Notebooks

Bioinformatics Club - 05/04/18

Jupyter notebook install

# Downloading virtualenv Python lib
$ curl -O https://pypi.python.org/packages/d4/0c/9840c08189e030873387a73b90ada981885010dd9aea134d6de30cd24cb8/virtualenv-15.1.0.tar.gz
$ tar xvfz virtualenv-15.1.0.tar.gz

# Installing a virtualenv
$ cd virtualenv-15.1.0
$ python virtualenv.py ~username/myfolder/Env01

# Activate the virtualenv
$ cd ~username/myfolder/Env01/bin
$ bash
$ source activate

# Install Jupyter
$ pip install Jupyter

Security breach (Jupyter)

• Jupyter notebook allow any user on a notebook to browse files from where the ipynb file is stored
• Potential solutions:
  • Embed the notebook in a docker
  • Use GitHub binder system

Jupyter - GitHub - Binder

• Since 2015, Jupyter Notebooks are correctly displayed on GitHub (static)
• Since 2017, interactive notebooks can be stored on GitHub through Binder
• Jupyter lab in Binder

Jupyter extensions

(jupyter_contrib_nbextensions)

• Clickable table content
• Hide code
• Pop-up cells
• etc.

Miscellaneous

• Shiny for R corresponds to Dash in Python
• Interactive with Jupyter: ipywidget lib
• For both platforms, plenty of good documentation
• Google Drive Jupyter maybe good for collaboration

Resources (1)

• A recent paper "Exploration and Explanation in Computational Notebooks"
• A gallery of interesting Jupyter Notebooks
• The book "Bioinformatics with Python Cookbook" made of Jupyter Notebooks
  • Basic sequence processing example
  • Working with FASTQ files

Resources (2)

• The paper "An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study" published all their analysis as a Jupyter Notebook for reproducibility