Academic Paper — Academic Paper Writing Full Pipeline

Full research pipeline for academic paper writing where an agent team collaborates to generate research design, experiment protocols, analysis, manuscript writing, and submission preparation. Use this skill for requests such as 'write an academic paper', 'research paper writing', 'help me write a paper', 'design a study', 'run statistical analysis', 'prepare journal submission', 'manuscript writing', 'research methodology design', 'hypothesis testing', 'academic writing', and other academic research paper tasks. Also supports analysis, rewriting, and submission preparation when existing data or drafts are available. However, actual data collection execution, official IRB submission, journal system login and upload, and running actual statistical software are outside the scope of this skill.

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

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

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

Data Transfer Protocol

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

Error Handling

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