{"slug":"brycewang-stanford-scientific-writing","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 structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.","long_description":"---\nname: scientific-writing\ndescription: 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.\nallowed-tools: Read Write Edit Bash\nlicense: MIT license\nmetadata:\n skill-author: K-Dense Inc.\n---\n\n\n\n# Scientific Writing\n\n## Overview\n\n**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.\n\nScientific 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.\n\n**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.\n\n## When to Use This Skill\n\nThis skill should be used when:\n- Writing or revising any section of a scientific manuscript (abstract, introduction, methods, results, discussion)\n- Structuring a research paper using IMRAD or other standard formats\n- Formatting citations and references in specific styles (APA, AMA, Vancouver, Chicago, IEEE)\n- Creating, formatting, or improving figures, tables, and data visualizations\n- Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews)\n- Drafting abstracts that meet journal requirements (structured or unstructured)\n- Preparing manuscripts for submission to specific journals\n- Improving writing clarity, conciseness, and precision\n- Ensuring proper use of field-specific terminology and nomenclature\n- Addressing reviewer comments and revising manuscripts\n\n## Visual Enhancement with Scientific Schematics\n\n**⚠️ MANDATORY: Every scientific paper MUST include a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.**\n\nThis is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document:\n1. **ALWAYS generate a graphical abstract** as the first visual element\n2. Generate at minimum ONE additional schematic or diagram using scientific-schematics\n3. Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)\n\n### Graphical Abstract (REQUIRED)\n\n**Every scientific writeup MUST include a graphical abstract.** This is a visual summary of your paper that:\n- Appears before or immediately after the text abstract\n- Captures the entire paper's key message in one image\n- Is suitable for journal table of contents display\n- Uses landscape orientation (typically 1200x600px)\n\n**Generate the graphical abstract FIRST:**\n```bash\npython scripts/generate_schematic.py \"Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]\" -o figures/graphical_abstract.png\n```\n\n**Graphical Abstract Requirements:**\n- **Content**: Visual summary showing workflow, key methods, main findings, and conclusions\n- **Style**: Clean, professional, suitable for journal TOC\n- **Elements**: Include 3-5 key steps/concepts with connecting arrows or flow\n- **Text**: Minimal labels, large readable fonts\n- Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary`\n\n### Additional Figures (GENERATE EXTENSIVELY)\n\n**⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.**\n\nEvery document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.\n\n**MINIMUM Figure Requirements:**\n\n| Document Type | Minimum | Recommended |\n|--------------|---------|-------------|\n| Research Papers | 5 | 6-8 |\n| Literature Reviews | 4 | 5-7 |\n| Market Research | 20 | 25-30 |\n| Presentations | 1/slide | 1-2/slide |\n| Posters | 6 | 8-10 |\n| Grants | 4 | 5-7 |\n| Clinical Reports | 3 | 4-6 |\n\n**Use scientific-schematics EXTENSIVELY for technical diagrams:**\n```bash\npython scripts/generate_schematic.py \"your diagram description\" -o figures/output.png\n```\n\n- Study design and methodology flowcharts (CONSORT, PRISMA, STROBE)\n- Conceptual framework diagrams\n- Experimental workflow illustrations\n- Data analysis pipeline diagrams\n- Biological pathway or mechanism diagrams\n- System architecture visualizations\n- Neural network architectures\n- Decision trees, algorithm flowcharts\n- Comparison matrices, timeline diagrams\n- Any technical concept that benefits from schematic visualization\n\n**Use generate-image EXTENSIVELY for visual content:**\n```bash\npython scripts/generate_image.py \"your image description\" -o figures/output.png\n```\n\n- Photorealistic illustrations of concepts\n- Medical/anatomical illustrations\n- Environmental/ecological scenes\n- Equipment and lab setup visualizations\n- Artistic visualizations, infographics\n- Cover images, header graphics\n- Product mockups, prototype visualizations\n- Any visual that enhances understanding or engagement\n\nThe AI will automatically:\n- Create publication-quality images with proper formatting\n- Review and refine through multiple iterations\n- Ensure accessibility (colorblind-friendly, high contrast)\n- Save outputs in the figures/ directory\n\n**When in Doubt, Generate a Figure:**\n- Complex concept → generate a schematic\n- Data discussion → generate a visualization\n- Process description → generate a flowchart\n- Comparison → generate a comparison diagram\n- Reader benefit → generate a visual\n\nFor detailed guidance, refer to the scientific-schematics and generate-image skill documentation.\n\n---\n\n## Core Capabilities\n\n### 1. Manuscript Structure and Organization\n\n**IMRAD Format**: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes:\n- **Introduction**: Establish research context, identify gaps, state objectives\n- **Methods**: Detail study design, populations, procedures, and analysis approaches\n- **Results**: Present findings objectively without interpretation\n- **Discussion**: Interpret results, acknowledge limitations, propose future directions\n\nFor detailed guidance on IMRAD structure, refer to `references/imrad_structure.md`.