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skills/brycewang-stanford/Auto-Empirical-Research-Skills/01-lishix520-academic-paper-skills-composer

academic-paper-composer

1
brycewang-stanford/Auto-Empirical-Research-Skills·Research·Audit passed·Snapshot 83f9da28deee

Summary

Systematic writing framework for philosophy and interdisciplinary academic papers from optimized outline to submission-ready manuscript. Use when users want to: (1) write a paper from a detailed outline, (2) ensure quality control during writing, (3) maintain consistency across chapters, (4) prepare a submission-ready manuscript, or (5) systematically execute a planned paper. Triggered by phrases like ''write the paper from this outline,'' ''compose the full manuscript,'' ''execute the outline,'' or when users have completed strategic planning (academic-paper-strategist skill) and are ready to write. Takes optimized outline as input; outputs complete manuscript with iterative quality checks.

SKILL.md

Academic Paper Composer

Overview

This skill provides a systematic framework for writing academic papers from optimized outline to submission-ready manuscript. It implements iterative quality control at both chapter-level and paper-level, ensuring consistent high quality throughout the writing process.

Input: Detailed, optimized paper outline (from academic-paper-strategist or equivalent)

Output: Complete, submission-ready manuscript with quality validation reports

Prerequisite: Use academic-paper-strategist skill first to create optimized outline (or provide equivalent detailed outline)


When to Use This Skill

Use academic-paper-composer when you need to:

Writing Stage:

  • Execute a detailed paper outline systematically
  • Write a complete academic paper chapter-by-chapter
  • Maintain quality control during writing process
  • Ensure consistency across all sections

Quality Assurance Stage:

  • Validate each chapter before proceeding
  • Check cross-chapter coherence
  • Perform final quality assessment
  • Verify submission readiness

Submission Preparation Stage:

  • Prepare manuscript for platform submission
  • Complete platform-specific checklists
Installs
0
  • Generate final submission package
  • Triggers:

    • "Write the paper from this outline"
    • "Compose the full manuscript"
    • "Execute the outline systematically"
    • "I have an outline, help me write the paper"
    • After completing academic-paper-strategist skill

    Workflow Overview

    Phase 4: SYSTEMATIC WRITING (Chapter-by-Chapter + Quality Gates)
        ↓
    Phase 5: QUALITY CONTROL (Final Validation + Submission Prep)
        ↓
    Output: Submission-Ready Manuscript + Quality Reports
    

    Quality Gates: After each chapter + final paper evaluation


    Required Input

    Before using this skill, you must provide:

    1. Optimized Detailed Outline

    Required structure:

    ## Abstract (250-300 words)
    - [Key points to cover]
    
    ## 1. Introduction (1,500 words)
    ### 1.1 Opening Puzzle (400 words)
    - [Content guidance]
    ### 1.2 Literature Review (600 words)
    - [Theories to discuss]
    ### 1.3 This Paper's Contribution (500 words)
    - [Specific claims]
    
    ## 2. [Main Chapter Title] (1,200 words)
    ### 2.1 [Section] (400 words)
    - [Argument structure]
    - [Key citations]
    ...
    
    [Complete structure with word counts and content guidance]
    

    Quality check: Outline should specify:

    • ✓ Chapter titles and word counts
    • ✓ Subsection structure (to 3rd level)
    • ✓ Content guidance for each section
    • ✓ Key citations to include
    • ✓ Argument structure notes

    If outline lacks these, consider using academic-paper-strategist first.

    2. Platform Writing Standards Guide

    From academic-paper-strategist Phase 1, or equivalent document specifying:

    • Platform style patterns (voice, terminology, citation format)
    • Structural conventions
    • Example papers for reference

    3. Literature Base (Optional but Recommended)

    • List of core papers to cite
    • Research gap analysis
    • Key concepts to emphasize

    Phase 4: Systematic Writing

    Goal

    Write complete manuscript chapter-by-chapter with iterative quality control.

