Metadata-Version: 1.1
Name: marsi
Version: 0.2.5
Summary: marsi - Metabolite Analogues for Rational Strain Improvement
Home-page: https://github.com/biosustain/marsi
Author: Joao Cardoso
Author-email: joaca@biosustain.dtu.dk
License: Apache License Version 2.0
Description: marsi - Metabolite Analogues for Strain Improvement
        ===================================================
        
        [![Build Status](https://travis-ci.org/biosustain/marsi.svg?branch=master)](https://travis-ci.org/biosustain/marsi)
        
        marsi is an open-source software to created to identify non-GMO strain design
        targets 
        
        Dependencies
        ------------
        * eigen3 >= 3.0
        * OpenBabel >= 2.2.3
        * RDKit >= 2016
        * mongodb
        * glpk
        * cplex (optional)
        * Cython >= 0.25
        * numpy >= 1.11
        
        
        Quick Start
        -----------
        
        1. Install the Dependencies
        2. `pip install marsi` 
        3. Run `marsi --help` from the command line
        
        More details in [Quick Start](QUICK_START.md)
        
        Initialization
        --------------
        
        *marsi* comes with a initialization command that will download all the necessary files
        and build the database. You can start by running `marsi db --help`.
        
        *marsi* will download the required files for you, setup the database and process the molecular structures. Just run `marsi db init`. **Make sure you have an stable internet 
        connection.** 
        
        
        The PubChem API does not provide a method for query. To retrieve the necessary files,
        go to [PubChem](https://pubchem.ncbi.nlm.nih.gov) and enter the following query:
         ```
            (antimetabolites) OR (analog) OR (analogue)     
         ```
         
        And download the summary file. You should save the file in data folder at *marsi*'s working 
        directory (`$HOME/.marsi/data` by default) with the name `pubchem_compound_analogs_antimetabolites.txt`.
        
        
        Find Metabolite Targets
        -----------------------
        
        
        License
        -------
        Apache License Version 2.0
        
        
        Databases and Software Tools
        ----------------------------
        
        All tools and databases are listed [here](CITATIONS.md)
        
Keywords: biology metabolism bioinformatics chemoinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3.4
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
