# 588 Scientific Skill Cae38a9f > Available Skills - Skill: `tools-only/588-scientific-skill-cae38a9f` (Agent Skill, multi-file: 3 files) - Install (CLI): `npx skillmds@latest add tools-only/588-scientific-skill-cae38a9f` - Raw SKILL.md: https://api.skillmd.com/api/skills/tools-only/588-scientific-skill-cae38a9f/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Research & Search - Author: tools-only (https://skillmd.com/u/tools-only) - Updated: 2026-09-22 - Page: https://skillmd.com/skills/tools-only/588-scientific-skill-cae38a9f --- # Available Skills **Scientific Writer is a deep research and writing tool** that combines AI-driven deep research with well-formatted written outputs. The skills below power this capability—from conducting literature searches and verifying citations to generating publication-ready documents in various formats. This document provides an overview of all skills available in the Scientific Writer CLI. ## Writing Skills ### 1. Scientific Writing **Location**: `.claude/skills/scientific-writing/` **Capabilities**: - IMRaD structure guidance (Introduction, Methods, Results, and Discussion) - Citation styles (APA, MLA, Chicago, Nature, Science, etc.) - Figure and table formatting best practices - Reporting guidelines for various study types - Writing principles for clarity, precision, and scientific rigor **References**: - `citation_styles.md`: Comprehensive guide to major citation formats - `figures_tables.md`: Best practices for presenting data - `imrad_structure.md`: Detailed guidance on each section - `reporting_guidelines.md`: Standards for clinical trials, observational studies, etc. - `writing_principles.md`: Core principles of scientific communication --- ### 2. Literature Review **Location**: `.claude/skills/literature-review/` **Capabilities**: - Conducting systematic literature searches - Database search strategies (PubMed, Web of Science, etc.) - Citation management and verification - Review synthesis and organization - PDF generation for literature summaries **References**: - `citation_styles.md`: Citation formatting guidelines - `database_strategies.md`: Effective search strategies **Scripts**: - `search_databases.py`: Automated database searching - `verify_citations.py`: Citation verification tools - `generate_pdf.py`: PDF generation for reviews **Assets**: - `review_template.md`: Template for literature review documents --- ### 3. Peer Review **Location**: `.claude/skills/peer-review/` **Capabilities**: - Identifying common issues in scientific manuscripts - Evaluating reporting standards compliance - Providing constructive feedback - Assessing methodology and statistical analysis - Checking adherence to journal guidelines **References**: - `common_issues.md`: Frequently found problems in manuscripts - `reporting_standards.md`: Required elements for different study types --- ### 4. Scholar Evaluation **Location**: `.claude/skills/scholar-evaluation/` **Capabilities**: - Systematic quantitative evaluation across 8 dimensions using ScholarEval framework - Scoring research papers, proposals, and literature reviews (1-5 scale) - Assessing publication readiness for target venues - Providing prioritized, actionable feedback with evidence-based recommendations - Identifying strengths and weaknesses across problem formulation, literature review, methodology, data collection, analysis, results, writing quality, and citations - Generating comprehensive evaluation reports with dimension scores **References**: - `evaluation_framework.md`: Detailed rubrics and quality indicators for all 8 evaluation dimensions **Scripts**: - `calculate_scores.py`: Calculate aggregate scores from dimension ratings, generate evaluation reports **Features**: - Research-backed framework (ScholarEval methodology from arXiv:2510.16234) - Quantitative scoring (1-5 scale per dimension) with weighted averaging - Dimension-specific rubrics for consistent evaluation - Publication readiness assessment - Strengths/weaknesses identification - Prioritized recommendations by impact - Contextual adjustments for work stage, venue, and discipline **When to Use**: - As a complement to peer review for quantitative assessment - Evaluating publication readiness before submission - Tracking improvement across multiple revisions - Benchmarking research quality against established criteria - Providing