burkesquires/build-a-reproducible-jupyter-workflow-from-scratch

Build a Reproducible Jupyter Workflow From Scratch (2017 NIH Hour of Code)

Build a Reproducible Workflow From Scratch (in about an hour)

NIH Hour of Code 2017

R. Burke Squires

NIAID Bioinformatics & Computational Biosciences Branch (BCBB)

https://nihlibrary.nih.gov/training/build-reproducible-workflow-scratch-jupyter-notebooks-about-hour

In this hands-on demonstration, we will utilize the Anaconda python distribution, Jupyter notebook, and python scientific stack to build a reproducible, bioinformatics workflow from scratch. From installation to automation, we will utilize the power of the Jupyter notebook and IPython kernel to seamlessly join a variety of existing components into a fully automated workflow that can be run with a single command. In this hands-on demonstration, we will utilize shell commands, popular bioinformatics applications, the Anaconda installer (conda), and the python programming language and scientific stack to assemble a workflow.

Prerequisites: none

If you'd like to follow along by webinar, you should have access to a computer with a Linux shell:

• Mac and Linux computers come with this installed
• Windows users may install git-bash, part of git for windows
• A recent installation of the Anaconda python distribution for python 3.6