Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
Core skill for the deep research and writing tool — combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill.
Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in the final manuscript. Use a two-stage process: first create section outlines with key points using research-lookup, then convert those outlines into complete paragraphs.
Guide papers through Introduction, Methods, Results, And Discussion. Support alternative structures for reviews, case reports, meta-analyses, methods papers, and theoretical/modeling papers. See references/imrad_structure.md for detailed section-by-section guidance.
Apply citation styles correctly: AMA (numbered superscript), Vancouver (numbered brackets), APA (author-date), Chicago (notes or author-date), IEEE (numbered brackets). Cite primary sources, include recent literature, and verify all citations against originals. See references/citation_styles.md for comprehensive style guides.
Use tables for precise numerical data; use figures for trends, patterns, and relationships. Each display item should be self-explanatory with complete captions, consistent formatting, labeled axes with units, and sample sizes. Follow the "one table/figure per 1000 words" guideline. See references/figures_tables.md for detailed best practices.
Follow established reporting standards for study-specific transparency: CONSORT (RCTs), STROBE (observational), PRISMA (systematic reviews), STARD (diagnostic accuracy), TRIPOD (prediction models), ARRIVE (animal research), CARE (case reports), SPIRIT (protocols), CHEERS (economic evaluations). See references/reporting_guidelines.md for checklists.
Clarity (precise language, defined terms, logical flow), conciseness (15-20 word average sentences, no redundancy), accuracy (exact values, consistent terminology), objectivity (no overstating, acknowledge conflicting evidence). See references/writing_principles.md for detailed guidance.
Adapt language and conventions to the target discipline — biomedical, molecular biology, chemistry, ecology, physics, neuroscience, social sciences. Match audience expertise level, define terms strategically, maintain consistency, avoid field-mixing errors. See references/field_terminology.md for domain-specific guidelines.
For non-journal documents (research reports, white papers, technical reports, grant reports), use the scientific_report.sty LaTeX style package. Provides Helvetica typography, colored box environments (keyfindings, methodology, recommendations, limitations), professional tables, and scientific notation commands. Compile with XeLaTeX. For journal manuscripts and conference papers, use the venue-templates skill instead. See references/professional_report_formatting.md for full documentation.
Adapt manuscripts to journal requirements: follow author guidelines for structure/length/format, apply journal-specific citation styles, meet figure/table specifications, include required statements (funding, conflicts, data availability, ethics), and adhere to word limits.
Stage 1 — Outline with Key Points: Use research-lookup to gather literature. Create a structured outline with bullet points marking main arguments, key citations, data points, and logical flow. These bullet points are scaffolding only — not the final manuscript.
Stage 2 — Convert to Full Paragraphs: Transform each bullet point into complete sentences. Add transitions between ideas (however, moreover, in contrast). Integrate citations naturally within sentences. Expand with context that bullet points omit. Ensure logical flow and vary sentence structure.
Rules:
Planning: Identify target journal, review author guidelines, determine applicable reporting guideline, outline structure, plan figures/tables.
Drafting (two-stage process for each section): Start with figures/tables (the core data story). Then draft Methods -> Results -> Discussion -> Introduction -> Abstract -> Title. For each section: first outline with research-lookup, then convert to prose.
Revision: Check logical flow and "red thread," verify terminology consistency, ensure figures/tables are self-explanatory, confirm reporting guideline adherence, verify citations, check word counts, proofread.
Final Preparation: Format to journal requirements, prepare supplementary materials, write cover letter, complete submission checklists.
Top rejection reasons: inappropriate/incomplete statistics, over-interpretation of results, poorly described methods, small/biased samples, poor writing quality, inadequate literature review, unclear figures/tables, failure to follow reporting guidelines.
Writing quality issues to avoid: mixing tenses inappropriately (past for methods/results, present for established facts), excessive jargon or undefined acronyms, paragraph breaks disrupting logical flow, missing transitions, inconsistent notation.
Use this skill for general scientific writing principles, then consult venue-templates for venue-specific style adaptation.