Metadata-Version: 2.1
Name: equilibrator-pathway
Version: 0.4.1b1
Summary: Pathway analysis tools by eQuilibrator
Home-page: https://gitlab.com/equilibrator/equilibrator-pathway/
Author: Elad Noor, Moritz E. Beber
Author-email: eladn@weizmann.ac.il, midnighter@posteo.net
License: MIT
Download-URL: https://pypi.org/project/equilibrator-pathway/
Project-URL: Source Code, https://gitlab.com/equilibrator/equilibrator-pathway/
Project-URL: Bug Tracker, https://gitlab.com/equilibrator/equilibrator-pathway/-/issues
Description: equilibrator-pathway
        ====================
        [![pipeline status](https://gitlab.com/equilibrator/equilibrator-pathway/badges/master/pipeline.svg)](https://gitlab.com/equilibrator/equilibrator-pathway/commits/master)
        [![codecov](https://codecov.io/gl/equilibrator/equilibrator-pathway/branch/master/graph/badge.svg)](https://codecov.io/gl/equilibrator/equilibrator-pathway)
        [![PyPI version](https://badge.fury.io/py/equilibrator-pathway.svg)](https://badge.fury.io/py/equilibrator-pathway)
        [![conda-forge](https://anaconda.org/conda-forge/equilibrator-pathway/badges/version.svg)](https://anaconda.org/conda-forge/equilibrator-pathway)
        
        Pathway analysis tools based on thermodynamic and kinetic models.
        This package can run two different pathway analysis methods:
        - Max-min Driving Force (MDF)<sup>1</sup>: 
          objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force.
        - [Enzyme Cost Minimization (ECM)](https://www.metabolic-economics.de/enzyme-cost-minimization/)<sup>2, 3</sup>: 
          estimating the specific cost in enzymes for sustaining a flux, given a kinetic model.
        
        
        ## Installation
        
        The easiest way to install equilibrator-pathway is PyPI (and we recommend using a virtual environment):
        ```
        virtualenv -p python3 equilibrator
        source equilibrator/bin/activate
        pip install equilibrator-pathway
        ```
        or, if you prefer installing with conda:
        ```
        conda install -c conda-forge equilibrator-pathway
        ```
        
        The following [example Jupyter notebook](https://gitlab.com/equilibrator/equilibrator-pathway/-/tree/develop/examples)
        can help you get started.
        
        If you only want to try out MDF or ECM without installing anything locally, we have
        a simple web interface for you at [eQuilibrator](http://equilibrator.weizmann.ac.il/pathway/) <sup>4</sup>.
        
        
        References
        ----------
        1. E. Noor, A. Bar-Even, A. Flamholz, E. Reznik, W. Liebermeister, R. Milo (2014), *Pathway Thermodynamics Highlights Kinetic Obstaclesin Central Metabolism*, PLOS Comp. Biol., [DOI: 10.1371/journal.pcbi.1003483](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930492/)
        2. [https://www.metabolic-economics.de/enzyme-cost-minimization/](https://www.metabolic-economics.de/enzyme-cost-minimization/)
        3. E. Noor, A. Flamholz, A. Bar-Even, D. Davidi, R. Milo, W. Liebermeister (2016), *The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization*, PLOS Comp. Biol., [DOI: 10.1371/journal.pcbi.1005167](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5094713/)
        4. Flamholz, E. Noor, A. Bar-Even, R. Milo (2012) *eQuilibrator - the biochemical thermodynamics calculator*, Nucleic Acids Res, [DOI: 10.1093/nar/gkr874](http://bioinformatics.oxfordjournals.org/content/28/15/2037.long)
        
Keywords: biochemical reaction,eQuilibrator,pathway analysis,enzyme cost minimization,max-min driving force
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: test
Provides-Extra: development
Provides-Extra: deployment