\n\n**Alternative Structures**: Support discipline-specific formats including:\n- Review articles (narrative, systematic, scoping)\n- Case reports and case series\n- Meta-analyses and pooled analyses\n- Theoretical/modeling papers\n- Methods papers and protocols\n\n### 2. Section-Specific Writing Guidance\n\n**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.\n\n**Introduction Development**: Build compelling introductions that:\n- Establish the research problem's importance\n- Review relevant literature systematically\n- Identify knowledge gaps or controversies\n- State clear research questions or hypotheses\n- Explain the study's novelty and significance\n\n**Methods Documentation**: Ensure reproducibility through:\n- Detailed participant/sample descriptions\n- Clear procedural documentation\n- Statistical methods with justification\n- Equipment and materials specifications\n- Ethical approval and consent statements\n\n**Results Presentation**: Present findings with:\n- Logical flow from primary to secondary outcomes\n- Integration with figures and tables\n- Statistical significance with effect sizes\n- Objective reporting without interpretation\n\n**Discussion Construction**: Synthesize findings by:\n- Relating results to research questions\n- Comparing with existing literature\n- Acknowledging limitations honestly\n- Proposing mechanistic explanations\n- Suggesting practical implications and future research\n\n### 3. Citation and Reference Management\n\nApply citation styles correctly across disciplines. For comprehensive style guides, refer to `references/citation_styles.md`.\n\n**Major Citation Styles:**\n- **AMA (American Medical Association)**: Numbered superscript citations, common in medicine\n- **Vancouver**: Numbered citations in square brackets, biomedical standard\n- **APA (American Psychological Association)**: Author-date in-text citations, common in social sciences\n- **Chicago**: Notes-bibliography or author-date, humanities and sciences\n- **IEEE**: Numbered square brackets, engineering and computer science\n\n**Best Practices:**\n- Cite primary sources when possible\n- Include recent literature (last 5-10 years for active fields)\n- Balance citation distribution across introduction and discussion\n- Verify all citations against original sources\n- Use reference management software (Zotero, Mendeley, EndNote)\n\n### 4. Figures and Tables\n\nCreate effective data visualizations that enhance comprehension. For detailed best practices, refer to `references/figures_tables.md`.\n\n**When to Use Tables vs. Figures:**\n- **Tables**: Precise numerical data, complex datasets, multiple variables requiring exact values\n- **Figures**: Trends, patterns, relationships, comparisons best understood visually\n\n**Design Principles:**\n- Make each table/figure self-explanatory with complete captions\n- Use consistent formatting and terminology across all display items\n- Label all axes, columns, and rows with units\n- Include sample sizes (n) and statistical annotations\n- Follow the \"one table/figure per 1000 words\" guideline\n- Avoid duplicating information between text, tables, and figures\n\n**Common Figure Types:**\n- Bar graphs: Comparing discrete categories\n- Line graphs: Showing trends over time\n- Scatterplots: Displaying correlations\n- Box plots: Showing distributions and outliers\n- Heatmaps: Visualizing matrices and patterns\n\n### 5. Reporting Guidelines by Study Type\n\nEnsure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to `references/reporting_guidelines.md`.\n\n**Key Guidelines:**\n- **CONSORT**: Randomized controlled trials\n- **STROBE**: Observational studies (cohort, case-control, cross-sectional)\n- **PRISMA**: Systematic reviews and meta-analyses\n- **STARD**: Diagnostic accuracy studies\n- **TRIPOD**: Prediction model studies\n- **ARRIVE**: Animal research\n- **CARE**: Case reports\n- **SQUIRE**: Quality improvement studies\n- **SPIRIT**: Study protocols for clinical trials\n- **CHEERS**: Economic evaluations\n\nEach guideline provides checklists ensuring all critical methodological elements are reported.\n\n### 6. Writing Principles and Style\n\nApply fundamental scientific writing principles. For detailed guidance, refer to `references/writing_principles.md`.\n\n**Clarity**:\n- Use precise, unambiguous language\n- Define technical terms and abbreviations at first use\n- Maintain logical flow within and between paragraphs\n- Use active voice when appropriate for clarity\n\n**Conciseness**:\n- Eliminate redundant words and phrases\n- Favor shorter sentences (15-20 words average)\n- Remove unnecessary qu","tagline":"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/V","category":"research","tags":["agent-skill"],"author":"brycewang-stanford","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"github candidate review","sourceDetail":"brycewang-stanford/Auto-Empirical-Research-Skills","creatorName":"brycewang-stanford","creatorUrl":"https://github.com/brycewang-stanford","sourceUrl":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. Creators can claim the listing to update ownership signals."