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
Installation
First install NGLview using pip, then install ssbio
pip install nglview
jupyter-nbextension enable nglview --py --sys-prefix
pip install ssbioUpdating
pip install ssbio --upgradeUninstalling
pip uninstall ssbioDependencies
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 maintainer
Metadata
1 maintainer
Release files for ssbio 0.9.9.8.post1
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Release files / ssbio-0.9.9.8.post1.tar.gz
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