Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
This is the 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.
Scientific writing is a process for communicating research with precision and clarity. Write manuscripts using IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA). Apply this skill for research papers and journal submissions.
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.
When to Use This Skill
This skill should be used when:
Writing or revising any section of a scientific manuscript (abstract, introduction, methods, results, discussion)
Structuring a research paper using IMRAD or other standard formats
Formatting citations and references in specific styles (APA, AMA, Vancouver, Chicago, IEEE)
Creating, formatting, or improving figures, tables, and data visualizations
Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews)
Drafting abstracts that meet journal requirements (structured or unstructured)
Preparing manuscripts for submission to specific journals
Improving writing clarity, conciseness, and precision
Ensuring proper use of field-specific terminology and nomenclature
Addressing reviewer comments and revising manuscripts
Visual Enhancement with Scientific Schematics
⚠️ MANDATORY: Every scientific paper MUST include at least 1-2 AI-generated figures using the scientific-schematics skill.
This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document:
Generate at minimum ONE schematic or diagram using scientific-schematics
Create publication-quality images with proper formatting
Review and refine through multiple iterations
Ensure accessibility (colorblind-friendly, high contrast)
Save outputs in the figures/ directory
When to add schematics:
Study design and methodology flowcharts (CONSORT, PRISMA, STROBE)
Conceptual framework diagrams
Experimental workflow illustrations
Data analysis pipeline diagrams
Biological pathway or mechanism diagrams
System architecture visualizations
Any complex concept that benefits from visualization
For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
Core Capabilities
1. Manuscript Structure and Organization
IMRAD Format: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes:
Introduction: Establish research context, identify gaps, state objectives
Methods: Detail study design, populations, procedures, and analysis approaches
Results: Present findings objectively without interpretation
For detailed guidance on IMRAD structure, refer to references/imrad_structure.md.
Alternative Structures: Support discipline-specific formats including:
Review articles (narrative, systematic, scoping)
Case reports and case series
Meta-analyses and pooled analyses
Theoretical/modeling papers
Methods papers and protocols
2. Section-Specific Writing Guidance
Abstract Composition: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.
Figures: Trends, patterns, relationships, comparisons best understood visually
Design Principles:
Make each table/figure self-explanatory with complete captions
Use consistent formatting and terminology across all display items
Label all axes, columns, and rows with units
Include sample sizes (n) and statistical annotations
Follow the "one table/figure per 1000 words" guideline
Avoid duplicating information between text, tables, and figures
Common Figure Types:
Bar graphs: Comparing discrete categories
Line graphs: Showing trends over time
Scatterplots: Displaying correlations
Box plots: Showing distributions and outliers
Heatmaps: Visualizing matrices and patterns
5. Reporting Guidelines by Study Type
Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to references/reporting_guidelines.md.
Each guideline provides checklists ensuring all critical methodological elements are reported.
6. Writing Principles and Style
Apply fundamental scientific writing principles. For detailed guidance, refer to references/writing_principles.md.
Clarity:
Use precise, unambiguous language
Define technical terms and abbreviations at first use
Maintain logical flow within and between paragraphs
Use active voice when appropriate for clarity
Conciseness:
Eliminate redundant words and phrases
Favor shorter sentences (15-20 words average)
Remove unnecessary qualifiers
Respect word limits strictly
Accuracy:
Report exact values with appropriate precision
Use consistent terminology throughout
Distinguish between observations and interpretations
Acknowledge uncertainty appropriately
Objectivity:
Present results without bias
Avoid overstating findings or implications
Acknowledge conflicting evidence
Maintain professional, neutral tone
7. Writing Process: From Outline to Full Paragraphs
CRITICAL: Always write in full paragraphs, never submit bullet points in scientific papers.
