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
Install
The skill file stays in the publisher's repository.
Paste the copied command in a terminal. It installs this SKILL.md into that agent.
npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing -a cursor -y
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.
Questions
How do I install scientific-writing?
Download skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does scientific-writing live?
The publisher keeps it at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.
Which agents can use scientific-writing?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.
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.
name: scientific-writing
description: 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.
allowed-tools: Read Write Edit Bash
license: MIT license
metadata:
skill-author: K-Dense Inc.
Scientific Writing
Overview
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 a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.
This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document:
ALWAYS generate a graphical abstract as the first visual element
Generate at minimum ONE additional schematic or diagram using scientific-schematics
Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)
Graphical Abstract (REQUIRED)
Every scientific writeup MUST include a graphical abstract. This is a visual summary of your paper that:
Appears before or immediately after the text abstract
Captures the entire paper's key message in one image
Any visual that enhances understanding or engagement
The AI will automatically:
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 in Doubt, Generate a Figure:
Complex concept → generate a schematic
Data discussion → generate a visualization
Process description → generate a flowchart
Comparison → generate a comparison diagram
Reader benefit → generate a visual
For detailed guidance, refer to the scientific-schematics and generate-image 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
Never in: Abstract, Introduction, Results, Discussion, Conclusions
Abstract Format Rule:
❌ NEVER use labeled sections (Background:, Methods:, Results:, Conclusions:)
✅ ALWAYS write as flowing paragraph(s) with natural transitions
Exception: Only use structured format if journal explicitly requires it in author guidelines
Integration with Research Lookup:
The research-lookup skill is essential for Stage 1 (creating outlines):
Search for relevant papers using research-lookup
Extract key findings, methods, and data
Organize findings as bullet points in your outline
Then convert the outline to full paragraphs in Stage 2
This two-stage process ensures you:
Gather and organize information systematically
Create logical structure before writing
Produce polished, publication-ready prose
Maintain focus on the narrative flow
8. Professional Report Formatting (Non-Journal Documents)
For research reports, technical reports, white papers, and other professional documents that are NOT journal manuscripts, use the scientific_report.sty LaTeX style package for a polished, professional appearance.
When to Use Professional Report Formatting:
Research reports and technical reports
White papers and policy briefs
Grant reports and progress reports
Industry reports and technical documentation
Internal research summaries
Feasibility studies and project deliverables
When NOT to Use (Use Venue-Specific Formatting Instead):
Journal manuscripts → Use venue-templates skill
Conference papers → Use venue-templates skill
Academic theses → Use institutional templates
The scientific_report.sty Style Package Provides:
Feature
Description
Typography
Helvetica font family for modern, professional appearance
Color Scheme
Professional blues, greens, and accent colors
Box Environments
Colored boxes for key findings, methods, recommendations, limitations
Tables
Alternating row colors, professional headers
Figures
Consistent caption formatting
Scientific Commands
Shortcuts for p-values, effect sizes, confidence intervals
Box Environments for Content Organization:
% Key findings (blue) - for major discoveries
egin{keyfindings}[Title]
Content with key findings and statistics.
nd{keyfindings}
% Methodology (green) - for methods highlights
egin{methodology}[Study Design]
Description of methods and procedures.
nd{methodology}
% Recommendations (purple) - for action items
egin{recommendations}[Clinical Implications]
egin{enumerate}
\item Specific recommendation 1
\item Specific recommendation 2
nd{enumerate}
nd{recommendations}
% Limitations (orange) - for caveats and cautions
egin{limitations}[Study Limitations]
Description of limitations and their implications.
nd{limitations}
Professional Table Formatting:
egin{table}[htbp]
How do I install scientific-writing?
Download skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does scientific-writing live?
The publisher keeps it at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.
Which agents can use scientific-writing?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.