Writing Better Plain-English Pseudocode for Bioinformatics

Part 1: Background

1.1. What is a plain-English pseudocode?

Plain-English pseudocode is a way of planning an algorithm or computational workflow using natural, human-readable language rather than the syntax of a specific programming language. It is not meant to be executed by a computer. Instead, it serves as a bridge between your conceptual understanding of a problem and the formal code you will eventually write.

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Good pseudocode emphasizes what needs to happen and in what order, without committing to how a specific language enforces that logic.

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1.2. Why is plain-English pseudocode important in bioinformatics, especially in the age of generative AI?

Bioinformatics problems are often complex, multi-step, and data-dependent. Writing plain-English pseudocode helps you:

• Clarify your own understanding of the biological and computational problem before coding.
• Communicate your plan clearly to collaborators who may use different programming languages.
• Identify missing steps, assumptions, or edge cases early.

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In the age of generative AI, pseudocode plays an additional role: it acts as a high-quality prompt. When you can clearly describe your logic in plain English, you are much more likely to obtain correct, useful, and maintainable code from an AI system. Vague ideas lead to vague prompts; precise pseudocode leads to precise implementations.

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1.3. Characteristics of good plain-English pseudocode

A strong pseudocode usually has the following properties:

• It is written for humans, not machines.
• It ignores language-specific syntax (no braces, semicolons, or keywords).
• Each step describes a single logical action.
• Steps are written in a clear, sequential order.