Week 2: Project organization, OSC, and Markdown
Overview
This week is a bit of a potpourri of shorter topics, introducing you to tools and strategies you’ll use throughout the course.
You will explore best practices for project file organization, get introduced to the Ohio Supercomputer Center (OSC), and learn how to write Markdown files. Along the way, you will also get to know VS Code, the text editor you’ll spend a lot of time in during this course.
Learning goals & lectures
This week’s content is divided into the following four lectures, during which you will learn:
A) Project file organization and documentation for reproducible research (Monday)
- Best practices for organizing and managing your research project files.
- Best practices for documenting your research project.
B) The Ohio Supercomputer Center (OSC) (Monday, continued Wednesday)
- What supercomputers are, and why they are useful.
- What resources OSC provides.
- How to access OSC resources through its OnDemand web portal.
C) An introduction to the VS Code editor (Wednesday)
- What VS Code is, and why we use it in this course.
- How to start VS Code at OSC, and find your way around its interface.
D) An introduction to Markdown (Wednesday)
- What Markdown is and why it’s useful for research documentation (and beyond).
- The most common Markdown syntax, and how to preview rendered Markdown in VS Code.
We may not finish all of session D’s content. If we don’t, this material is suitable for self-study, and you should read and practice with the remaining slides on your own. There are anyway already several slides at the end that are marked as “self-study material” (see below), and any additional content not covered in class would add to that.
Assignments & exercises
- Exercises: Markdown and project organization
- No assignments this week
Readings
The self-study material slides at the end of the Markdown lecture (starting here: Markdown self-study slides).
Markowetz (2015): Five selfish reasons to work reproducibly (OSU proxy link )
This short paper gives a light-hearted overview of self-interested reasons to perform your research in a reproducible way.
Optional self-study material
Books for the entire course
Throughout the course, chapters from these two books are optional readings. With OSU credentials, both can be freely accessed online via the links below.
Buffalo (2015): Bioinformatics Data Skills
This week: Preface, Chapter 1 – How to Learn Bioinformatics, Chapter 2 – Setting Up and Managing a Bioinformatics Project.Allesina and Wilmes (2019): Computing Skills for Biologists
This week: Chapter 0 – Building a Computing Toolbox (Introduction & Section 0.1 only).
Other
Noble (2009): A quick guide to organizing computational biology projects (open access link )
Wilson et al. (2017): Good enough practices in scientific computing (open access link )