README · Data Science in Omics Introduction

Data Science in Omics Introduction was created with the:

Data Carpentry for Biologists - Semester Course

You can cite the material used in this course using the follwing DOI:

Because of the many contributors, an omission is likely and unintentional. Please contact me to be included.

This course version is a forkable set of teaching materials for teaching biologists how to work with data through the shell, programming, and computing more generally.

This repository contains the complete teaching materials and a website for a university style and self-guided course teaching computational data skills to biologists. The course was originally designed to work as a flipped classroom, with students reading and viewing videos before coming to class and then spending the bulk of class time working on exercises with the teacher answering questions and demoing the concepts.

We will primarily operate this course as an online or hybrid class due to the ongoing COVID pandemic that started in 2020.

The developers encourage collaborative development. This repository was used originally by @ethanwhite to teach a version of this course and Helpful information is available regarding the structure and function of the course and website materials for customized development and delivery of the course. Key site and course materials are available as templates for contributions of new materials.

Here are some other examples of customized courses:
- Introduction to Ecology by Andrew Tredennick
- Data Science for Agriculture by Phillip Alderman

Where is everything

Core teaching materials are stored in exercises/, lectures/, and materials/.

Class specific materials are stored in the syllabus, schedule and assignments/.

Most of the other folders and files support creating the course website using Jekyll.

How to contribute

We use standard GitHub flow, so fork the repository, add or change material, and submit a pull request.

The goal of making this course forkable is to facilitate collaboration on developing this kind of material and instructors can then select from a rich pool of exercises the ones that fit the topics, languages, and scientific domains that best fit the material they want to cover for university courses.

Our philosophy is to use and improve these external resources when available instead of creating new versions of the same content. In particularly we actively use Data Carpentry and Software Carpentry workshop materials. However, in cases where the necessary material doesn’t exist elsewhere it can certainly be added here.

Using Jekyll to build your own course website

Simple setup

The website is setup to be easy to run automatically through GitHub:

Fork or import the repository to https://github.com/yourusername/semester-biology.
Update # Setup information in _config.yml in the main directory for proper site rendering.
- You must push this change to your repository to build and browse your forked version.
- In a few minutes you should be able to see the site at: https://yourusername.github.io/semester-biology/
Edit any of the markdown (.md) files
Commit and push the changes
- The changes should now be reflected on the website
If you want to use a custom domain name instead of github.io, follow GitHub’s instructions for setting up a custom domain.

If you have any problems please let us know and we’ll be happy to help.

Previewing changes locally

If you want to view your changes locally, before pushing them to the live website, you’ll need to setup Jekyll locally. GitHub provides a good introduction on how to do this.

If you have Jekyll properly installed, you can then run

bundle exec jekyll serve --baseurl ''

from the command line and navigate to http://localhost:4000/ in your browser to preview the current state of the website. Any changes made to _config.yml will require that you restart Jekyll to view them locally.

Creating new pages

If you want to add new exercises, lecture notes, etc. you do this by creating a markdown file in the appropriate directory. Each markdown file needs to start with some information that tells Jekyll what the page is. This is done using something called YAML, and the standard YAML for a new exercise would look like this:

---
layout: exercise
topic: Topic group of exercise
title: Name of exercise
language: [R, Python, SQL]
---

This is placed at the very beginning of the markdown file and provides information on what kind of content it is (e.g., exercise, page, etc.), the title of the page, and what language it applies to.

The page should then be available at a url based on where the file is located and what the file name is. So if you created a new exercise in the exercises/ folder called my_awesome_exercise.md it would be located at:

Locally: http://localhost:4000/exercises/my_awesome_exercise

After pushing to GitHub: https://yourusername.github.io/semester-biology/exercises/my_awesome_exercise

Acknowledgements

Development of this material is funded by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4563 to Ethan White and the National Science Foundation as part of a CAREER award to Ethan White.