    Workflow

    Step 4.1: Writing Environment Setup

    Before writing, I will:

    1. Verify outline completeness:

      • All chapters specified with word counts
      • Content guidance provided
      • Argument structure clear
    2. Load reference documents:

      • Platform writing standards
      • Section writing guides (references/section_guides.md)
      • Quality standards (references/writing_standards.md)
    3. Create writing tracker:

      # Writing Progress Tracker
      - [ ] Abstract (250 words)
      - [ ] Chapter 1: Introduction (1,500 words)
      - [ ] Chapter 2: [Title] (1,200 words)
      ...
      - [ ] Conclusion (1,000 words)
      - [ ] References
      

    Decision Point 1: Confirm outline and standards loaded, ready to begin writing.

    Step 4.2: Chapter-by-Chapter Writing

    For each chapter, I will follow this sequence:

    A. Pre-Writing Review

    Before writing chapter N:

    1. Review outline specification for this chapter:

      • Word count target
      • Subsection structure
      • Content guidance
      • Key arguments/citations
    2. Review previous chapter (if N>1):

      • Last paragraph of chapter N-1
      • Key concepts introduced
      • Promises to fulfill
    3. Check section guide:

      • Load appropriate template from references/section_guides.md
      • Review quality markers for this section type
    B. Writing Execution

    I will write the chapter following:

    Content principles:

    • Follow outline exactly: Respect structure and word counts
    • Include specified citations: Use literature from outline
    • Maintain platform style: Match voice and terminology
    • Use section templates: Follow appropriate guide from section_guides.md

    Quality targets (pre-emptive):

    • Argument quality: Clear thesis, justified premises
    • Citation quality: All claims supported, proper format
    • Clarity: Precise prose, terms defined, good transitions
    • Structure: Logical flow, proper proportions
    • Style conformity: Match platform conventions

    Output: Complete chapter draft

    C. Post-Writing Evaluation

    After completing chapter draft, I will:

    1. Create evaluation document:

      python scripts/chapter_quality_check.py
      # Option 1: Create template for this chapter
      
    2. Perform 5-dimension assessment:

      • Argument Quality (1-4): Thesis clear? Premises justified? Objections addressed?
      • Citation Quality (1-4): All claims cited? Format consistent? Key literature included?
      • Clarity & Readability (1-4): Prose clear? Terms defined? Transitions smooth?
      • Structure & Flow (1-4): Logical progression? Proper proportions? Follows outline?
      • Platform Conformity (1-4): Style match? Voice consistent? Format correct?
    3. Generate quality report:

      python scripts/chapter_quality_check.py
      # Option 2: Generate report from evaluation
      

      This produces:

      • Total score (X/20)
      • Pass/fail (threshold: ≥16/20)
      • Weak dimensions identified
      • Specific revision recommendations

    Quality Gate 4A (After Each Chapter):

    • ✓ Score ≥16/20 (80%)
    • ✓ All dimensions ≥3/4 (or revisions implemented)
    • ✓ Word count within ±10% of target

    If Failed: Implement revisions before proceeding to next chapter

    D. Iteration (If Needed)

    If chapter scores <16/20:

    1. Identify weak dimension(s): Which scored <3/4?

    2. Implement targeted revisions:

      • Argument quality issue → Add justifications, address objections
      • Citation quality issue → Add supporting citations, fix format
      • Clarity issue → Simplify prose, add definitions, improve transitions
      • Structure issue → Reorganize paragraphs, adjust proportions
      • Style issue → Adjust voice, terminology, format
    3. Re-evaluate: Generate new quality report

    4. Repeat until passing (typically 1-2 iterations)

    Important: Do not proceed to next chapter until current chapter passes quality gate.

    E. Chapter Completion

    Once chapter passes quality gate:

    1. Mark chapter complete in writing tracker
    2. Save chapter with quality report
    3. Note key concepts introduced (for coherence check later)
    4. Preview next chapter requirements

    Decision Point 2 (After Major Chapters): After completing each main body chapter, I will:

    • Present completed chapter summary
    • Show quality score
    • Ask: Proceed to next chapter or revise further?

