A collection of tutorials in the form of iPython Jupyter notebooks, detailing how to work with SPARC vagus scaffolds and data.
Python version 3.7+ for which jupyter and cmlibs.zinc are available on https://pypi.org.
| Package | Installation | More info |
|---|---|---|
| jupyter | pip install jupyter | https://jupyter-notebook.readthedocs.io/en/latest/ |
| cmlibs.zinc | pip install cmlibs.zinc | Zinc Library for Finite Element model representation and visualization. API documentation is at: https://cmlibs.org/documentation. |
| cmlibs.utils | pip install cmlibs.utils | Python support utilities for using with Zinc. |
| cmlibs.maths | pip install cmlibs.maths | Useful mathematical functions for working with Zinc in Python. |
| ssvtools | pip install ssvtools | High-level tools for querying and transforming vagus scaffolds. https://github.com/ABI-Software/ssvtools |
At the command line in the top folder of this downloaded repository, with your python environment activated, enter:
jupyter notebook
The above should open a window in your default browser. Click on and run through the notebook files, in suggested order:
1_introduction_ssv_scaffolds.ipynb 2_query_structure.ipynb
More details on using jupyter notebooks can be found at https://docs.jupyter.org/en/latest/running.html