Metadata-Version: 1.1
Name: ssbio
Version: 0.9.9
Summary: Tools to enable structural systems biology
Home-page: http://github.com/SBRG/ssbio
Author: Nathan Mih
Author-email: nmih@ucsd.edu
License: MIT
Download-URL: https://github.com/SBRG/ssbio/archive/v0.9.9.tar.gz
Description-Content-Type: UNKNOWN
Description: *************************************************
        ssbio: A Framework for Structural Systems Biology
        *************************************************
        
        Introduction
        ============
        
        This Python package provides a collection of tools for people with questions in the realm of structural systems biology. The main goals of this package are to:
        
        #. Provide an easy way to map genes to their encoded proteins sequences and structures
        #. Directly link structures to genome-scale SBML models
        #. Prepare structures for downstream analyses, such as their use in molecular modeling software
        #. Demonstrate fully-featured Python scientific analysis environments in Jupyter notebooks
        
        Example questions you can (start to) answer with this package:
        
        - How can I determine the number of protein structures available for my list of genes?
        - What is the best, representative structure for my protein?
        - Where, in a metabolic network, do these proteins work?
        - Where do popular mutations show up on a protein?
        - How can I compare the structural features of entire proteomes?
        - How can I zoom in and visualize the interactions happening in the cell at the molecular level?
        - How do structural properties correlate with my experimental datasets?
        - How can I improve the contents of my model with structural data?
        - and more...
        
        Installation
        ============
        
        First install NGLview using pip:
        
        .. code-block:: bash
        
            pip install nglview
        
        Then install ssbio:
        
        .. code-block:: bash
        
            pip install ssbio
        
        **Updating**
        
        .. code-block:: bash
        
            pip install ssbio --upgrade
        
        **Uninstalling**
        
        .. code-block:: bash
        
            pip uninstall ssbio
        
        
        Dependencies
        ------------
        
        See: `Software Installations <https://github.com/SBRG/ssbio/wiki/Software-Installations>`_ for additional programs to install. Most of these additional programs are used to predict or calculate properties of proteins.
        
        
        Tutorials
        =========
        
        Check out some Jupyter notebook tutorials at :ref:`protein` and :ref:`gempro`.
        
        
        Citation
        ========
        
        The manuscript for the ``ssbio`` package can be found and cited at [1]_.
        
        .. [1] Mih, N. et al. ssbio: A Python Framework for Structural Systems Biology. bioRxiv 165506 (2017). doi:10.1101/165506
Platform: UNKNOWN
