JHI/IBioIC Introduction to Bioinformatics

Table of Contents

1. Introduction
2. Schedule
3. Forthcoming presentations
4. Run on MyBinder
5. Set up the course materials on your own machine

Introduction

Welcome to the GitHub repository for the JHI/IBioIC Introduction to Bioinformatics course. This document provides a record of previous presentations, and a schedule for the forthcoming presentation.

You can run the Jupyter notebook content of this course by following the link to MyBinder in the button below.

We also provides instructions in the Setup section below to help you download and set up the course materials for your own use, so that there are the minimum of technical issues.

Schedule: 16th-17th March 2017, MC407 McCance Building, University of Strathclyde

Thursday 16th March, 0930-1230

• Welcome and introduction (Leighton, Sue, Peter)
• Introduction to Linux, Jupyter and Python (Peter)
• Introduction to sequence data and bioinformatics (Peter)

Thursday 16th March, 1330-1700

• Mining bioinformatics databases (Leighton)

Friday 17th March, 0930-1230

• Reproducible research (Leighton)
• Worked example (Peter, Leighton, Sue)

Friday 17th March, 1330-1700

• Structural bioinformatics (Sue)
• Conclusion and wrap-up (Leighton, Peter, Sue)

Forthcoming presentations

• 16th-17th March 2017: University of Strathclyde, Glasgow

Run on MyBinder

MyBinder is a cloud-based service that allows you to run Jupyter notebooks 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:

Set up the course materials on your own machine

Setting up the course materials on your own machine involves following stages:

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

You can, if you choose, shortcut the process by downloading a pre-prepared Ubuntu virtual machine, which comes with course materials and tool prerequisites.

• Download Ubuntu VM

Cloning the repository

To clone the repository, run the following commands in the terminal. We are doing the clone in your home directory to ensure The paths in the examples will match your system.

cd ~
git clone git@github.com:widdowquinn/Teaching-IBioIC-Intro-to-Bioinformatics.git

This will download the repository in a subdirectory of your home directory called Teaching-IBioIC-Intro-to-Bioinformatics. You can change working location to this directory with the command:

cd ~/Teaching-IBioIC-Intro-to-Bioinformatics

Install packages: Create Virtual Environment

It is recommended to use a Python virtual environment to ensure that compatible libraries can be installed, separately from your system Python installation to avoid conflicts.

virtualenv

To create a new virtual environment, you can use the following command (if virtualenv is installed):

virtualenv venv-IBioIC -p python3.6

To start the virtual environment, issue the following:

source venv-IBioIC/bin/activate

Then, to install the required Python packages, you can use pip with the provided requirements.txt file:

pip install -r requirements.txt

Jupyter Kernel setup

To use the Jupyter notebooks with the version of Python and packages installed under your virtual environment, you will need to make a kernel for your virtualenv available. This can be done by activating your virtual machine, and then installing a kernel with the commands below.

$ source venv-IBioIC/bin/activate
$ python -m ipykernel install --user --name Python3_ibioic_course --display-name "Python 3 (IBioIC)"