# Scientific Writing - Detailed Guide > This file contains the detailed procedure and reference material extracted from `SKILL.md` for focused loading. The root skill defines activation, examples, safety constraints, and limitations. ## Overview **This is the core skill for the deep research and writing tool**—combining AI-driven deep research with well-formatted written outputs. A comprehensive literature search and verified citations require actual source access and a documented search; this skill alone does not provide them. 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. **Style principle:** Prefer clear connected prose; lists, structured abstracts and contribution statements are appropriate when the venue/style requires them. Use a two-stage process: first create section outlines with key points using research-lookup, then convert those outlines into complete paragraphs. ## Figures appropriate to the evidence and venue Follow the target journal's current author and image/AI policies. A graphical abstract is required only when the venue requests it; no universal figure quota applies. Use reproducible plotting tools for actual data and label conceptual schematics as illustrations. Never generate or alter microscopy, gels, patient images, measurements, sample counts or results to manufacture evidence. If using an approved image tool for a conceptual diagram, verify every label, arrow, anatomical detail, unit and causal claim against the study/source; record the tool/version and disclose AI assistance as the venue requires. Accessibility, publication resolution and scientific accuracy require human verification, not an automatic generation claim. Obtain permission before sharing unpublished or identifiable material with external tools. No generation scripts are bundled. --- ## 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 - Choose the number of displays needed to communicate results within the venue limits - 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 **Use the target venue’s format, with prose for developed arguments and lists where appropriate.** 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 **Fictional example outline (Introduction section):** Smith/Jones/Lee/Chen citations, dataset counts and method/results statements below are invented teaching placeholders, not verified literature or research performed. Replace every such claim with supplied study evidence before reuse. ``` - 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 | **Final structure check:** Follow the actual journal requirements for abstract headings, Methods lists, contribution bullets and supplementary protocols. Do not impose a universal ban on lists or structured abstracts. **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 non-journal reports, use an available approved template. The scientific_report.sty package and supporting assets described below are not bundled, so its commands/environments will not compile without separately supplied definitions. Standard report/article classes are a fallback. Do not download a same-named package or enable shell escape automatically. **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) - Use the actual technique precisely (qPCR, RT-qPCR and real-time PCR are not interchangeable in every context) **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 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/` **Workflow**: First use this skill for general scientific writing principles (IMRAD, clarity, citations), then consult venue-templates for venue-specific style adaptation. ## References The following upstream reference names are not included in this tracked two-file bundle; verify availability before referencing or loading them: - `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` ## Assets The following upstream style assets are not included in this tracked bundle: - `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 **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 **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. Load these references as needed when working on specific aspects of scientific writing.