A Python framework for structural systems biology
ssbio: A Framework for Structural Systems Biology
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:
.. 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.
First install NGLview using pip, then install ssbio
.. code-block:: console
pip install nglview
jupyter-nbextension enable nglview --py --sys-prefix
pip install ssbio
.. code-block:: console
pip install ssbio --upgrade
.. code-block:: console
pip uninstall ssbio
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.
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_.
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