bps-kit 1.0.1 → 1.0.3

package/templates/vault/scientific-writing/SKILL.md

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----
-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...
-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:
-1. **ALWAYS generate a graphical abstract** as the first visual element
-2. Generate at minimum ONE additional schematic or diagram using scientific-schematics
-3. 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
-- Is suitable for journal table of contents display
-- Uses landscape orientation (typically 1200x600px)
-
-**Generate the graphical abstract FIRST:**
-```bash
-python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]" -o figures/graphical_abstract.png
-```
-
-**Graphical Abstract Requirements:**
-- **Content**: Visual summary showing workflow, key methods, main findings, and conclusions
-- **Style**: Clean, professional, suitable for journal TOC
-- **Elements**: Include 3-5 key steps/concepts with connecting arrows or flow
-- **Text**: Minimal labels, large readable fonts
-- Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary`
-
-### Additional Figures (GENERATE EXTENSIVELY)
-
-**⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.**
-
-Every document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.
-
-**MINIMUM Figure Requirements:**
-
-| Document Type | Minimum | Recommended |
-|--------------|---------|-------------|
-| Research Papers | 5 | 6-8 |
-| Literature Reviews | 4 | 5-7 |
-| Market Research | 20 | 25-30 |
-| Presentations | 1/slide | 1-2/slide |
-| Posters | 6 | 8-10 |
-| Grants | 4 | 5-7 |
-| Clinical Reports | 3 | 4-6 |
-
-**Use scientific-schematics EXTENSIVELY for technical diagrams:**
-```bash
-python scripts/generate_schematic.py "your diagram description" -o figures/output.png
-```
-
-- 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
-- Neural network architectures
-- Decision trees, algorithm flowcharts
-- Comparison matrices, timeline diagrams
-- Any technical concept that benefits from schematic visualization
-
-**Use generate-image EXTENSIVELY for visual content:**
-```bash
-python scripts/generate_image.py "your image description" -o figures/output.png
-```
-
-- Photorealistic illustrations of concepts
-- Medical/anatomical illustrations
-- Environmental/ecological scenes
-- Equipment and lab setup visualizations
-- Artistic visualizations, infographics
-- Cover images, header graphics
-- Product mockups, prototype visualizations
-- 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
-- **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
-
-**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):
-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. 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:**
-
-```latex
-% Key findings (blue) - for major discoveries
-\begin{keyfindings}[Title]
-Content with key findings and statistics.
-\end{keyfindings}
-
-% Methodology (green) - for methods highlights
-\begin{methodology}[Study Design]
-Description of methods and procedures.
-\end{methodology}
-
-% Recommendations (purple) - for action items
-\begin{recommendations}[Clinical Implications]
-\begin{enumerate}
-    \item Specific recommendation 1
-    \item Specific recommendation 2
-\end{enumerate}
-\end{recommendations}
-
-% Limitations (orange) - for caveats and cautions
-\begin{limitations}[Study Limitations]
-Description of limitations and their implications.