structured feedback for academic work **Key Guidance**: - Complements peer-review skill with systematic quantitative approach - Evaluates across 8 dimensions: Problem Formulation, Literature Review, Methodology, Data Collection, Analysis, Results, Writing Quality, Citations - Scores range from 1 (Poor) to 5 (Excellent) - Overall assessment thresholds: 4.5+ (Exceptional/Top-tier), 4.0-4.4 (Strong/Minor revisions), 3.5-3.9 (Good/Major revisions), 3.0-3.4 (Acceptable/Significant revisions), <3.0 (Needs major rework) --- ### 5. Research Grants **Location**: `.claude/skills/research-grants/` **Capabilities**: - Writing competitive research proposals for NSF, NIH, DOE, and DARPA - Agency-specific formatting and requirements - Review criteria understanding (Intellectual Merit, Broader Impacts, Significance, Innovation) - Budget preparation and justification - Specific Aims pages (NIH) - Project Summaries (NSF) - Broader Impacts strategies - Technology transition planning (DOE, DARPA) - Resubmission strategies **Focus Agencies**: - **NSF**: National Science Foundation (Intellectual Merit + Broader Impacts) - **NIH**: National Institutes of Health (R01, R21, K awards, etc.) - **DOE**: Department of Energy (Office of Science, ARPA-E, EERE) - **DARPA**: Defense Advanced Research Projects Agency (BAAs, SBIR) **References**: - `nsf_guidelines.md`: NSF proposal structure, broader impacts, review criteria - `nih_guidelines.md`: NIH mechanisms, specific aims, research strategy - `doe_guidelines.md`: DOE programs, TRLs, cost sharing, lab partnerships - `darpa_guidelines.md`: DARPA structure, Heilmeier Catechism, PM engagement - `broader_impacts.md`: Comprehensive NSF broader impacts strategies - `specific_aims_guide.md`: Complete guide to NIH Specific Aims page **Assets/Templates**: - `nsf_project_summary_template.md`: NSF Project Summary with Overview, Intellectual Merit, Broader Impacts - `nih_specific_aims_template.md`: NIH Specific Aims page template - `budget_justification_template.md`: Budget justification with agency-specific examples **Features**: - Agency-specific review criteria and scoring systems - Success rates and funding trends by agency - Timeline planning and milestone development - Budget preparation with personnel, equipment, travel, supplies - Broader impacts with measurable outcomes (NSF) - Preliminary data integration (NIH) - National laboratory collaboration (DOE) - Technology transition and commercialization (DOE, DARPA) - Resubmission and reviewer response strategies **Key Guidance**: - NSF: Equally weighted Intellectual Merit and Broader Impacts (must be substantive) - NIH: Specific Aims page is the most critical component (1 page) - DOE: Energy relevance, TRLs, cost sharing, commercialization pathway - DARPA: High-risk/high-reward, Heilmeier Catechism, PM engagement essential --- ### 6. Clinical Reports **Location**: `.claude/skills/clinical-reports/` **Capabilities**: - Writing clinical case reports following CARE (CAse REport) guidelines for journal publication - Creating diagnostic reports (radiology, pathology, laboratory) with professional standards - Documenting clinical trial data (SAE reports, Clinical Study Reports per ICH-E3) - Patient clinical documentation (SOAP notes, H&P, discharge summaries) - HIPAA compliance and de-identification verification - Regulatory compliance (FDA 21 CFR Part 11, ICH-GCP) - Medical terminology and coding standards (SNOMED-CT, LOINC, ICD-10, CPT) - Quality assurance and validation **Four Major Report Types**: 1. **Clinical Case Reports** - CARE-compliant case reports for medical journals 2. **Diagnostic Reports** - Radiology (ACR), pathology (CAP), laboratory reports 3. **Clinical Trial Reports** - SAE reports, CSRs, protocol deviations, DSMB reports 4. **Patient Documentation** - SOAP notes, H&P, discharge summaries, consultation notes **References**: - `case_report_guidelines.md`: CARE guidelines, journal requirements, de-identification - `diagnostic_reports_standards.md`: ACR/CAP/CLSI standards, structured reporting - `clinical_trial_reporting.md`: ICH-E3, CONSORT, SAE reporting, MedDRA coding - `patient_documentation.md`: SOAP, H&P, discharge summary standards - `regulatory_compliance.md`: HIPAA, 21 CFR Part 11, ICH-GCP, FDA requirements - `medical_terminology.md`: SNOMED-CT, LOINC, ICD-10, CPT, abbreviations - `data_presentation.md`: