README.md

BioJava in Jupyter Notebooks

This repository demonstrates how to run BioJava applications in a Jupyter Notebook and Jupyter Lab.

This project uses the Java Kernel developed by the BeakerX project, a collection of kernels that provide JVM support for Jupyter Notebook and Lab.

The nbviewer links below provide a non-interactive preview of notebooks and the launch links launch the notebooks in Jupyter Notebook and Jupyter Lab in your web browser using the Binder (mybinder.org) server (may be slow!).

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nbviewer	Jupyter Notebook	Jupyter Lab
ProteinChainShapeAnalysis.ipynb

By combining BioJava code with Python data analysis, machine leanrning, and visualization tools in a Jupyter Notebooks, a workflow can be shared, reproduced, and reused.

Local Installation

Install Anaconda

Open a terminal window

Clone this repository

git clone https://github.com/sbl-sdsc/biojava-notebooks.git

Create a conda environment

cd biojava-notebooks

conda env create -f binder/environment.yml

Activate the conda environment

conda activate biojava-notebooks

Launch Jupyter Notebook

jupyter notebook

After you are finished, deactivate the conda environment

conda deactivate

Anytime you want to use the environment, activate it again and start Jupyter Notebook

To permanently remove the biojava-notebooks environment

conda remove --name biojava-notebooks --all

How to Contribute

Do you have an idea for a new notebook? Please file an issue.

To contribute a new notebook, fork this repository and create pull-requests.

Please follow the Ten Simple Rules for Reproducible Research in Jupyter Notebooks.