Draft Paper

Write a research paper from analysis results, companion .md files, and iterative user input. Covers literature review, all manuscript sections, and LaTeX assembly.

Preconditions

Check for companion .md files in output/figures/ and output/tables/ (from /finalize-analysis). If found, use them as the basis for data/methods/results sections. If not found, read raw output files and ask user to describe findings for each.

When to Use

• •Analysis complete, want to write up results
• •User says "write paper", "draft manuscript", "start writing"
• •Turning completed figures and tables into a publication
• •Need literature review integrated with findings

When NOT to Use

• •Analysis still ongoing (use /finalize-analysis)
• •Single section in isolation (just write it directly)
• •Editing an existing draft (just edit directly)

Workflow

Phase 1: Synthesize Findings

Scan output/ for companion .md files. If none exist, read output files directly and ask user to describe each. Summarize all findings in a structured overview.

Done when: User confirms the summary captures the key results.

Phase 2: Abstract Drafting

AskUserQuestion about most significant findings, preferred framing, contribution to the field. Write 150-250 word abstract. Get approval.

Done when: User approves the abstract draft.

Phase 3: Literature Review Planning

Enter Plan mode. Ask user about preferred structure (thematic, theoretical, gap-driven). Identify search topics from findings. Ask detailed questions about theoretical framework, comparison studies, methodological precedents. Create search plan. See references/literature-review-workflow.md.

Done when: Search plan written with topics and user approves.

Phase 4: Execute Literature Review

Primary — /gemini: Invoke /gemini for each search topic to discover papers. If /gemini is unavailable, use WebSearch tool directly. For each paper found, extract key claims, methods, sample, relevance.

Secondary — Zotero MCP: Search the user's Zotero library using zotero_search_items and zotero_semantic_search to find papers already collected on each topic. For Zotero hits, use zotero_get_item_metadata with format: bibtex to export citations directly. Use zotero_get_item_fulltext for deeper reading when needed.

Build .bib incrementally: Export BibTeX from Zotero when available; hand-write entries (cite key: firstauthorYYYYkeyword) for papers found only via /gemini. Build literature matrix (see references/literature-review-workflow.md).

Done when: All topics searched, literature matrix complete, .bib has entries.

Phase 5: Analyze Literature vs Findings

Map findings against literature: knowledge gaps, methodological implications, theoretical implications, mechanisms/theories explaining discovered patterns.

Done when: Gap analysis documented and user confirms framing.

Phase 6: Write Introduction + Literature Review

Draft both sections. Invoke /codex for review (or ask user to review if unavailable). Ask user for feedback. Iterate.

Done when: User approves both sections.

Phase 7: Write Data/Methods/Results

Rewrite from companion .md files. AskUserQuestion about presentation level (technical vs accessible), emphasis, what to highlight or downplay, what to include or exclude from appendix.

Done when: User approves these sections.

Phase 8: Write Discussion + Conclusion

Connect findings to literature. AskUserQuestion about policy implications, limitations the user wants to acknowledge, future research directions.

Done when: User approves.

Phase 9: Revise Abstract + Assemble LaTeX

Update abstract to reflect final paper. Create manuscript/paper.tex using the ASR/Science-style template (see references/latex-template.md): title page, author bios, all sections, \input{} for tables, \includegraphics{} for figures, BibTeX references. Copy asr.bst and scicite.sty from skill assets/ to manuscript/. Compile with pdflatex + bibtex.

Done when: LaTeX compiles without errors.

Quick Reference

Common Mistakes