greenstick / bioinformatics_programming

A course covering Python fundamentals and tools for bioinformatics and scientific computing

Welcome to Bioinformatics Programming & Scripting

To get started, you'll need to clone this repository to your computer.

Cloning the Repo

The simplest way to get the class materials is to click the "Clone or download" button above and download a .zip archive of all the materials. However, this won't create a Git repository on your local machine (you'll simply be copying the files). Following the steps below to clone the repo on your local computer will give you some familiarity with Github and the Git version control system, which will definitely come in handy in the future.

Git on the Command-line

I encourage you to try using Git on the command-line. Mac and Linux users should already have git installed on their computers. You can check with the following command:

git --version

If you don't have Git installed, you can get it at the link below (available for all operating systems):

https://git-scm.com/downloads

https://git-scm.com/book/en/v2/Getting-Started-Installing-Git

Once you have Git installed, from the command-line you can simply change to the directory where you want to clone this repo and then run the following:

git clone https://github.com/mooneymi/bioinformatics_programming.git

Github Desktop

If you're not comfortable using the command-line, there is a Github Desktop app available at the link below:

https://desktop.github.com/

To clone this repository, follow the instructions here (note: keep this page open, because you'll need to click the "Clone or download" button above):

https://help.github.com/desktop/guides/contributing/cloning-a-repository-from-github-to-github-desktop/

Running the Jupyter Notebooks

Note: Please make sure you have installed the Anaconda Python distribution (https://www.continuum.io/downloads) before trying to run the Jupyter Notebooks.

Once you've cloned the repo to you computer, open a terminal and go to the directory containing the repo. Then type the following command to start the Jupyter Notebook server:

jupyter notebook

A new tab should open in your web browser that lists all the available lectures. Click on the link for "BMI565_Week1_Data_Types_Operators.ipynb". This should open the notebook for lecture #1 in a new tab.

Viewing the Lectures Online

If you simply want to view the lecture materials online (note: you won't be able to interact with the code examples), you can do so using the Jupyter nbviewer site:

https://nbviewer.jupyter.org/

To view any lecture, go to the site above and enter "mooneymi/bioinformatics_programming" in the search box. Then click the link for any of the .ipynb files (Jupyter notebooks) listed.