Clinical tables, figures, Kaplan-Meier curves, forest plots - `peer_review_standards.md`: Review criteria for clinical manuscripts **Templates (12 comprehensive templates)**: - `case_report_template.md`: CARE-compliant case report structure - `soap_note_template.md`: SOAP progress note format - `history_physical_template.md`: Complete H&P template - `discharge_summary_template.md`: Hospital discharge summary - `consult_note_template.md`: Consultation note format - `radiology_report_template.md`: Structured radiology report - `pathology_report_template.md`: Surgical pathology with synoptic reporting - `lab_report_template.md`: Clinical laboratory report - `clinical_trial_sae_template.md`: Serious adverse event report - `clinical_trial_csr_template.md`: Clinical study report (ICH-E3) - `quality_checklist.md`: QA checklist for all report types - `hipaa_compliance_checklist.md`: Privacy compliance verification **Scripts (8 validation and automation tools)**: - `validate_case_report.py`: Check CARE guideline compliance - `check_deidentification.py`: Scan for 18 HIPAA identifiers - `validate_trial_report.py`: Verify ICH-E3 structure - `format_adverse_events.py`: Generate AE summary tables - `generate_report_template.py`: Interactive template generator - `extract_clinical_data.py`: Parse structured clinical data - `compliance_checker.py`: Regulatory compliance verification - `terminology_validator.py`: Medical terminology and coding validation **Features**: - Comprehensive coverage of all clinical report types - Regulatory compliance built-in (HIPAA, FDA, ICH-GCP) - Professional templates based on industry standards - Automated validation and quality checking - Privacy protection and de-identification tools - Integration with scientific-writing and peer-review skills **Key Guidance**: - Always obtain informed consent for case reports - Remove all 18 HIPAA identifiers before publication - Follow CARE guidelines for case reports - Use structured reporting for diagnostic reports (BI-RADS, Lung-RADS, etc.) - Meet regulatory timelines for SAE reporting (7-day, 15-day) - Document medical necessity for billing support - Maintain ALCOA-CCEA principles for clinical trial data **When to Use**: - Publishing clinical case reports in medical journals - Writing radiology, pathology, or laboratory reports - Documenting adverse events in clinical trials - Preparing regulatory submissions (CSR, IND safety reports) - Creating patient progress notes and summaries - Ensuring HIPAA compliance in clinical documentation **Example Usage**: ### Writing a Clinical Case Report ``` > Create a clinical case report for a patient with unusual presentation of acute appendicitis ``` Claude will use the clinical-reports skill to create a CARE-compliant case report with proper de-identification. ### Generating Diagnostic Reports ``` > Generate a radiology report template for chest CT scan > Create a pathology report for breast biopsy specimen ``` Claude will use structured reporting templates (ACR, CAP) with appropriate medical terminology. ### Clinical Trial Documentation ``` > Write an SAE report for serious adverse event in phase 3 trial > Create a clinical study report outline following ICH-E3 ``` Claude will ensure regulatory compliance and proper causality assessment. ### Patient Documentation ``` > Create a SOAP note for follow-up visit > Generate a discharge summary for heart failure patient ``` Claude will use standard clinical documentation formats with billing support. ### Validation and Compliance ``` > Check this case report for HIPAA identifiers > Validate clinical trial report against ICH-E3 structure ``` Claude will use validation scripts to ensure compliance and quality. --- ### 7. Clinical Decision Support **Location**: `.claude/skills/clinical-decision-support/` **Capabilities**: - Generate professional clinical decision support (CDS) documents for medical professionals - Create patient cohort analyses stratified by biomarkers or clinical characteristics - Develop evidence-based treatment recommendation reports with GRADE methodology - Build clinical decision algorithms and pathways with TikZ flowcharts - Produce biomarker-guided therapy selection reports - Support three document types: individual treatment plans, cohort analyses, and recommendation reports - LaTeX/PDF output with compact professional formatting (0.5in margins) **Document Types**: 1. **Individual Patient Treatment Plans** - Personalized treatment protocols for specific conditions - Medication dosing, monitoring schedules, follow-up plans - HIPAA-compliant de-identification 2. **Patient Cohort Analysis** - Biomarker-stratified group analyses (e.g., PD-L1 expression levels, molecular subtypes) - Outcome comparisons with statistical testing (OS, PFS, ORR, safety) - Pharmaceutical-grade reports for clinical research 3. **Treatment Recommendation Reports** - Evidence-based clinical guidelines with GRADE grading - Treatment algorithms and decision pathways - Biomarker-guided therapy selection **References (6 comprehensive guides)**: - `patient_cohort_analysis.md`: Stratification methods, biomarkers, outcome metrics, statistical comparisons - `treatment_recommendations.md`: Evidence grading (GRADE), treatment sequencing, monitoring protocols - `clinical_decision_algorithms.md`: Decision trees, risk stratification tools, TikZ flowcharts - `biomarker_classification.md`: Genomic biomarkers, molecular subtypes, companion diagnostics, actionability frameworks - `outcome_analysis.md`: Survival analysis (Kaplan-Meier, Cox regression), response assessment (RECIST), statistical methods - `evidence_synthesis.md`: Guideline integration (NCCN, ASCO, ESMO), systematic reviews, GRADE methodology **Templates (4 LaTeX templates)**: - `cohort_analysis_template.tex`: Patient group analysis with demographics, biomarker profile, outcomes, statistics - `treatment_recommendation_template.tex`: Evidence-based guidelines with color-coded recommendation boxes - `clinical_pathway_template.tex`: TikZ flowcharts for clinical decision algorithms (landscape format) - `biomarker_report_template.tex`: Comprehensive genomic profiling reports with therapy matching **Scripts (5 analysis tools)**: - `generate_survival_analysis.py`: Kaplan-Meier curves, log-rank tests, hazard ratios, LaTeX table generation - `create_cohort_tables.py`: Baseline characteristics, efficacy outcomes, safety tables with statistical tests - `build_decision_tree.py`: Automated TikZ flowchart generation from JSON/text specifications - `biomarker_classifier.py`: Patient stratification algorithms (PD-L1, HER2, molecular subtypes) - `validate_cds_document.py`: Quality checks for evidence citations, GRADE format, HIPAA compliance **Assets**: - `example_gbm_cohort.md`: GBM molecular subtype analysis example (Mesenchymal-Immune-Active vs Other) - `recommendation_strength_guide.md`: GRADE framework guide with examples and wording templates - `color_schemes.tex`: Standardized color definitions for recommendations, urgency, biomarkers **Features**: - **Evidence-Based**: GRADE methodology for recommendation strength and evidence quality - **Biomarker Integration**: Genomic alterations, expression profiles, molecular subtypes - **Statistical Rigor**: Proper hypothesis testing, confidence intervals, survival analysis - **Professional Output**: Compact LaTeX/PDF matching pharmaceutical industry standards - **Guideline Concordance**: Integration with NCCN, ASCO, ESMO, AHA/ACC guidelines - **Clinical Actionability**: Tier-based classification (FDA-approved, investigational, VUS) **When to Use**: - Creating treatment plans for individual patients - Analyzing patient cohorts stratified by biomarkers - Generating evidence-based clinical recommendations - Producing pharmaceutical-grade clinical analysis documents - Developing clinical pathways and decision algorithms - Reporting biomarker-guided therapy selection **Example Usage**: ### Individual Treatment Plan ``` > Create a treatment plan for a 55-year-old patient with newly diagnosed type 2 diabetes and hypertension ``` Claude will generate a personalized treatment protocol with monitoring and follow-up. ### Patient Cohort Analysis ``` > Analyze a cohort of 45 NSCLC patients stratified by PD-L1 expression (<1%, 1-49%, ≥50%) including ORR, PFS, and OS outcomes > Generate cohort analysis for 30 GBM patients classified into mesenchymal-immune-active and proneural molecular subtypes with treatment outcomes ``` Claude will create comprehensive cohort reports with biomarker profiles, outcome comparisons, statistical analysis, and clinical recommendations. ### Treatment Recommendation Report ``` > Create evidence-based treatment recommendations for HER2-positive metastatic