},"stats":{"stars":3651,"forks":467,"verified_installs":0,"successful_runs":0,"total_outcomes":0,"rating":0,"review_count":0,"quality_score":48.19},"quality":{"score":83,"tier":"strong","label":"Strong","summary":"Solid option that is likely worth shortlisting for production workflows.","signals":[{"label":"GitHub stars","value":"3.7K","tone":"positive"},{"label":"Freshness","value":"6d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"MIT license","tone":"neutral"}],"warnings":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable."]},"trust":{"version":"trust-score-v5","score":63,"base_score":71,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.","recommendedAction":"Run only in a sandbox and compare close alternatives before using it for real work.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Compare alternatives before installing.","reasoning":["63/100 Trust Score v5","71/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human review.","Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":86,"weight":0.13,"status":"pass","detail":"3.7K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":83,"weight":0.08,"status":"pass","detail":"3.7K stars, 467 forks; 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require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"3.7K GitHub stars","repoActivity":"3.7K stars, 467 forks","lastPushed":"6d since push","license":"MIT license","repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","install":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Usable metadata, review docs","agentOutcomes":"No agent outcome data yet","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":true,"command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","6d since push","Financial domain: human review is required before use in a live investment workflow.","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["research","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","trust_score":63,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["research","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":71,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v5":{"version":"trust-score-v5","score":63,"base_score":71,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. 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require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"3.7K GitHub stars","repoActivity":"3.7K stars, 467 forks","lastPushed":"6d since push","license":"MIT license","repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","install":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Usable metadata, review docs","agentOutcomes":"No agent outcome data yet","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":true,"command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","6d since push","Financial domain: human review is required before use in a live investment workflow.","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["research","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","trust_score":63,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["research","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":71,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v4":{"version":"trust-score-v4","score":71,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection.","recommendedAction":"Inspect the repository, license, and recent activity before connecting it to agent workflows.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":86,"weight":0.13,"status":"pass","detail":"3.7K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":83,"weight":0.08,"status":"pass","detail":"3.7K stars, 467 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"6d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"MIT license"},{"id":"documentation","label":"README/SKILL.md completeness","score":76,"weight":0.14,"status":"info","detail":"Public metadata needs stronger README/SKILL.md context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":72,"weight":0.12,"status":"info","detail":"command execution surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":48,"weight":0.07,"status":"warn","detail":"shell or command execution, filesystem or document access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"pass","label":"GitHub adoption","detail":"3.7K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"3.7K stars, 467 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"6d since push"},{"status":"pass","label":"License clarity","detail":"MIT license"},{"status":"info","label":"README/SKILL.md completeness","detail":"Public metadata needs stronger README/SKILL.md context"},{"status":"info","label":"Dependency/runtime risk","detail":"command execution surface"},{"status":"pass","label":"Install availability","detail":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Meaningful GitHub adoption signal","Install command has no obvious high-risk pattern"],"warnings":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"],"evidence":{"stars":"3.7K GitHub stars","repoActivity":"3.7K stars, 467 forks","lastPushed":"6d since push","license":"MIT license","repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","install":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Usable metadata, review docs","agentOutcomes":"No agent outcome data yet"},"installReadiness":{"ready":true,"command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","6d since push","Financial domain: human review is required before use in a live investment workflow."