    Step 4.3: Writing Sequence

    Recommended order:

    1. Introduction (write first)

      • Establishes thesis and roadmap
      • Use introduction guide from section_guides.md
      • Quality check: Abstract promises, literature coverage, clear contribution
    2. Main Body Chapters (in outline order)

      • Follow outline sequence
      • Quality check after each
      • Build on previous chapters
    3. Conclusion (write after main body)

      • Synthesizes findings
      • Addresses introduction promises
      • Use conclusion guide from section_guides.md
    4. Abstract (write last)

      • Summarizes complete paper
      • Use abstract guide from section_guides.md
      • Quality check: Standalone, accurate, compelling
    5. References (compile throughout)

      • Format according to platform standards
      • Verify all citations present

    Step 4.4: Cross-Chapter Coherence Check

    After all chapters written, before final evaluation:

    1. Terminology consistency:

      • Extract key terms from each chapter
      • Verify consistent usage throughout
      • Check definitions consistent
    2. Argument flow:

      • Verify chapter N+1 builds on chapter N
      • Check roadmap (intro) matches execution
      • Ensure conclusion addresses introduction promises
    3. Citation patterns:

      • Check for uneven citation distribution
      • Verify key works cited where relevant
      • Ensure bibliography complete

    Output: Cross-chapter coherence report identifying any inconsistencies


    Phase 5: Quality Control

    Goal

    Perform comprehensive final evaluation and prepare submission-ready manuscript.

    Workflow

    Step 5.1: Content Completeness Check

    Using structured checklist, verify:

    Structural Completeness:

    • Abstract (250-300 words)
    • Introduction with all required elements
    • All outlined main chapters present
    • Conclusion with all required elements
    • References section formatted correctly

    Content Completeness:

    • All introduction promises fulfilled
    • All claims supported by evidence or argument
    • All technical terms defined
    • All objections addressed
    • All limitations acknowledged

    Citation Completeness:

    • Every citation in text has bibliography entry
    • Every bibliography entry cited in text
    • Citation format consistent throughout
    • All citations include necessary information

    Format Completeness:

    • Title page (if required)
    • Section numbering consistent
    • Heading hierarchy logical
    • Figure/table captions (if applicable)

    Output: Completeness checklist report

    Step 5.2: Final 7-Dimension Evaluation

    I will perform comprehensive evaluation using:

    python scripts/final_evaluation.py
    # Create evaluation template
    

    7 Dimensions (10 points each, 70 total):

    1. Overall Argument Quality (1-10)

      • Thesis clarity throughout
      • Chapter integration
      • Logical completeness
      • Objections addressed
    2. Literature Integration (1-10)

      • Citation count (40-60 typical for philosophy)
      • Key literature covered
      • Citations well-integrated
      • Critical engagement present
    3. Clarity & Accessibility (1-10)

      • Prose clarity
      • Complex ideas explained
      • Appropriate for audience
      • Technical terms defined
    4. Originality & Contribution (1-10)

      • Clear original contribution
      • Advance over literature
      • Significance established
      • Innovation present
    5. Methodological Rigor (1-10)

      • Method explicit and justified
      • Consistently applied
      • Appropriate for question
      • Limitations acknowledged
    6. Structure & Organization (1-10)

      • Logical flow
      • Optimal organization
      • Proportions balanced
      • Transitions seamless
    7. Platform & Style Conformity (1-10)

      • Style matches platform
      • Format correct
      • Voice consistent
      • Citation format perfect

    Scoring Process:

    1. Evaluate each dimension (1-10)
    2. Provide detailed notes for each
    3. Complete completeness checklist
    4. List any specific issues

    Generate report:

    python scripts/final_evaluation.py
    # Generate final report
    

    This produces:

    • Total score (X/70)
    • Pass/fail (threshold: ≥56/70)
    • Weak dimensions identified
    • Completeness assessment
    • Prioritized revision recommendations
    • Submission readiness decision

    Quality Gate 5 (Final):

