Tools to enable structural systems biology
Project 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
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
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