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"bestFor":["research","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"outcome_stats":null,"safety":{"score":54,"level":"avoid_auto_install","label":"Avoid automatic install","safety_tier":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","summary":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","auto_install_policy":"review","reasons":["High-risk permission hints: Shell or command execution","54/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"needs_review","permission_hints":[{"id":"shell","label":"Shell or command execution","reason":"Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.","severity":"high"},{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"}],"policy_warnings":["High-risk permission hints: Shell or command execution","Permission surface may require sandboxing"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","auto_install_policy":"review","auto_install_allowed":false,"blocked":false,"human_review_required":true,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","reasons":["High-risk permission hints: Shell or command execution","54/100 agent safety score"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":75,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Permission surface: shell or command execution, filesystem or document access","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Permission surface: shell or command execution, filesystem or document access"],"warnings":["Trust score: Potentially useful, but at least one trust signal needs human inspection.","Audit score: Needs review","Agent safety gate: Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","High-risk permission hints: Shell or command execution","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","The skill mandates a minimum number of figures for each document type, which may be overly prescriptive and could lead to unnecessary resource consumption or forced visual elements that do not add value.","No explicit limitations or safe operating boundaries are documented in SKILL.md, though the skill is primarily instructional and not inherently risky.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review"],"validation_plan":["Inspect repository, README/SKILL.md, license, and recent commits before production use.","Install in an isolated workspace or sandbox with no production secrets available.","Run the smallest representative task and record files touched, commands run, network access, and outputs.","Compare the selected skill against at least one alternative when the eval status is review or failed.","Promote only after the agent reports a successful verification result and unresolved warnings are accepted."],"checks":[{"id":"task_fit","label":"Task fit","status":"pass","score":94,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate scientific-writing before installing it in an agent workflow","research","Research agents workflows; Claude Code teams; teams that value GitHub adoption signals"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing"]},{"id":"install_safety","label":"Install command safety","status":"pass","score":92,"required_for_auto_install":true,"detail":"standard package or runtime install path","evidence":["npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing"]},{"id":"trust_score","label":"Trust score","status":"warn","score":71,"required_for_auto_install":true,"detail":"Potentially useful, but at least one trust signal needs human inspection.","evidence":["Manual review","3.7K GitHub stars","MIT license"]},{"id":"audit_score","label":"Audit score","status":"warn","score":82,"required_for_auto_install":true,"detail":"Needs review","evidence":["Permission surface may require sandboxing"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"warn","score":54,"required_for_auto_install":true,"detail":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","evidence":["Test manually in an isolated workspace and compare against safer alternatives.","High-risk permission hints: Shell or command execution"]},{"id":"readme_skillmd_completeness","label":"README/SKILL.md completeness","status":"warn","score":76,"required_for_auto_install":false,"detail":"Public metadata needs stronger README/SKILL.md context","evidence":["Usable metadata, review docs"]},{"id":"license_clarity","label":"License clarity","status":"pass","score":86,"required_for_auto_install":true,"detail":"MIT license","evidence":["MIT license"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"6d since push","evidence":["6d since push"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":48,"required_for_auto_install":true,"detail":"shell or command execution, filesystem or document access","evidence":["Shell or command execution: high","Network access: medium","Filesystem access: medium"]},{"id":"alternatives","label":"Alternatives available","status":"info","score":55,"required_for_auto_install":false,"detail":"No close alternatives were found in the current shortlist.","evidence":[]}],"endpoints":{"web":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing/evals","api":"/api/agent/evals?slug=brycewang-stanford-scientific-writing","text":"/api/agent/evals?slug=brycewang-stanford-scientific-writing&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"brycewang-stanford-scientific-writing","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 structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.","category":"research","url":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing","repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","github_repo":"brycewang-stanford/Auto-Empirical-Research-Skills"},"suited_tasks":["Research agents workflows","Claude Code teams","teams that value GitHub adoption signals","Search sources","Extract claims","Synthesize findings","Chunk documents","Create embeddings"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add brycewang-stanford-scientific-writing"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"scientific-writing\" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"scientific-writing\" as a Claude Code skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"scientific-writing\" from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/brycewang-stanford-scientific-writing/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/brycewang-stanford-scientific-writing"},"trust":{"score":71,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"3.7K GitHub stars","repoActivity":"3.7K stars, 467 forks","lastPushed":"6d since push","license":"MIT license","repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","install":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Usable metadata, review docs","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["research","agent-skill"],"known_risks":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":82,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","The skill mandates a minimum number of figures for each document type, which may be overly prescriptive and could lead to unnecessary resource consumption or forced visual elements that do not add value.","No explicit limitations or safe operating boundaries are documented in SKILL.md, though the skill is primarily instructional and not inherently risky.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":83,"label":"Strong"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"6d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The skill mandates a minimum number of figures for each document type, which may be overly prescriptive and could lead to unnecessary resource consumption or forced visual elements that do not add value."],"agent_contract":{"task_input":"Use scientific-writing in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 71/100 Manual review","Audit: 82/100 Needs review","Safety: 54/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"brycewang-stanford-scientific-writing (scientific-writing)","install_command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"","skill_slug":"brycewang-stanford-scientific-writing","task":"Use scientific-writing in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing","api":"https://www.openagentskill.com/api/agent/skills/brycewang-stanford-scientific-writing","audit":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=brycewang-stanford-scientific-writing&task=Use%20scientific-writing%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20scientific-writing%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20scientific-writing%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/brycewang-stanford-scientific-writing/install","manifest":"https://www.openagentskill.com/api/registry/manifest/brycewang-stanford-scientific-writing"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"brycewang-stanford-scientific-writing","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 structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.","category":"research","url":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing","repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","github_repo":"brycewang-stanford/Auto-Empirical-Research-Skills"},"suited_tasks":["Research agents workflows","Claude Code teams","teams that value GitHub adoption signals","Search sources","Extract claims","Synthesize findings","Chunk documents","Create embeddings"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add brycewang-stanford-scientific-writing"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"scientific-writing\" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"scientific-writing\" as a Claude Code skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"scientific-writing\" from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/brycewang-stanford-scientific-writing/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/brycewang-stanford-scientific-writing"},"trust":{"score":71,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"3.7K GitHub stars","repoActivity":"3.7K stars, 467 forks","lastPushed":"6d since push","license":"MIT license","repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","install":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Usable metadata, review docs","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["research","agent-skill"],"known_risks":["Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":82,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","The skill mandates a minimum number of figures for each document type, which may be overly prescriptive and could lead to unnecessary resource consumption or forced visual elements that do not add value.","No explicit limitations or safe operating boundaries are documented in SKILL.md, though the skill is primarily instructional and not inherently risky.