    • ✓ Score ≥56/70 (80%)
    • ✓ All completeness checklist items complete
    • ✓ All high-priority issues addressed

    If Failed: Implement revisions and re-evaluate

    Step 5.3: Revision Implementation (If Needed)

    If final score <56/70 or completeness incomplete:

    1. Prioritize revisions:

      • HIGH priority: All issues affecting score or completeness
      • MEDIUM priority: Issues improving quality
      • LOW priority: Optional enhancements
    2. Implement systematically:

      • Address high-priority first
      • Document changes
      • Maintain style consistency
    3. Re-evaluate:

      • Generate new final report
      • Verify score ≥56/70
      • Check completeness 100%
    4. Iterate until passing

    Decision Point 3: After final evaluation, I will:

    • Present final score and assessment
    • Show submission readiness status
    • Recommend: Submit immediately / Implement optional improvements / Required revisions
    • Ask: Proceed with submission or implement further improvements?

    Step 5.4: Submission Package Preparation

    Once final evaluation passes:

    1. Platform-specific checklist:

      • PhilArchive/PhilPapers:

        • PDF format
        • Abstract <500 words
        • Metadata (title, keywords, classification)
        • Author information complete
      • arXiv:

        • LaTeX or PDF format
        • Abstract <1920 characters
        • Category selection correct
        • No font embedding issues
      • PhilSci-Archive:

        • PDF format
        • Subject classification
        • Keywords (3-5)
        • No copyright issues
    2. Generate final outputs:

      • Formatted manuscript (PDF or LaTeX)
      • Abstract (separate file if needed)
      • Metadata file
      • Cover letter (if applicable)
    3. Pre-submission verification:

      • Re-read complete paper
      • Check all formatting
      • Verify all links/citations work
      • Proofread for typos

    Output: Complete submission package ready for platform upload


    Complete Output Package

    Upon completion of both phases, you receive:

    Quality Reports

    1. Chapter Quality Reports (one per chapter)

      • 5-dimension scores
      • Pass/fail status
      • Revision recommendations implemented
    2. Cross-Chapter Coherence Report

      • Terminology consistency check
      • Argument flow verification
      • Citation pattern analysis
    3. Final Evaluation Report ⭐ Key Document

      • 7-dimension comprehensive assessment
      • Completeness checklist (100%)
      • Submission readiness decision
      • Platform-specific checklist

    Manuscript Files

    1. Complete Manuscript ⭐ Main Deliverable

      • All chapters integrated
      • Properly formatted
      • Citations complete
      • Submission-ready
    2. Abstract (separate file)

      • Standalone 250-300 words
      • Platform-formatted
    3. Metadata Document

      • Title, keywords, classification
      • Author information
      • Platform-specific requirements

    Supporting Documentation

    1. Writing Progress Tracker

      • All chapters completed
      • Quality scores logged
      • Revision history
    2. Citation List

      • All references used
      • Formatted for platform
      • Verified complete

    Quality Assurance System

    Quality Standards Reference

    For detailed evaluation criteria, all standards are defined in:

    references/writing_standards.md
    

    This document provides:

    • Chapter-level quality standards (5 dimensions)
    • Final quality standards (7 dimensions)
    • Section-specific quality criteria
    • Scoring rubrics
    • Issue identification and fixes

    Section Writing Guides

    For guidance on writing each section type:

    references/section_guides.md
    

    This provides:

    • Abstract writing template and checklist
    • Introduction structure (6 subsections)
    • Main body chapter templates (4 types)
    • Conclusion structure
    • Transition strategies
    • Platform-specific style guidance
    • Common mistakes and fixes

    Evaluation Scripts

    Two Python scripts support quality validation:

    1. Chapter Quality Check

    python scripts/chapter_quality_check.py
    

    Function: Evaluates individual chapters against 5-dimension standards

    • Creates evaluation templates
    • Calculates scores and pass/fail
    • Identifies weak dimensions
    • Generates revision recommendations
    • Supports multi-chapter comparison

    When to Use: After writing each chapter (Step 4.2.C)

