Zhehao’s Cookbook

Welcome

This is my collection of manuals, cookbooks, and operation notes. It’s the practical counterpart of my notebook (currently a WIP mess), with focus on how to get things done (properly) over how things work. Likewise, the thematic focus is on deep-sea biology, from in situ to in silico.

Philosophy

As I am establishing a toolkit, I try to make sense of my choice. If possible, I always use tools that has matching community (meaning developers and users can engage with each other, and the users share similar profiles with me), and value reproducibility, robustness, scalability, and automation.

• Lacking reproducibility, same methods on the same data might produce different results every time, or one just forgets how one did the work half a year ago.
• Lacking robustness, the analyses are usually subjective and one cannot convince others about the methods.
• Lacking scalability, required effort grows linearly, even exponentially with the amount of data.
• Lacking automation, precious human power and time is wasted by doing the repetitive works.

These aspects have made my workflow to be heavily local and code-based. You might still find workflows centered around GUI here, it’s either because it’s required for interactive workflow, or I just haven’t established an alternative.

Environment

Programming Languages

The primary language I use is R. You know what it is if you work in biology. Python is also in my toolkit. I recommend installing them if you haven’t done so yet.

• The R Project
• I personally use the newer Positron IDE because it supports every language I use and is deeper integrated in the Posit ecosystems.

Program Ecosystems

Other programs I recommend having on your machine:

• Homebrew: Package manager for many conventional tools. Once set up, you only need one-liners to install programs managed by it.