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.
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:
Setting up the course materials on your own machine involves following stages:
You can, if you choose, shortcut the process by downloading a pre-prepared Ubuntu virtual machine, which comes with course materials and tool prerequisites.
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 email@example.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:
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.
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:
Then, to install the required Python packages, you can use
pip with the provided
pip install -r requirements.txt
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)"