    2. Final Paper Evaluation

    python scripts/final_evaluation.py
    

    Function: Evaluates complete paper against 7-dimension standards

    • Comprehensive quality assessment
    • Completeness checklist validation
    • Submission readiness determination
    • Platform-specific preparation
    • Generates final report with recommendations

    When to Use: After all chapters complete (Step 5.2)


    Decision Points (Interactive)

    This skill has 3 key decision points where I pause for your input:

    Decision Point 1: Writing Commencement (Step 4.1)

    I provide: Loaded outline, standards, and writing plan You confirm: Ready to begin writing / Need adjustments

    Decision Point 2: Chapter Completion (Step 4.2.E)

    I provide: Completed chapter with quality score You decide: Proceed to next / Revise further / Adjust approach

    Frequency: After each main body chapter (3-5 times typically)

    Decision Point 3: Final Submission (Step 5.3)

    I provide: Final evaluation report with score and readiness assessment You decide: Submit immediately / Implement optional improvements / Additional revisions


    Example Usage

    User Request

    "I have the optimized outline from the strategist skill. Please write the complete paper on self-continuity during sleep."

    Skill Response

    Phase 4: Systematic Writing

    1. Setup: Outline loaded (6 chapters, 9,600 words total). Platform: PhilArchive. Standards loaded. ✓

    2. Chapter 1 - Introduction (1,500 words):

      • Writing... [follows outline structure]
      • Self-evaluation: Argument 4/4, Citation 3/4, Clarity 4/4, Structure 3/4, Style 4/4
      • Score: 18/20 ✓ PASS
      • Decision Point 2: Proceed to Chapter 2?
    3. Chapter 2 - Narrative Compression Framework (1,200 words):

      • Writing... [develops theoretical framework]
      • Self-evaluation: All dimensions 3-4
      • Score: 17/20 ✓ PASS
      • Decision Point 2: Proceed to Chapter 3?
    4. Chapter 3-5: [Similar process for each chapter]

    5. Chapter 6 - Conclusion (1,000 words):

      • Writing... [synthesizes findings]
      • Score: 18/20 ✓ PASS
    6. Abstract (280 words):

      • Writing... [summarizes complete paper]
      • Score: 19/20 ✓ PASS
    7. Cross-Chapter Coherence: Terminology consistent ✓, Argument flow verified ✓, Citations complete ✓

    Phase 5: Quality Control

    1. Completeness Check: All items complete ✓ (18/18)

    2. Final Evaluation:

      • Overall Argument: 9/10
      • Literature Integration: 8/10 (48 citations)
      • Clarity: 9/10
      • Originality: 8/10
      • Methodology: 8/10
      • Structure: 9/10
      • Platform Fit: 9/10
      • Total: 60/70 (85.7%) ✓ PASS
    3. Decision Point 3: Paper scored 60/70 (Good quality, ready for submission). Submit now or implement optional improvements?

    4. Submission Package: PDF generated, metadata prepared, PhilArchive checklist complete ✓

    Output: Submission-ready manuscript + comprehensive quality reports


    Tips for Best Results

    Provide Complete Outline

    • The more detailed your outline, the better the writing quality
    • Include content guidance for each section
    • Specify key citations and argument structure
    • Indicate expected word counts

    Trust the Iterative Process

    • Chapter-level quality gates ensure each section is solid
    • Don't skip quality checks (they prevent cascading problems)
    • Revisions at chapter-level are easier than whole-paper revisions

    Engage at Decision Points

    • Your input at decision points shapes the final manuscript
    • Feel free to request additional revisions even if chapter passes
    • Provide feedback on style or emphasis

    Use Quality Reports

    • Chapter reports show specific weaknesses
    • Final report provides objective submission readiness assessment
    • Use reports to track improvement across chapters

    Leverage Section Guides

    • I reference section_guides.md for each section type
    • You can review these guides directly if you want to understand the approach
    • Guides include templates, examples, and common mistakes

    Integration with Academic-Paper-Strategist

    This skill is designed to work seamlessly with academic-paper-strategist:

    Ideal workflow:

    1. Use academic-paper-strategist to:

      • Identify optimal platform
      • Conduct literature search
      • Identify research gaps
      • Assess originality
      • Generate optimized detailed outline
    2. Use academic-paper-composer (this skill) to:

      • Execute the outline systematically
      • Maintain quality control during writing
      • Produce submission-ready manuscript

    Can be used standalone: If you already have a detailed outline from another source, you can use this skill directly (skip strategist).