breast cancer including first-line and second-line options > Generate treatment algorithm for heart failure management based on NYHA class and ejection fraction with GDMT protocols ``` Claude will develop recommendation reports with GRADE-graded options, decision algorithms, and monitoring protocols. ### Biomarker Report ``` > Create a genomic profiling report for NSCLC patient with EGFR L858R mutation including FDA-approved therapies and clinical trial matching ``` Claude will generate biomarker reports with tier-based actionability and personalized treatment recommendations. ### Validation ``` > Validate this cohort analysis document for evidence citations and statistical reporting completeness ``` Claude will use validation scripts to check quality and compliance. --- ### 8. LaTeX Research Posters (DEFAULT) **Location**: `.claude/skills/latex-posters/` **⚠️ This is the DEFAULT skill for all poster requests.** Use this unless user explicitly requests PPTX/PowerPoint format. **Capabilities**: - Creating professional research posters using LaTeX (beamerposter, tikzposter, baposter) - AI-powered visual element generation (generate figures BEFORE assembling poster) - Conference poster design and layout - Full-page poster templates with proper spacing - Color schemes and visual design principles - Typography and readability optimization - PDF generation and quality control - Accessibility and inclusive design - Poster size configuration (A0, A1, 36×48", etc.) - Overflow prevention and content density guidelines **References**: - `latex_poster_packages.md`: Detailed comparison of beamerposter, tikzposter, and baposter - `poster_design_principles.md`: Typography, color theory, visual hierarchy, and accessibility - `poster_layout_design.md`: Grid systems, spatial organization, and visual flow - `poster_content_guide.md`: Content strategy, writing style, and section-specific guidance **Scripts**: - `review_poster.sh`: Automated PDF quality check script **Assets**: - `beamerposter_template.tex`: Classic academic poster template - `tikzposter_template.tex`: Modern, colorful poster template - `baposter_template.tex`: Structured multi-column poster template - `poster_quality_checklist.md`: Comprehensive pre-printing checklist **Features**: - **AI-Powered Visual Generation**: Generate all figures using scientific-schematics before creating poster - **Poster-Size Font Requirements**: Guidelines for readable text in AI-generated graphics (72pt+ for key numbers) - **Overflow Prevention**: Content limits (5-6 sections max, 300-800 words) to prevent cutoff - Ensures posters span the full page without excessive margins - PDF review and quality control guidelines with overflow check - Automated checking scripts for page size, fonts, and images - Reduced-scale print testing instructions - Color contrast and accessibility verification - Common issues troubleshooting guide **For PPTX/PowerPoint posters**: Use `pptx-posters` skill ONLY when user explicitly requests PPTX format. Located at `.claude/skills/pptx-posters/`. --- ### 9. Scientific Slides and Presentations **Location**: `.claude/skills/scientific-slides/` **Capabilities**: - Create stunning PDF slide decks using Nano Banana Pro AI - Structure presentations for different contexts (5-60 minute talks) - AI-generated slides with publication-quality visuals - Optimize data visualizations for presentation context - Timing and pacing guidance with practice strategies - Visual review workflow with automated validation - Integration with research-lookup for proper citations **Talk Types Supported**: - **Conference talks** (10-20 min): Brief, focused on key findings - **Academic seminars** (45-60 min): Comprehensive, detailed methods - **Thesis defenses** (45-60 min): Complete dissertation overview - **Grant pitches** (15-20 min): Emphasis on significance and feasibility - **Journal clubs** (20-45 min): Critical analysis of published work - **Lightning talks** (5 min): Ultra-focused single message **References**: - `presentation_structure.md`: Structure for all talk types, timing allocation, narrative arc - `slide_design_principles.md`: Typography, color theory, layout, accessibility - `data_visualization_slides.md`: Simplifying figures for presentations - `talk_types_guide.md`: Specific guidance for each presentation type - `visual_review_workflow.md`: PDF to