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":83,"label":"Strong"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"6d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The skill mandates a minimum number of figures for each document type, which may be overly prescriptive and could lead to unnecessary resource consumption or forced visual elements that do not add value."],"agent_contract":{"task_input":"Use scientific-writing in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 71/100 Manual review","Audit: 82/100 Needs review","Safety: 54/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"brycewang-stanford-scientific-writing (scientific-writing)","install_command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"","skill_slug":"brycewang-stanford-scientific-writing","task":"Use scientific-writing in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing","api":"https://www.openagentskill.com/api/agent/skills/brycewang-stanford-scientific-writing","audit":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=brycewang-stanford-scientific-writing&task=Use%20scientific-writing%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20scientific-writing%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20scientific-writing%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/brycewang-stanford-scientific-writing/install","manifest":"https://www.openagentskill.com/api/registry/manifest/brycewang-stanford-scientific-writing"}},"supply_profile":{"track":{"slug":"research","label":"Research and knowledge work","shortLabel":"Research","description":"Deep research, source comparison, literature review, RAG, knowledge search, and reports."},"scenario":{"label":"Research agents","description":"I need my agent to research a topic, compare sources, and produce a concise report.","useCases":[{"slug":"research-agents","title":"Research agents"},{"slug":"rag-knowledge","title":"RAG and knowledge"},{"slug":"github-automation","title":"GitHub automation"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":3651,"starsLabel":"3.7K","forks":467,"license":"MIT license","qualityScore":83,"trustScore":71,"auditScore":82},"maintenance":{"status":"fresh","label":"6d since push","daysSincePush":6,"lastPushedAt":"2026-09-01T14:28:11+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","The skill mandates a minimum number of figures for each document type, which may be overly prescriptive and could lead to unnecessary resource consumption or forced visual elements that do not add value.","No explicit limitations or safe operating boundaries are documented in SKILL.md, though the skill is primarily instructional and not inherently risky."]},"coverageTags":["Research","Research agents","agent-skill"]},"audit":{"audit_score":82,"risk_level":"needs_review","risk_label":"Needs review","quality_score":83,"trust_score":71,"maintenance_score":100,"security_score":77,"install_score":92,"warnings":["Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","Skill references external skills (research-lookup, scientific-schematics) that are not included in this submission, which may cause runtime failures if those skills are unavailable.","The skill mandates a minimum number of figures for each document type, which may be overly prescriptive and could lead to unnecessary resource consumption or forced visual elements that do not add value.","No explicit limitations or safe operating boundaries are documented in SKILL.md, though the skill is primarily instructional and not inherently risky.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"quality_signals":{"model":"v2","star_score":24.94,"usage_score":0,"review_score":5.25,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"rag-knowledge","title":"RAG and knowledge","url":"https://www.openagentskill.com/use-cases/rag-knowledge"},{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"},{"slug":"content-automation","title":"Content automation","url":"https://www.openagentskill.com/use-cases/content-automation"}],"stacks":[{"slug":"research-report-agent","title":"Research report agent","url":"https://www.openagentskill.com/collections/research-report-agent"},{"slug":"rag-knowledge-base","title":"RAG knowledge base","url":"https://www.openagentskill.com/collections/rag-knowledge-base"},{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"}],"install":"npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill scientific-writing","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add brycewang-stanford-scientific-writing","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"scientific-writing\" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"scientific-writing\" as a Claude Code skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"scientific-writing\" from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"brycewang-stanford-scientific-writing\",\"task\":\"Install scientific-writing\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","github_repo":"brycewang-stanford/Auto-Empirical-Research-Skills","version":"1.0.0","license":"MIT license","urls":{"web":"https://www.openagentskill.com/skills/brycewang-stanford-scientific-writing","repository":"https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/03-K-Dense-AI-claude-scientific-skills/scientific-writing","api":"/api/agent/skills/brycewang-stanford-scientific-writing","install_api":"/api/skills/brycewang-stanford-scientific-writing/install"},"meta":{"created_at":"2026-09-02T10:03:08.668385+00:00","updated_at":"2026-09-02T10:03:08.747775+00:00","agent_friendly":true}}