    Limitations and Notes

    • Requires detailed outline: Vague outlines produce lower-quality output; specificity is key
    • Iterative process takes time: Quality writing with validation requires patience; typical timeline: 1-2 days for 10,000-word paper
    • Quality checks are systematic, not perfect: Final human review recommended before submission
    • Platform-specific formatting: I adapt to platform standards, but you should verify final format
    • Complementary to strategist skill: Best results come from using both skills in sequence

    Common Issues and Solutions

    Issue 1: Chapter Fails Quality Gate

    Symptom: Score <16/20 after writing chapter

    Solution:

    1. Review weak dimension(s) from report
    2. Implement specific recommendations
    3. Re-evaluate chapter
    4. Typical fix time: 30-60 minutes

    Prevention: Follow section guides closely during initial writing

    Issue 2: Inconsistent Style Across Chapters

    Symptom: Some chapters feel different in tone or voice

    Solution:

    1. Run cross-chapter coherence check (Step 4.4)
    2. Identify inconsistent terminology or voice
    3. Revise to match dominant style
    4. Re-run check to verify

    Prevention: Reference platform standards before writing each chapter

    Issue 3: Low Final Score (<56/70)

    Symptom: Paper fails final quality gate

    Solution:

    1. Identify weak dimensions from final report
    2. Focus on dimensions scoring <7/10
    3. Implement high-priority revisions systematically
    4. Re-evaluate after revisions

    Common causes: Insufficient literature integration, unclear contribution, poor coherence

    Issue 4: Completeness Checklist Incomplete

    Symptom: Missing required elements

    Solution:

    1. Review which category has incomplete items
    2. Add missing elements (e.g., missing objections section, incomplete references)
    3. Re-run completeness check

    Prevention: Use writing tracker throughout; check outline completeness before starting


    Platform-Specific Notes

    PhilArchive / PhilPapers

    • Style: First-person acceptable ("I argue")
    • Length: 5,000-12,000 words typical
    • Citations: APA or Chicago author-year
    • Quality focus: Philosophical rigor, argument clarity

    arXiv (Philosophy-adjacent)

    • Style: More formal, passive voice common
    • Length: Varies widely (3,000-20,000)
    • Citations: Varies by subcategory
    • Quality focus: Interdisciplinary clarity, technical precision

    PhilSci-Archive

    • Style: Bridges philosophical and scientific
    • Length: 6,000-15,000 words typical
    • Citations: Author-year typical
    • Quality focus: Integration of philosophy + science

    Summary

    academic-paper-composer transforms an optimized outline into a submission-ready manuscript through:

    1. Systematic Writing (Phase 4): Chapter-by-chapter execution with 5-dimension quality checks after each (≥16/20 threshold)
    2. Quality Control (Phase 5): Final 7-dimension assessment (≥56/70 threshold) + completeness validation + submission preparation

    Quality Assurance: Iterative evaluation at chapter and paper levels ensures consistent quality throughout.

    Output: Submission-ready manuscript with comprehensive quality reports documenting systematic validation.

    Estimated Time: 1-2 days for systematic writing and validation of 8,000-12,000 word paper (varies with outline detail and revision needs).


    Related Skills

    Prerequisite: academic-paper-strategist

    • Produces the optimized outline that this skill executes
    • Highly recommended to use first for best results

    This skill can be used standalone: If you have a detailed outline from another source, you can proceed directly with this skill.

    Related skills

    r-reproducibility-guideAnswering Research QuestionsBuilding Paper Screening RubricsChina-CF-StudyCleaning Up Research Sessions