Manuscript Writing Guide

This guide covers the structure and organization of academic research papers following the IMRaD format (Introduction, Methods, Results, and Discussion).

When to Use This Skill

• •Starting a new research paper
• •Organizing existing research into manuscript form
• •Writing or revising specific sections
• •Drafting abstracts and titles

Combine with: human-writing for prose style, scientific-style for citations and hedging.

IMRaD Overview

Title Construction

Strong titles follow these patterns:

Declarative (states the finding):

• •"Gene X regulates metabolic pathway Y in species Z"
• •Best for clear, significant results

Descriptive (states the topic):

• •"Regulation of metabolic pathway Y in species Z"
• •Best when results are complex or exploratory

Question (poses the research question):

• •"Does gene X regulate metabolic pathway Y?"
• •Use sparingly; can seem uncertain

Title Checklist

• • Contains key terms for searchability
• • Avoids abbreviations (except universally known ones)
• • No colons unless necessary for subtitles
• • Specific enough to distinguish from similar papers
• • Accurate representation of content

Section-by-Section Guidance

Introduction

Goal: Move from broad context to specific research question.

Structure (funnel shape):

1. •Opening hook - Why does this topic matter?
2. •Background - What do we already know?
3. •Gap - What remains unknown?
4. •Objective - What does this study address?
5. •Approach - How did you address it? (brief)

Common mistakes:

• •Too much background, too little gap identification
• •Burying the research question
• •Citing exhaustively rather than selectively
• •No clear statement of objectives

Methods

Goal: Enable replication.

Key principles:

• •Describe what you did, not why
• •Use past tense throughout
• •Include enough detail for replication
• •Cite established protocols rather than re-describing

Standard subsections:

• •Study design/overview
• •Participants/samples
• •Data collection/procedures
• •Data analysis
• •Ethics statement (if applicable)

Results

Goal: Report findings without interpretation.

Key principles:

• •Lead with most important findings
• •State results, then reference supporting figure/table
• •Report effect sizes, not just significance
• •Present results systematically (by hypothesis, by variable, etc.)

Structure each paragraph:

1. •Topic sentence stating the result
2. •Supporting statistics
3. •Reference to figure or table

Discussion

Goal: Interpret findings and place in context.

Structure:

1. •Summary - Restate key findings (1-2 sentences)
2. •Interpretation - What do results mean?
3. •Context - How do they fit existing literature?
4. •Implications - Why do they matter?
5. •Limitations - What are the caveats?
6. •Future directions - What comes next?
7. •Conclusion - Final take-home message

Common mistakes:

• •Repeating results without interpretation
• •Overstating conclusions
• •Ignoring contradictory literature
• •Limitations section that undermines the entire study

Abstract Types

See ABSTRACT_TEMPLATES.md for templates.

Structured abstract (with headings):

• •Background/Introduction
• •Methods
• •Results
• •Conclusions

Unstructured abstract (single paragraph):

• •Same content, flowing prose
• •Typically follows same order

Key Transitions

See SECTION_TRANSITIONS.md for phrases to move between sections.

Quality Checks

Before submission, verify each section:

• • Title - Searchable, accurate, appropriate length
• • Abstract - Stands alone, within word limit, no citations
• • Introduction - Clear gap and objectives
• • Methods - Replicable, complete, properly cited
• • Results - Systematic, properly referenced figures/tables
• • Discussion - Interprets (not repeats), acknowledges limitations

Related Files

• •IMRAD_STRUCTURE.md - Detailed checklists for each section
• •ABSTRACT_TEMPLATES.md - Templates with word budgets
• •SECTION_TRANSITIONS.md - Transition phrases