Assembler

Combines all drafted sections into a final manuscript, applies formatting and word limits, and generates the complete reference list.

Critical Prerequisite: Academic Reviewer Approval

Do NOT proceed with assembly until the academic reviewer has signed off.

Before assembling:

1. Check notes/reviewer-feedback.md exists
2. Verify all critical issues have been addressed
3. Confirm sign-off status is "Approved" or "Approved with minor revisions"

If reviewer sign-off is missing or issues remain unresolved:

## Assembly Blocked

The academic reviewer has not approved this manuscript for assembly.

**Status**: [Not reviewed / Critical issues pending / User input required]

**Outstanding Issues**:
1. [Issue from reviewer-feedback.md]
2. [Issue from reviewer-feedback.md]

**Action Required**:
- Address the issues listed in notes/reviewer-feedback.md
- Re-run the academic reviewer (/writer:review)
- Obtain sign-off before proceeding

Assembly cannot continue until these issues are resolved.

Prerequisites

Required files:

• scope.md - Constraints (word limit, journal, citation style)
• notes/reviewer-feedback.md - Academic reviewer sign-off (REQUIRED)
• notes/statistical-review.md - Statistical reviewer sign-off
• notes/ethics-summary.md - Ethics document summary (optional, provides ethics statement)
• drafts/abstract.md - Abstract and title options
• drafts/introduction.md - Introduction section
• drafts/methods.md - Methods section
• drafts/results.md - Results section
• drafts/discussion.md - Discussion section
• notes/papers-library/*.pdf - All source PDFs
• notes/bibliography.md - Master reference list
• All notes/papers/*.md for reference details

Workflow

[Verify Academic Reviewer Sign-Off] ─── REQUIRED
     │
     ▼
[Verify Biostatistician Sign-Off] ─── REQUIRED
     │
     ▼
[Load all drafts]
     │
     ▼
[Compile reference list] ─── From notes/bibliography.md
     │
     ▼
[Assemble manuscript] ─── Combine in order
     │
     ▼
[Apply word limit] ─── Trim if needed
     │
     ▼
[Final formatting] ─── Apply journal style
     │
     ▼
[Output] ─── manuscript.md

Step 0: Verify Sign-Offs

Academic Reviewer Sign-Off

Read notes/reviewer-feedback.md and confirm:

## Sign-Off Verification

**Academic Reviewer**:
- Sign-off status: [Approved / Approved with minor revisions / NOT APPROVED]
- Critical issues: [0] remaining
- Major issues: [X] addressed, [Y] acknowledged
- Date: [timestamp]

**Proceed?**: [ ] Yes / [ ] No — [reason if no]

Statistical Reviewer Sign-Off

Read notes/statistical-review.md and confirm:

**Statistical Reviewer**:
- Sign-off status: [Approved / NOT APPROVED]
- Statistical issues: [0] remaining
- Date: [timestamp]

**Proceed?**: [ ] Yes / [ ] No — [reason if no]

If either sign-off is missing or not approved, STOP and report to user.

Step 1: Compile Reference List

Collect All Citations

From each notes/papers/*.md, extract:

• Full citation string
• Citation number used in text

Order References

Vancouver/ICMJE style: Number in order of first appearance in text

Scan through drafts in order:

1. Introduction
2. Methods
3. Results
4. Discussion

Assign numbers [1], [2], [3]... as each new source appears.

Format Reference List

Based on scope.md citation style:

AMA/Vancouver:

1. Smith JA, Jones BB, Wilson CC. Title of article. Journal. Year;Vol:Pages. doi:XX
2. Author AA, Author BB. Title. Journal. Year;Vol:Pages.

APA:

Author, A. A., & Author, B. B. (Year). Title. Journal, Vol(Issue), Pages. https://doi.org/XX

Step 2: Assemble Manuscript

Create manuscript.md with this structure:

# [Title from drafts/abstract.md]

**Authors**: [To be added]

**Affiliations**: [To be added]

**Corresponding Author**: [To be added]

---

## Abstract

[Content from drafts/abstract.md]

**Keywords**: [keywords from abstract]

---

## Introduction

[Content from drafts/introduction.md]

---

## Methods

[Content from drafts/methods.md]

---

## Results

[Content from drafts/results.md]

---

## Discussion

[Content from drafts/discussion.md - includes Conclusion if combined]

---

## Conclusion

[If separate from Discussion - extract from drafts/discussion.md]

---

## Acknowledgments

[Placeholder]

---

## Ethics Statement

[Auto-populated from notes/ethics-summary.md if available, otherwise placeholder]

This study was approved by [Institution/Ethics Board] (approval number: [from ethics-summary.md]). [Informed consent statement as appropriate for study type.]

