academic-paper

Academic Paper — Academic Paper Writing Full Pipeline

An agent team collaborates to generate research design, experiment protocols, analysis, manuscript writing, and submission preparation for an academic paper.

Execution Mode

Agent Team — 5 members communicate directly via SendMessage and cross-validate each other's work.

Agent Roster

Agent	File	Role	Type
research-designer	.claude/agents/research-designer.md	Research questions, hypotheses, methodology, prior literature	general-purpose
experiment-manager	.claude/agents/experiment-manager.md	Experiment protocols, data collection planning	general-purpose
statistical-analyst	.claude/agents/statistical-analyst.md	Statistical analysis, code generation, visualization	general-purpose
paper-writer	.claude/agents/paper-writer.md	IMRaD-structured writing, citation management	general-purpose
submission-preparer	.claude/agents/submission-preparer.md	Journal selection, formatting, cover letter	general-purpose

Workflow

Phase 1: Preparation (Performed Directly by Orchestrator)

1. Extract from user input:
   • Research Topic: Research field, core keywords
   • Research Level (optional): Undergraduate/Master's/Doctoral/Faculty level
   • Target Journal (optional): Journal name, IF range
   • Existing Materials (optional): Data, drafts, literature lists
   • Constraints (optional): Deadline, length, special considerations
2. Create the _workspace/ directory at the project root
3. Organize the input and save it as _workspace/00_input.md
4. If existing files are provided, copy them to _workspace/ and skip the corresponding phase
5. Determine the execution mode based on the scope of the request

Phase 2: Team Assembly and Execution

Order	Task	Owner	Dependencies	Deliverable
1	Research Design	designer	None	_workspace/01_research_design.md
2	Experiment Protocol	experiment	Task 1	_workspace/02_experiment_protocol.md
3	Statistical Analysis	analyst	Tasks 1, 2	_workspace/03_analysis_report.md
4	Manuscript Writing	writer	Tasks 1, 2, 3	_workspace/04_manuscript.md
5	Submission Preparation	preparer	Tasks 1, 4	_workspace/05_submission_package.md
6	Integrated Review	orchestrator	All	_workspace/06_review_report.md

Inter-Agent Communication Flow:

• designer completes -> delivers variables and sampling plan to experiment, hypotheses and analysis direction to analyst, theoretical background to writer, research field to preparer
• experiment completes -> delivers data structure to analyst, Methods materials to writer
• analyst completes -> delivers Results materials (APA format + Tables/Figures) to writer, analysis code to preparer
• writer completes -> delivers completed manuscript to preparer
• orchestrator cross-validates overall consistency (hypotheses <-> analysis <-> results <-> discussion)

Phase 3: Integration and Final Deliverables

1. Verify consistency across all files in _workspace/
2. Validate logical consistency of hypotheses-analysis-results-discussion chain
3. Generate the integrated review report
4. Report the final summary to the user

Execution Modes by Scope

User Request Pattern	Execution Mode	Agents Deployed
"Write a paper", "Research paper writing"	Full Pipeline	All 5 agents
"Just design the study"	Design Mode	designer only
"Analyze this data" + data	Analysis Mode	analyst + writer
"Polish this manuscript draft" + draft	Rewriting Mode	writer + preparer
"Prepare for submission" + manuscript	Submission Mode	preparer only
"Continue with the rest using this design" + design doc	Continuation Mode	experiment -> analyst -> writer -> preparer

Using Existing Files: When the user provides data, drafts, or design documents, copy them to _workspace/ and skip the corresponding phase.

Data Transfer Protocol

Strategy	Method	Purpose
File-Based	_workspace/ directory	Store and share main deliverables
Message-Based	SendMessage	Real-time key information delivery, correction requests
Task-Based	TaskCreate/TaskUpdate	Progress tracking, dependency management

File naming convention: {order}_{deliverable}.{extension}

Error Handling

Error Type	Strategy
Prior literature search failure	Work from user-provided references, note "Limited literature review"
Vague research topic	Propose 3 specific sub-topics and request user selection
No data available	Provide analysis strategy and code only, instruct "Run after data collection"
Agent failure	Retry once -> if still fails, proceed without that deliverable, note omission in review
Hypothesis-results mismatch	Paper writer addresses in Discussion, suggests post-hoc analyses

Test Scenarios

Normal Flow

Prompt: "Write a paper studying the effect of social media usage time on college students' academic achievement. Survey-based." Expected Results:

• Design: Cross-sectional survey design, social media time (IV) -> GPA (DV), control variables included
• Protocol: Questionnaire (using existing validated scales), online collection procedure
• Analysis: Multiple regression code (R/Python), APA-format results
• Manuscript: Complete IMRaD structure, prior study citations
• Submission: 3 SSCI journal recommendations, cover letter

Existing File Flow

Prompt: "Analyze this data and write the paper" + CSV data attached Expected Results:

• Identify variable structure from the data to develop analysis strategy
• Lightly deploy designer to reverse-extract research framework
• Proceed in order: analyst -> writer -> preparer

Error Flow

Prompt: "Write a paper, but I haven't decided on a topic yet" Expected Results:

• designer asks about the user's area of interest, or
• suggests 3 research topics based on recent trends
• Review report notes "Topic undetermined — proceeded on example basis"

Agent Extension Skills

Extension Skill	Path	Target Agent	Role
research-methodology	.claude/skills/research-methodology/skill.md	research-designer, statistical-analyst	Research design, sampling, statistical analysis, ethics
citation-standards	.claude/skills/citation-standards/skill.md	paper-writer, submission-preparer	APA/IEEE/Chicago citation, IMRaD, submission preparation