---
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: (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."
allowed-tools: [Read, Write, Edit, Bash]
---

# 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 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:
1. Generate at minimum ONE schematic or diagram using scientific-schematics
2. Prefer 2-3 figures for comprehensive papers (methods flowchart, results visualization, conceptual diagram)

**How to generate figures:**
- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
- Simply describe your desired diagram in natural language
- Nano Banana Pro will automatically generate, review, and refine the schematic

**How to generate schematics:**
```bash
python scripts/generate_schematic.py "your diagram description" -o figures/output.png
```

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 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
- **Discussion**: Interpret results, acknowledge limitations, propose future directions

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.

**Introduction Development**: Build compelling introductions that:
- Establish the research problem's importance
- Review relevant literature systematically
- Identify knowledge gaps or controversies
- State clear research questions or hypotheses
- Explain the study's novelty and significance

**Methods Documentation**: Ensure reproducibility through:
- Detailed participant/sample descriptions
- Clear procedural documentation
- Statistical methods with justification
- Equipment and materials specifications
- Ethical approval and consent statements

**Results Presentation**: Present findings with:
- Logical flow from primary to secondary outcomes
- Integration with figures and tables
- Statistical significance with effect sizes
- Objective reporting without interpretation

**Discussion Construction**: Synthesize findings by:
- Relating results to research questions
- Comparing with existing literature
- Acknowledging limitations honestly
- Proposing mechanistic explanations
- Suggesting practical implications and future research

### 3. Citation and Reference Management

Apply citation styles correctly across disciplines. For comprehensive style guides, refer to `references/citation_styles.md`.

**Major Citation Styles:**
- **AMA (American Medical Association)**: Numbered superscript citations, common in medicine
- **Vancouver**: Numbered citations in square brackets, biomedical standard
- **APA (American Psychological Association)**: Author-date in-text citations, common in social sciences
- **Chicago**: Notes-bibliography or author-date, humanities and sciences
- **IEEE**: Numbered square brackets, engineering and computer science

**Best Practices:**
- Cite primary sources when possible
- Include recent literature (last 5-10 years for active fields)
- Balance citation distribution across introduction and discussion
- Verify all citations against original sources
- Use reference management software (Zotero, Mendeley, EndNote)

### 4. Figures and Tables

Create effective data visualizations that enhance comprehension. For detailed best practices, refer to `references/figures_tables.md`.

**When to Use Tables vs. Figures:**
- **Tables**: Precise numerical data, complex datasets, multiple variables requiring exact values
- **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`.

**Key Guidelines:**
- **CONSORT**: Randomized controlled trials
- **STROBE**: Observational studies (cohort, case-control, cross-sectional)
- **PRISMA**: Systematic reviews and meta-analyses
- **STARD**: Diagnostic accuracy studies
- **TRIPOD**: Prediction model studies
- **ARRIVE**: Animal research
- **CARE**: Case reports
- **SQUIRE**: Quality improvement studies
- **SPIRIT**: Study protocols for clinical trials
- **CHEERS**: Economic evaluations

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:
1. Use the research-lookup skill to gather relevant literature and data
2. 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
3. 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:

1. **Transform bullet points into complete sentences** with subjects, verbs, and objects
2. **Add transitions** between sentences and ideas (however, moreover, in contrast, subsequently)
3. **Integrate citations naturally** within sentences, not as lists
4. **Expand with context and explanation** that bullet points omit
5. **Ensure logical flow** from one sentence to the next within each paragraph
6. **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
- **Supplementary Materials**: Extended protocols, equipment lists, detailed parameters
- **Never in**: Abstract, Introduction, Results, Discussion, Conclusions

**Integration with Research Lookup:**

The research-lookup skill is essential for Stage 1 (creating outlines):
1. Search for relevant papers using research-lookup
2. Extract key findings, methods, and data
3. Organize findings as bullet points in your outline
4. 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. Journal-Specific Formatting

