SfAM ECS 2017 Presentation and Workshop

Table of Contents

1. Introduction
2. Schedule
3. Presentations
4. Workshop Notebooks
5. Run Workshop in the Cloud on MyBinder
6. Run Workshop on Your Own Machine

Introduction

Welcome to the "Not All Bioinformatics is NGS" part of the SfAM ECS symposium. This document describes the contents of this repository, provides useful links, and instructions for how to reproduce the workshop materials on your own machine, or run them in the cloud.

Schedule

• [poster]

Presentations

The links below will take you to the presentations in an interactive form, in your browser.

• My Life in Sequences
• Reproducible Research

Workshop Notebooks

The links below will take you to the workshop notebooks as live notebooks, in your browser.

• 00 - Introduction to Jupyter (25min)
• 01 - Thinking Statistically (30min)
  • 01a - Correlations
  • 01b - Classifiers
• 02 - Automation (20min)
  • 02a - Python Basics
  • 02b - Automating BLAST
• 03 - Integrating Data (20min)

Run Workshop in the Cloud on MyBinder

MyBinder is a service that allows you to run Jupyter notebooks in the cloud (i.e. on someone else's hardware). This course is provided as interactive notebooks via this service, and you can start up an instance by clicking on the button below:

This approach has the advantage that it requires no further configuration: all materials and tools are pre-installed, and ready to go.

Run Workshop on Your Own Machine

Setting up the course materials to run on your own machine involves following stages, which will be described one-by-one below:

1. Clone the repository
2. Ensure the bioinformatics package prerequisites are installed
3. Create a virtual environment for the Jupyter notebooks

To install and run these materials locally, you will require:

• The Anaconda Python distribution [download]

Download the materials

The course materials (notebooks, presentations, data) are available for download at the link below:

• https://github.com/widdowquinn/Teaching-SfAM-ECS/archive/v1.0.zip

Download the compressed (.zip) file to a suitable location and unpack it. This will place the materials in a subdirectory called Teaching-SfAM-ECR.

Alternatively, if you have git installed, you can clone the most current version of the materials to your local machine with the command:

git clone https://github.com/widdowquinn/Teaching-SfAM-ECS.git

Run the materials

• Open a terminal on your machine
• Navigate to a convenient location and create a new directory for the course materials (e.g. sfam-workshop)

mkdir sfam-workshop
cd sfam-workshop

• Download or clone the course materials to this location (see above) and extract them, if necessary
• Change directory to the course materials

cd Teaching-SfAM-ECS        # if you cloned the repository
cd Teaching-SfAM-ECS-1.0    # if you extracted the .zip/.tar.gz file

• Add a new Anaconda channel for bioconda

conda config --add channels bioconda

• Install Jupyter in the conda environment

conda install jupyter

• Create a new conda environment called sfam, installing the necessary Python libraries (accept the changes requested).

conda create --name sfam python=3 jupyter numpy pandas seaborn bioservices biopython

• Activate the conda environment:

On Windows:

activate sfam

On OSX/Linux

source activate sfam

You should see that your command-line prompt has changed, and now starts with (sfam). This indicates that you are now working within a 'protected' Python environment, specific for this workshop.

• Add a new kernel to Jupyter, and enable iPython widgets

python -m ipykernel install --user --name Python3_SfAM --display-name "Python 3 (SfAM)"
jupyter nbextension enable --py --sys-prefix widgetsnbextension

• Start the notebooks with jupyter notebook index.ipynb to begin at the top page of the workshop

jupyter notebook index.ipynb