Metadata-Version: 1.1
Name: ssbio
Version: 0.9.9.8a0
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/v0.9.9.8a.tar.gz
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 hundreds or thousands of genes to their encoded protein sequences and structures
        #. Directly link protein structures to genome-scale metabolic models
        #. 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 do structural properties correlate with my experimental datasets?
        - How can I improve the contents of my metabolic model with structural data?
        
        
        Try it without installing
        =========================
        
        .. image:: https://mybinder.org/badge.svg
            :target: https://mybinder.org/v2/gh/SBRG/ssbio/master?filepath=Binder.ipynb
        
        
        .. note:: Binder notebooks are still in beta, but they mostly work! Third-party programs are also preinstalled in the Binder notebooks except I-TASSER and TMHMM due to licensing restrictions.
        
        
        Installation
        ============
        
        First install NGLview using pip, then install ssbio
        
        .. code-block:: console
        
            pip install nglview
            jupyter-nbextension enable nglview --py --sys-prefix
            pip install ssbio
        
        Updating
        --------
        
        .. code-block:: console
        
            pip install ssbio --upgrade
        
        Uninstalling
        ------------
        
        .. code-block:: console
        
            pip uninstall ssbio
        
        Dependencies
        ------------
        
        See: Software_ for a list of external programs to install, along with the functionality that they add. Most of these additional programs are used to predict or calculate properties of proteins, and are only required if you desire to calculate the described properties.
        
        
        Tutorials
        =========
        
        Check out some Jupyter notebook tutorials for a single Protein_ and or for many in a GEM-PRO_ model. See a list of all Tutorials_.
        
        
        Citation
        ========
        
        The manuscript for the *ssbio* package can be found and cited at [1]_.
        
        .. [1] Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO. 2018. ssbio: A Python Framework for Structural Systems Biology. Bioinformatics. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty077/4850940.
        
        .. Links
        .. _Protein: http://ssbio.readthedocs.io/en/latest/protein.html
        .. _GEM-PRO: http://ssbio.readthedocs.io/en/latest/gempro.html
        .. _Software: http://ssbio.readthedocs.io/en/latest/software.html
        .. _Tutorials: http://ssbio.readthedocs.io/en/latest/tutorials.html
Platform: UNKNOWN
