File paths and project management
Pre-class work
Please work through Episodes 1–4 of the Software Carpentry Unix Shell exercises available at this link.1
1 I encourage you to explore additional exercises available in the Carpentries Curriculum. These are high-quality materials that are used to teach core programming/data management and analysis skills to scientists across the world.
In-class sides
In-class exercise: Project organization and management
Project audit
To begin this exercise, please consider a single project (either ongoing or recently completed) that you wish to have as a reproducible and open entity.
Answer the following questions about the project:
In 3–4 sentences, what are the overall questions you hope to address through this project?
In 3–4 sentences, what are the general steps you have taken so far (or will take) to achieve these objectives?
Please provide a list of all the files you have generated (or anticipate generating) related to this project. Try to be as thorough as possible – e.g. do you have physical and/or digital meeting notes from brainstorming conversations? Data files collected in the lab or in the field? What kinds of scripts does the analysis require, and what files do your analyses generate (e.g. figures, intermediate files, etc.)?
What is your current or anticipated organizational scheme for these files? How often do you conduct data backups?
With whom do you currently share or anticipate sharing project-related files? Which of the files that you are generating do you feel are important to share along with the final “product” to come out of this work (e.g. resulting journal article) to ensure its reproducibility?
What are some “pain points” in your project organization scheme? Are these particular issues that you find yourself confronting on a regular basis? Is there any way to streamline your project organization/setup to help ease this pain point?