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:

• Generate at minimum ONE schematic or diagram using scientific-schematics
• 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:

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.

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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:

• 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 approac