images, systematic inspection, iteration **Assets**: - `timing_guidelines.md`: Comprehensive timing, pacing, and practice strategies **Scripts**: - `validate_presentation.py`: Check slide count, timing, fonts, file size - `pdf_to_images.py`: Convert PDF to images for visual inspection **Features**: - **Nano Banana Pro AI**: Generate stunning PDF slides with AI-powered visuals - **Research-lookup integration**: Automatically gather citations for background and discussion - **Visual validation workflow**: Convert to images, inspect systematically, iterate - **Timing guidance**: One-slide-per-minute rule with adjustments - **Design principles**: Minimal text (24pt+), high contrast, color-blind safe - **Practice strategies**: Systematic rehearsal with timing checkpoints **When to Use**: - Creating any scientific presentation or slide deck - Preparing conference talks or research seminars - Developing thesis defense presentations - Making grant pitch slides - Building lecture or tutorial presentations - Converting papers to presentation format **Example Usage**: ### Conference Talk ``` > Create a 15-minute conference presentation on my machine learning research ``` Claude will use research-lookup to gather citations, structure the talk, and generate stunning PDF slides using Nano Banana Pro AI. ### Seminar Presentation ``` > Help me build a 45-minute seminar on CRISPR gene editing with comprehensive methods ``` Claude will structure a detailed academic seminar with proper citations and timing guidance. ### Thesis Defense ``` > Create slides for my dissertation defense covering three studies ``` Claude will structure a comprehensive defense presentation following academic standards. ### Visual Validation ``` > Convert my presentation to images and review for layout issues ``` Claude will use scripts to convert PDF to images and systematically inspect for text overflow, overlap, and design issues. ### Timing Check ``` > Validate my 20-slide presentation for a 15-minute talk ``` Claude will check if slide count is appropriate and provide timing recommendations. **Key Principles**: - **Structure**: Spend 40-50% of time on results, follow clear story arc - **Design**: Minimal text, large fonts (24pt+), one idea per slide - **Citations**: Use research-lookup to gather 8-12 papers for proper context - **Timing**: Practice 3-5 times, set checkpoints, never skip conclusions - **Validation**: Visual review workflow to catch overflow and overlap issues --- ### 10. Scientific Schematics and Diagrams **Location**: `.claude/skills/scientific-schematics/` **Capabilities**: - Create methodology flowcharts (CONSORT diagrams for clinical trials) - Generate circuit diagrams and electrical schematics - Visualize biological pathways and signaling cascades - Design system architecture and block diagrams - Create process flow diagrams and decision trees - Network diagrams and graph visualizations - Publication-quality vector graphics with TikZ/LaTeX - Programmatic diagram generation with Python (Schemdraw, NetworkX, Matplotlib) **References**: - `tikz_guide.md`: Comprehensive TikZ syntax, positioning, styles, and techniques - `diagram_types.md`: Catalog of scientific diagram types with use cases and examples - `best_practices.md`: Publication standards, accessibility, and colorblind-safe design - `python_libraries.md`: Guide to Schemdraw, NetworkX, and Matplotlib for programmatic generation **Scripts**: - `generate_flowchart.py`: Convert text descriptions to TikZ flowcharts - `circuit_generator.py`: Generate circuit diagrams using Schemdraw - `pathway_diagram.py`: Create biological pathway diagrams with Matplotlib - `compile_tikz.py`: Standalone TikZ compilation utility (PDF/PNG output) **Assets**: - `tikz_styles.tex`: Reusable style definitions with Okabe-Ito colorblind-safe palette - `flowchart_template.tex`: CONSORT-style methodology flowchart template - `circuit_template.tex`: Electrical circuit diagram template with CircuitikZ - `pathway_template.tex`: Biological pathway diagram template - `block_diagram_template.tex`: System architecture diagram template **Features**: - Colorblind-safe Okabe-Ito color palette throughout - Vector graphics for infinite scalability - LaTeX integration for consistent typography - Automated flowchart generation from numbered lists - Publication-ready output (PDF, SVG, PNG) - Accessible