Scientific papers must be written in complete, flowing prose. Use this two-stage approach for effective writing:
Stage 1: Create Section Outlines with Key Points
When starting a new section:
Use the research-lookup skill to gather relevant literature and data
Create a structured outline with bullet points marking:
Main arguments or findings to present
Key studies to cite
Data points and statistics to include
Logical flow and organization
These bullet points serve as scaffolding—they are NOT the final manuscript
Example outline (Introduction section):
- Background: AI in drug discovery gaining traction
* Cite recent reviews (Smith 2023, Jones 2024)
* Traditional methods are slow and expensive
- Gap: Limited application to rare diseases
* Only 2 prior studies (Lee 2022, Chen 2023)
* Small datasets remain a challenge
- Our approach: Transfer learning from common diseases
* Novel architecture combining X and Y
- Study objectives: Validate on 3 rare disease datasets
Stage 2: Convert Key Points to Full Paragraphs
Once the outline is complete, expand each bullet point into proper prose:
Transform bullet points into complete sentences with subjects, verbs, and objects
Add transitions between sentences and ideas (however, moreover, in contrast, subsequently)
Integrate citations naturally within sentences, not as lists
Expand with context and explanation that bullet points omit
Ensure logical flow from one sentence to the next within each paragraph
Vary sentence structure to maintain reader engagement
Example conversion to prose:
Artificial intelligence approaches have gained significant traction in drug discovery
pipelines over the past decade (Smith, 2023; Jones, 2024). While these computational
methods show promise for accelerating the identification of therapeutic candidates,
traditional experimental approaches remain slow and resource-intensive, often requiring
years of laboratory work and substantial financial investment. However, the application
of AI to rare diseases has been limited, with only two prior studies demonstrating
proof-of-concept results (Lee, 2022; Chen, 2023). The primary obstacle has been the
scarcity of training data for conditions affecting small patient populations.
To address this challenge, we developed a transfer learning approach that leverages
knowledge from well-characterized common diseases to predict therapeutic targets for
rare conditions. Our novel neural architecture combines convolutional layers for
molecular feature extraction with attention mechanisms for protein-ligand interaction
modeling. The objective of this study was to validate our approach across three
independent rare disease datasets, assessing both predictive accuracy and biological
interpretability of the results.
Key Differences Between Outlines and Final Text:
Outline (Planning Stage)
Final Manuscript
Bullet points and fragments
Complete sentences and paragraphs
Telegraphic notes
Full explanations with context
List of citations
Citations integrated into prose
Abbreviated ideas
Developed arguments with transitions
For your eyes only
For publication and peer review
Common Mistakes to Avoid:
❌ Never leave bullet points in the final manuscript
❌ Never submit lists where paragraphs should be
❌ Don't use numbered or bulleted lists in Results or Discussion sections (except for specific cases like study hypotheses or inclusion criteria)
❌ Don't write sentence fragments or incomplete thoughts
✅ Do use occasional lists only in Methods (e.g., inclusion/exclusion criteria, materials lists)
✅ Do ensure every section flows as connected prose
✅ Do read paragraphs aloud to check for natural flow
When Lists ARE Acceptable (Limited Cases):
Lists may appear in scientific papers only in specific contexts:
Methods: Inclusion/exclusion criteria, materials and reagents, participant characteristics
Include required statements (funding, conflicts of interest, data availability, ethical approval)
Adhere to word limits for each section
Format according to template requirements when provided
9. Field-Specific Language and Terminology
Adapt language, terminology, and conventions to match the specific scientific discipline. Each field has established vocabulary, preferred phrasings, and domain-specific conventions that signal expertise and ensure clarity for the target audience.
Identify Field-Specific Linguistic Conventions:
Review terminology used in recent high-impact papers in the target journal
Note field-specific abbreviations, units, and notation systems
Identify preferred terms (e.g., "participants" vs. "subjects," "compound" vs. "drug," "specimens" vs. "samples")
Observe how methods, organisms, or techniques are typically described
Biomedical and Clinical Sciences:
Use precise anatomical and clinical terminology (e.g., "myocardial infarction" not "heart attack" in formal writing)
