git:20260721.831d49e to v2.0

- description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.

- allowed-tools: Read Write Edit Bash

- license: MIT license

- required_environment_variables: [{"name": "OPENROUTER_API_KEY", "prompt": "OpenRouter API key for the skill's LLM-powered steps.", "required_for": "optional features"}]

- metadata: {"version": "1.2", "skill-author": "K-Dense Inc.", "openclaw": {"primaryEnv": "OPENROUTER_API_KEY", "envVars": [{"name": "OPENROUTER_API_KEY", "required": false, "description": "OpenRouter API key for the skill's LLM-powered steps."}]}}

- ## 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:

- 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

- 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

- **Workflow**: First use this skill for general scientific writing principles (IMRAD, clarity, citations), then consult venue-templates for venue-specific style adaptation.

- ## References

- This skill includes comprehensive reference files covering specific aspects of scientific writing:

- - `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

- This skill includes LaTeX style packages and templates for professional report formatting:

- - `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.