Novo Nordisk Foundation Center for Biosustainability.
        * Free software distributed under the `Apache Software License 2.0
          <https://www.apache.org/licenses/LICENSE-2.0>`_.
        
        
        Cite us
        =======
        
        If you use multitfa in a scientific publication, please cite `doi:10.1101/2020.12.01.407387 <https://doi.org/10.1101/2020.12.01.407387>`_.
        
        References
        ==========
        
        .. [1] Henry, Christopher S., Linda J. Broadbelt, and Vassily Hatzimanikatis.
            "Thermodynamics-Based Metabolic Flux Analysis."
            *Biophysical Journal* 92, no. 5 (March 1, 2007): 1792–1805.
            https://doi.org/10.1529/biophysj.106.093138.
        
        .. [2] Vishnuvardhan Mahamkali, Tim McCubbin, Moritz Emanuel Beber, Esteban Marcellin, Lars Keld Nielsen. 
            "multiTFA: a Python package for multi-variate Thermodynamics-based Flux Analysis."
            *bioRxiv* 2020.12.01.407387;
            https://doi.org/10.1101/2020.12.01.407387
        
        .. summary-end
        
Keywords: thermodynamics,multivariate,flux analysis,metabolic,TMFA,TFA,multiTFA
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: development