-\end{limitations}
-```
-
-**Professional Table Formatting:**
-
-```latex
-\begin{table}[htbp]
-\centering
-\caption{Results Summary}
-\begin{tabular}{@{}lccc@{}}
-\toprule
-\textbf{Variable} & \textbf{Treatment} & \textbf{Control} & \textbf{p} \\
-\midrule
-Outcome 1 & \meansd{42.5}{8.3} & \meansd{35.2}{7.9} & <.001\sigthree \\
-\rowcolor{tablealt} Outcome 2 & \meansd{3.8}{1.2} & \meansd{3.1}{1.1} & .012\sigone \\
-Outcome 3 & \meansd{18.2}{4.5} & \meansd{17.8}{4.2} & .58\signs \\
-\bottomrule
-\end{tabular}
-
-{\small \siglegend}
-\end{table}
-```
-
-**Scientific Notation Commands:**
-
-| Command | Output | Purpose |
-|---------|--------|---------|
-| `\pvalue{0.023}` | *p* = 0.023 | P-values |
-| `\psig{< 0.001}` | ***p* = < 0.001** | Significant p-values (bold) |
-| `\CI{0.45}{0.72}` | 95% CI [0.45, 0.72] | Confidence intervals |
-| `\effectsize{d}{0.75}` | d = 0.75 | Effect sizes |
-| `\samplesize{250}` | *n* = 250 | Sample sizes |
-| `\meansd{42.5}{8.3}` | 42.5 ± 8.3 | Mean with SD |
-| `\sigone`, `\sigtwo`, `\sigthree` | *, **, *** | Significance stars |
-
-**Getting Started:**
-
-```latex
-\documentclass[11pt,letterpaper]{report}
-\usepackage{scientific_report}
-
-\begin{document}
-\makereporttitle
-    {Report Title}
-    {Subtitle}
-    {Author Name}
-    {Institution}
-    {Date}
-
-% Your content with professional formatting
-\end{document}
-```
-
-**Compilation**: Use XeLaTeX or LuaLaTeX for proper Helvetica font rendering:
-```bash
-xelatex report.tex
-```
-
-For complete documentation, refer to:
-- `assets/scientific_report.sty`: The style package
-- `assets/scientific_report_template.tex`: Complete template example
-- `assets/REPORT_FORMATTING_GUIDE.md`: Quick reference guide
-- `references/professional_report_formatting.md`: Comprehensive formatting guide
-
-### 9. 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
-
-### 10. 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 a consistent system for abbreviations (decide on "PCR" or "polymerase chain reaction" after first definition)
-- Apply the same nomenclature system throughout (especially for genes, species, chemicals)
-
-**Avoid Field Mixing Errors:**
-- Don't use clinical terminology for basic science (e.g., don't call mice "patients")
-- Avoid colloquialisms or overly general terms in place of precise field terminology
-- Don't import terminology from adjacent fields without ensuring proper usage
-
-**Verify Terminology Usage:**
-- Consult field-specific style guides and nomenclature resources
-- Check how terms are used in recent papers from the target journal
-- Use domain-specific databases and ontologies (e.g., Gene Ontology, MeSH terms)
-- When uncertain, cite a key reference that establishes terminology
-
-### 11. Common Pitfalls to Avoid
-
-**Top Rejection Reasons:**
-1. Inappropriate, incomplete, or insufficiently described statistics
-2. Over-interpretation of results or unsupported conclusions
-3. Poorly described methods affecting reproducibility
-4. Small, biased, or inappropriate samples
-5. Poor writing quality or difficult-to-follow text
-6. Inadequate literature review or context
-7. Figures and tables that are unclear or poorly designed
-8. Failure to follow reporting guidelines
-
-**Writing Quality Issues:**
-- Mixing tenses inappropriately (use past tense for methods/results, present for established facts)
-- Excessive jargon or undefined acronyms
-- Paragraph breaks that disrupt logical flow
-- Missing transitions between sections
-- Inconsistent notation or terminology
-
-## Workflow for Manuscript Development
-
-**Stage 1: Planning**
-1. Identify target journal and review author guidelines
-2. Determine applicable reporting guideline (CONSORT, STROBE, etc.)
-3. Outline manuscript structure (usually IMRAD)
-4. Plan figures and tables as the backbone of the paper
-
-**Stage 2: Drafting** (Use two-stage writing process for each section)
-1. Start with figures and tables (the core data story)
-2. For each section below, follow the two-stage process:
-   - **First**: Create outline with bullet points using research-lookup
-   - **Second**: Convert bullet points to full paragraphs with flowing prose
-3. Write Methods (often easiest to draft first)
-4. Draft Results (describing figures/tables objectively)
-5. Compose Discussion (interpreting findings)
-6. Write Introduction (setting up the research question)
-7. Craft Abstract (synthesizing the complete story)
-8. Create Title (concise and descriptive)
-
-**Remember**: Bullet points are for planning only—the final manuscript must be in complete paragraphs.