---

## Conflicts of Interest

[Placeholder]

---

## Funding

[Placeholder]

---

## References

[Compiled reference list]

---

## Figure Legends

[From drafts/results.md]

---

## Tables

[From drafts/results.md]

---

## Supplementary Materials

[If applicable]

Step 2b: Populate Ethics Statement

If notes/ethics-summary.md exists:

Extract from the ethics summary:

• Approval Number: Use exact number from "Study Identification" section
• Approving Body: IRB, IACUC, Ethics Committee, etc.
• Institution Name: If available, otherwise use "[Institution]" placeholder
• Approval Date: Include if journal requires it

Generate ethics statement:

## Ethics Statement

This study was approved by [Institution Name] [Approving Body]
(Protocol #[Approval Number], approved [Approval Date]).
[Informed consent / waiver of consent statement based on study type].

Consent Statement Templates

Based on study type from notes/ethics-summary.md:

Prospective with consent:

Written informed consent was obtained from all participants prior to enrollment.

Retrospective/waiver:

The requirement for informed consent was waived due to the retrospective nature of this study.

Secondary data analysis:

This study used de-identified data and was exempt from consent requirements.

Animal research:

All procedures were approved by [Institution] Institutional Animal Care and Use Committee (IACUC).

Computational/simulation:

This study did not involve human subjects or animals and did not require ethics approval.

If notes/ethics-summary.md does NOT exist:

Leave placeholder for user to complete:

## Ethics Statement

[PLACEHOLDER - Please provide:]
- Approval number: ___
- Approving body: ___
- Institution name: ___
- Consent statement: ___

Notify user: "No ethics document was provided. Please complete the Ethics Statement section with your approval information, or indicate if ethics approval was not required."

Step 3: Apply Word Limit

Count Words

# Approximate word count (excluding references, figures, tables)

Count sections:

• Abstract: [n] words (typically excluded from limit)
• Introduction: [n] words
• Methods: [n] words
• Results: [n] words
• Discussion: [n] words
• Total body: [n] words

Compare to Limit

From scope.md:

• Word limit: [n]
• Current count: [n]
• Delta: [over/under by n]

If Over Limit

Strategies to reduce word count:

1. Discussion (usually easiest to trim):

   • Reduce speculative language
   • Consolidate similar points
   • Remove redundant transitions

2. Methods (if detailed):

   • Move supplementary details to Supplementary Materials
   • Combine sentences
   • Remove obvious steps

3. Results (carefully):

   • Keep all statistics
   • Reduce narrative around clear findings
   • Move secondary findings to Supplementary

4. Introduction (last resort):

   • Reduce background breadth
   • Tighten gap statement

Do NOT cut:

• Key statistics
• Primary findings
• Essential methods for reproducibility

Step 4: Final Formatting

Journal-Specific Adjustments

Based on scope.md target journal, apply:

Radiology / RSNA journals:

• Structured abstract (Background, Purpose, Materials and Methods, Results, Conclusion)
• "Materials and Methods" not just "Methods"
• Abbreviations defined in abstract and again in text

JAMA network:

• Key Points box (Question, Findings, Meaning)
• Structured abstract
• Strict word limits

Nature/Science:

• Very concise
• Methods often separate/supplementary
• References in specific format

Section Headings

Verify correct heading style:

• All caps vs title case
• Numbered vs unnumbered
• Combined "Results and Discussion" vs separate

Citation Format

Verify all citations match required style:

• Superscript¹ vs brackets [1]
• Author-date (Smith, 2023) if APA
• Correct punctuation around citations

Step 5: Quality Checks

Consistency Checks

• All figures referenced in text
• All tables referenced in text
• All references cited in text appear in reference list
• All references in list are cited in text
• Abbreviations defined on first use
• Numbers in abstract match numbers in text
• No contradictions between sections

Formatting Checks

• Heading levels consistent
• Citation format consistent throughout
• Statistical reporting format consistent
• Line spacing/margins per journal (if specified)

Final Proofread Notes

Flag for user attention:

• Author names and order
• Affiliations
• Corresponding author details
• Acknowledgments
• COI disclosures
• Funding statement
• Ethics statement / IRB number

Output

Primary Output

Save to: manuscript.md

Word Count Summary

## Word Count Summary

| Section | Words |
|---------|-------|
| Abstract | XXX |
| Introduction | XXX |
| Methods | XXX |
| Results | XXX |
| Discussion | XXX |
| **Body Total** | **XXX** |
| Target | XXX |
| Status | ✓ Under / ⚠️ Over by X |

Completion Summary

Return to user:

"Manuscript assembled. Here's the summary:

Title: [title] Word Count: [n] / [limit] words References: [n] sources cited Figures: [n] Tables: [n]

Needs your input:

• Author list and affiliations
• Acknowledgments
• Conflicts of interest
• Funding statement

The manuscript is saved to manuscript.md."

Files Generated

Final project structure:

project/
├── papers/
├── data/
├── figures/
├── code/
├── notes/
│   ├── papers/*.md
│   ├── search/*.md
│   ├── code-analysis.md
│   └── data-analysis.md
├── drafts/
│   ├── introduction.md
│   ├── methods.md
│   ├── results.md
│   ├── discussion.md
│   └── abstract.md
├── config.md
├── inventory.md
├── scope.md
└── manuscript.md          ← Final output