Adapt manuscripts to journal requirements:
- Follow author guidelines for structure, length, and format
- Apply journal-specific citation styles
- Meet figure/table specifications (resolution, file formats, dimensions)
- 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)
- Follow standardized disease nomenclature (ICD, DSM, SNOMED-CT)
- Specify drug names using generic names first, brand names in parentheses if needed
- Use "patients" for clinical studies, "participants" for community-based research
- Follow Human Genome Variation Society (HGVS) nomenclature for genetic variants
- Report lab values with standard units (SI units in most international journals)

**Molecular Biology and Genetics:**
- Use italics for gene symbols (e.g., *TP53*), regular font for proteins (e.g., p53)
- Follow species-specific gene nomenclature (uppercase for human: *BRCA1*; sentence case for mouse: *Brca1*)
- Specify organism names in full at first mention, then use accepted abbreviations (e.g., *Escherichia coli*, then *E. coli*)
- Use standard genetic notation (e.g., +/+, +/-, -/- for genotypes)
- Employ established terminology for molecular techniques (e.g., "quantitative PCR" or "qPCR," not "real-time PCR")

**Chemistry and Pharmaceutical Sciences:**
- Follow IUPAC nomenclature for chemical compounds
- Use systematic names for novel compounds, common names for well-known substances
- Specify chemical structures using standard notation (e.g., SMILES, InChI for databases)
- Report concentrations with appropriate units (mM, μM, nM, or % w/v, v/v)
- Describe synthesis routes using accepted reaction nomenclature
- Use terms like "bioavailability," "pharmacokinetics," "IC50" consistently with field definitions

**Ecology and Environmental Sciences:**
- Use binomial nomenclature for species (italicized: *Homo sapiens*)
- Specify taxonomic authorities at first species mention when relevant
- Employ standardized habitat and ecosystem classifications
- Use consistent terminology for ecological metrics (e.g., "species richness," "Shannon diversity index")
- Describe sampling methods with field-standard terms (e.g., "transect," "quadrat," "mark-recapture")

**Physics and Engineering:**
- Follow SI units consistently unless field conventions dictate otherwise
- Use standard notation for physical quantities (scalars vs. vectors, tensors)
- Employ established terminology for phenomena (e.g., "quantum entanglement," "laminar flow")
- Specify equipment with model numbers and manufacturers when relevant
- Use mathematical notation consistent with field standards (e.g., ℏ for reduced Planck constant)

**Neuroscience:**
- Use standardized brain region nomenclature (e.g., refer to atlases like Allen Brain Atlas)
- Specify coordinates for brain regions using established stereotaxic systems
- Follow conventions for neural terminology (e.g., "action potential" not "spike" in formal writing)
- Use "neural activity," "neuronal firing," "brain activation" appropriately based on measurement method
- Describe recording techniques with proper specificity (e.g., "whole-cell patch clamp," "extracellular recording")

**Social and Behavioral Sciences:**
- Use person-first language when appropriate (e.g., "people with schizophrenia" not "schizophrenics")
- Employ standardized psychological constructs and validated assessment names
- Follow APA guidelines for reducing bias in language
- Specify theoretical frameworks using established terminology
- Use "participants" rather than "subjects" for human research

**General Principles:**

**Match Audience Expertise:**
- For specialized journals: Use field-specific terminology freely, define only highly specialized or novel terms
- For broad-impact journals (e.g., *Nature*, *Science*): Define more technical terms, provide context for specialized concepts
- For interdisciplinary audiences: Balance precision with accessibility, define terms at first use

**Define Technical Terms Strategically:**
- Define abbreviations at first use: "messenger RNA (mRNA)"
- Provide brief explanations for specialized techniques when writing for broader audiences
- Avoid over-defining terms well-known to the target audience (signals unfamiliarity with field)
- Create a glossary if numerous specialized terms are unavoidable

**Maintain Consistency:**
- Use the same term for the same concept throughout (don't alternate between "medication," "drug," and "pharmaceutical")
- Follow