Metadata-Version: 2.1
Name: antivirals
Version: 0.0.1
Summary: Finding antivirals for the novel coronavirus.
Home-page: https://www.github.com/bnext-iqt/antivirals
Author: JJ Ben-Joseph
Author-email: jbenjoseph@iqt.org
License: Apache
Description: .. image:: coronavirus.png
           :alt: The novel coronavirus
        
        Coronavirus Antivirals
        ~~~~~~~~~~~~~~~~~~~~~~
        
        This project hopes to discover an antiviral that can treat the novel
        coronavirus disease. This project will use newer approaches in machine learning to 
        model and optimize for the properties needed in candidate therapeutics.
        
        In therapeutic drug development the properties we minimize are toxicity and 
        side-effects (also called “off-target effects”). Properties we maximize are 
        bioactivity on target (also called "on-target effects"), absorption, 
        synthesizability, and large-scale manufacturability. 
        
        We aim to search the molecular space (both drug-like molecules, and 
        already approved drugs) for drug candidates maximizing these properties.
        
        How to Contribute
        ~~~~~~~~~~~~~~~~~
        
        We need your help if you have one of the following skills:
        
        * Software development in Python
        * Machine learning
        * Web development (for the UI)
        * DevOps -- especially with Kubernetes and Helm
        
        Fork the project and create a new branch:
        
        ::
        
            git checkout -b feature/my_new_feature
        
        Push your changes and use GitHub to submit a pull request.
        
        Any contributions are helpful. Look at the open issues for inspiration 
        on what to work on.
        
        License
        ~~~~~~~
        
        Apache 2. See LICENSE file for details.
        
        Installation
        ~~~~~~~~~~~~
        
        Using the system through Docker is highly recommended:
        
        :: 
        
            docker run -v my_host_data_directory:/app/data -it inqtel/antivirals up sqlite:////app/data/antivirals.db
        
        
        Alternatively, a package is also available:
        
        ::
        
            pip install antivirals
        
        
        
        Archiecture
        ~~~~~~~~~~~
        The system is structured in a quazi Model-View-Controller archiecture.
        
        * __init__.py: Executes operations like training and inference. The "controller" layer in MVC archiecture.
        * schema.py: Contains all the code for adding to and querying the molecular database. The "model" layer in MVC archiecture.
        * __main__.py: A command-line user interface. The "view" layer in MVC archiecture.
        * data.py: Maps from public datasets (eg. ZINC Clean Leads, Tox21) to the molecular database schema.
        * chem.py: The actual cheminformatics machine learning algorithms.
        
        There is also work to make it function as part of Docker and Kubernetes. Help is needed!
        
        Usage
        ~~~~~
        
        The Coronavirus Antivirals project comes bundled with a command line tool.
        
        You must have a `SQLAlchemy compatible database <https://docs.sqlalchemy.org/en/13/core/engines.html>`_ 
        running. Otherwise everything gets stored in volitile memory. Any database string can be used in theory, 
        but it has only been tested with SQLite.
        
        To completely set up the project and run an agent that runs indefinitely doing antivirals experiments, simply run:
        
        ::
        
            antivirals up sqlite:///path/to/your/db
        
        This command sets up the whole Coronavirus Antivirals system de novo (downloading data, training models, etc).
        
        Any models generated will be dumped in the current working directory in "data". When you use Docker 
        or Kubernetes you want to mount the /app/data folder in the container to a volume.
        
        There is some more advanced usage. Inline documentation about other actions is available:
        
        ::
        
            antivirals -h
        
        Acknowledgment
        ~~~~~~~~~~~~~~
        
        A project of `B.Next <https://www.bnext.org/>`_.
Keywords: machine_learning artificial_intelligence medicine devops
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Provides-Extra: gpu
Provides-Extra: cpu