-
-**Stage 3: Revision**
-1. Check logical flow and "red thread" throughout
-2. Verify consistency in terminology and notation
-3. Ensure figures/tables are self-explanatory
-4. Confirm adherence to reporting guidelines
-5. Verify all citations are accurate and properly formatted
-6. Check word counts for each section
-7. Proofread for grammar, spelling, and clarity
-
-**Stage 4: Final Preparation**
-1. Format according to journal requirements
-2. Prepare supplementary materials
-3. Write cover letter highlighting significance
-4. Complete submission checklists
-5. Gather all required statements and forms
-
-## Integration with Other Scientific Skills
-
-This skill works effectively with:
-- **Data analysis skills**: For generating results to report
-- **Statistical analysis**: For determining appropriate statistical presentations
-- **Literature review skills**: For contextualizing research
-- **Figure creation tools**: For developing publication-quality visualizations
-- **Venue-templates skill**: For venue-specific writing styles and formatting (journal manuscripts)
-- **scientific_report.sty**: For professional reports, white papers, and technical documents
-
-### Professional Reports vs. Journal Manuscripts
-
-**Choose the right formatting approach:**
-
-| Document Type | Formatting Approach |
-|---------------|---------------------|
-| Journal manuscripts | Use `venue-templates` skill |
-| Conference papers | Use `venue-templates` skill |
-| Research reports | Use `scientific_report.sty` (this skill) |
-| White papers | Use `scientific_report.sty` (this skill) |
-| Technical reports | Use `scientific_report.sty` (this skill) |
-| Grant reports | Use `scientific_report.sty` (this skill) |
-
-### Venue-Specific Writing Styles
-
-**Before writing for a specific venue, consult the venue-templates skill for writing style guides:**
-
-Different venues have dramatically different writing expectations:
-- **Nature/Science**: Accessible, story-driven, broad significance
-- **Cell Press**: Mechanistic depth, graphical abstracts, Highlights
-- **Medical journals (NEJM, Lancet)**: Structured abstracts, evidence language
-- **ML conferences (NeurIPS, ICML)**: Contribution bullets, ablation studies
-- **CS conferences (CHI, ACL)**: Field-specific conventions
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-The venue-templates skill provides:
-- `venue_writing_styles.md`: Master style comparison
-- Venue-specific guides: `nature_science_style.md`, `cell_press_style.md`, `medical_journal_styles.md`, `ml_conference_style.md`, `cs_conference_style.md`
-- `reviewer_expectations.md`: What reviewers look for at each venue
-- Writing examples in `assets/examples/`
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-**Workflow**: First use this skill for general scientific writing principles (IMRAD, clarity, citations), then consult venue-templates for venue-specific style adaptation.
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-## References
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-This skill includes comprehensive reference files covering specific aspects of scientific writing:
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-- `references/imrad_structure.md`: Detailed guide to IMRAD format and section-specific content
-- `references/citation_styles.md`: Complete citation style guides (APA, AMA, Vancouver, Chicago, IEEE)
-- `references/figures_tables.md`: Best practices for creating effective data visualizations
-- `references/reporting_guidelines.md`: Study-specific reporting standards and checklists
-- `references/writing_principles.md`: Core principles of effective scientific communication
-- `references/professional_report_formatting.md`: Guide to professional report styling with `scientific_report.sty`
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-## Assets
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-This skill includes LaTeX style packages and templates for professional report formatting:
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-- `assets/scientific_report.sty`: Professional LaTeX style package with Helvetica fonts, colored boxes, and attractive tables
-- `assets/scientific_report_template.tex`: Complete report template demonstrating all style features
-- `assets/REPORT_FORMATTING_GUIDE.md`: Quick reference guide for the style package
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-**Key Features of `scientific_report.sty`:**
-- Helvetica font family for modern, professional appearance
-- Professional color scheme (blues, greens, oranges, purples)
-- Box environments: `keyfindings`, `methodology`, `resultsbox`, `recommendations`, `limitations`, `criticalnotice`, `definition`, `executivesummary`, `hypothesis`
-- Tables with alternating row colors and professional headers
-- Scientific notation commands for p-values, effect sizes, confidence intervals
-- Professional headers and footers
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-**For venue-specific writing styles** (tone, voice, abstract format, reviewer expectations), see the **venue-templates** skill which provides comprehensive style guides for Nature/Science, Cell Press, medical journals, ML conferences, and CS conferences.
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-Load these references as needed when working on specific aspects of scientific writing.
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