design following WCAG standards - Grayscale compatibility verification **Use Cases**: - **CONSORT diagrams**: Participant flow for clinical trials - **Electronics papers**: Circuit schematics and signal processing diagrams - **Biology papers**: Signaling cascades, metabolic pathways, gene networks - **Engineering papers**: System architecture, data flow, block diagrams - **Methodology sections**: Study design, data processing pipelines - **Conceptual frameworks**: Process flows, decision trees --- ### 11. Market Research Reports **Location**: `.claude/skills/market-research-reports/` **Capabilities**: - Generate comprehensive market research reports (50+ pages) in consulting-firm style - Professional LaTeX formatting with custom `market_research.sty` style package - Extensive visual generation (25-30 diagrams per report) using scientific-schematics - Multi-framework strategic analysis (Porter's Five Forces, PESTLE, SWOT, BCG Matrix) - TAM/SAM/SOM market sizing with data-driven projections - Competitive landscape analysis with positioning matrices - Risk assessment with heatmaps and mitigation frameworks - Strategic recommendations with implementation roadmaps - Investment thesis development with financial projections **References**: - `report_structure_guide.md`: Detailed section-by-section content requirements for all 11 chapters - `visual_generation_guide.md`: Complete prompts for generating all 28 standard report visuals - `data_analysis_patterns.md`: Templates for Porter's, PESTLE, SWOT, BCG Matrix, TAM/SAM/SOM **Scripts**: - `generate_market_visuals.py`: Batch generate all standard market report visuals with a single command **Assets**: - `market_research.sty`: LaTeX style package with professional colors, box environments, and formatting - `market_report_template.tex`: Complete 50+ page LaTeX template with all chapters pre-structured - `FORMATTING_GUIDE.md`: Quick reference for box environments, colors, tables, and styling **Features**: - **Comprehensive Length**: Reports designed for 50+ pages with no token constraints - **Visual Density**: 25-30 generated images/diagrams (approximately 1 per 2 pages) - **Data-Driven**: Deep integration with research-lookup for market data and statistics - **Multi-Framework**: Porter's Five Forces, PESTLE, SWOT, BCG Matrix, Value Chain Analysis - **Professional Formatting**: Consulting-firm quality typography, colors, and layout - **Actionable Recommendations**: Strategic focus with prioritization matrices and implementation roadmaps **Report Structure (50+ Pages)**: - Front Matter: Cover page, TOC, Executive Summary (5 pages) - Core Analysis: Market Overview, Market Size & Growth, Industry Drivers, Competitive Landscape, Customer Analysis, Technology Landscape, Regulatory Environment, Risk Analysis (35 pages) - Strategic Recommendations: Opportunities, Implementation Roadmap, Investment Thesis (10 pages) - Back Matter: Methodology, Data Tables, Company Profiles, References (5 pages) **When to Use**: - Creating comprehensive market analysis for investment decisions - Developing industry reports for strategic planning - Analyzing competitive landscapes and market dynamics - Conducting market sizing exercises (TAM/SAM/SOM) - Evaluating market entry opportunities - Preparing due diligence materials for M&A activities - Creating thought leadership content - Developing go-to-market strategy documentation **Example Usage**: ### Generate Market Research Report ``` > Create a comprehensive market research report on the Electric Vehicle Charging Infrastructure market ``` Claude will use the market-research-reports skill to create a 50+ page professional report with extensive visuals. ### Market Sizing Analysis ``` > Analyze the AI in Healthcare market with TAM/SAM/SOM breakdown and 10-year projections ``` Claude will provide comprehensive market sizing with growth trajectory charts and regional breakdowns. ### Competitive Landscape Report ``` > Create a competitive landscape analysis for the Cloud Computing market including Porter's Five Forces and positioning matrix ``` Claude will generate competitive analysis with strategic frameworks and visualizations. --- ## Document Manipulation Skills ### 12. MarkItDown - Universal File to Markdown Converter **Location**: `.claude/skills/markitdown/` **Capabilities**: - Convert 15+ file formats to Markdown (PDF, DOCX, PPTX, XLSX, images, audio, etc.) - AI-enhanced image descriptions using advanced vision models - OCR for scanned documents and images - Speech-to-text transcription for audio files - YouTube video transcription extraction - Batch processing with parallel execution - Azure Document Intelligence integration for complex PDFs - Plugin system for custom converters **References**: - `api_reference.md`: Complete API documentation and class references - `file_formats.md`: Format-specific conversion guides and best practices **Scripts**: - `batch_convert.py`: Parallel batch conversion of multiple files - `convert_with_ai.py`: AI-enhanced conversions with custom prompts - `convert_literature.py`: Scientific literature conversion with metadata extraction **Assets**: - `example_usage.md`: Comprehensive examples for common use cases **Features**: - Token-efficient Markdown output optimized for LLM processing - Supports optional dependencies for specific file formats - Custom prompts for scientific, medical, and data visualization contexts - Metadata extraction and organization - Error handling and robust batch processing - Integration with scientific workflows **Source**: https://github.com/microsoft/markitdown (MIT License) --- ### 13. DOCX (Word Documents) **Location**: `.claude/skills/document-skills/docx/` **Capabilities**: - Create and edit Word documents programmatically - Work with OOXML format - Manage comments and track changes - Validate document structure - Handle templates **Scripts**: - `document.py`: Core document manipulation - `utilities.py`: Helper functions - OOXML validation and manipulation tools **References**: - `docx-js.md`: JavaScript integration guide - `ooxml.md`: OOXML format specification --- ### 14. PDF Documents **Location**: `.claude/skills/document-skills/pdf/` **Capabilities**: - Extract text and metadata from PDFs - Check bounding boxes and layout - Work with fillable PDF forms - Convert PDFs to images - Extract form field information **Scripts**: - `check_bounding_boxes.py`: Analyze PDF layout - `check_fillable_fields.py`: Identify form fields - `fill_fillable_fields.py`: Populate PDF forms - `convert_pdf_to_images.py`: PDF to image conversion - `extract_form_field_info.py`: Extract form metadata **References**: - `forms.md`: Working with PDF forms - `reference.md`: PDF manipulation reference --- ### 15. PPTX (PowerPoint Presentations) **Location**: `.claude/skills/document-skills/pptx/` **Capabilities**: - Create and modify PowerPoint presentations - Convert HTML to PowerPoint - Manage slides and layouts - Work with OOXML format - Generate thumbnails **Scripts**: - `html2pptx.js`: HTML to PowerPoint conversion - `inventory.py`: Presentation inventory management - `rearrange.py`: Slide reordering - `replace.py`: Content replacement - `thumbnail.py`: Thumbnail generation **References**: - `html2pptx.md`: HTML conversion guide - `ooxml.md`: OOXML format specification --- ### 16. XLSX (Excel Spreadsheets) **Location**: `.claude/skills/document-skills/xlsx/` **Capabilities**: - Read and write Excel files - Manage formulas and calculations - Handle complex spreadsheet operations - Recalculate formulas **Scripts**: - `recalc.py`: Formula recalculation utility --- ## How Skills Are Used When you interact with the Scientific Writer CLI, Claude automatically: 1. **Detects relevant skills**: Based on your request, Claude identifies which skills to use 2. **Loads resources**: Accesses reference materials, scripts, and templates 3. **Applies best practices**: Follows the guidelines and standards in each skill 4. **Executes tools**: Uses scripts when needed for document manipulation or data processing ## Skill Integration All skills are loaded from the `.claude/skills/` directory and are automatically available when you run the CLI. You don't need to manually select or activate them - Claude will use the appropriate skills based on your requests. ## Example Usage ### Using Scientific Writing Skill ``` > Help me structure a methods section for a randomized controlled trial ``` Claude will use the scientific-writing skill to provide IMRaD-compliant guidance. ### Using Literature Review Skill ``` > Create a literature review on CRISPR gene editing in agriculture ``` Claude will use literature-review skill to structure a comprehensive review. ### Using Document Skills ``` > Extract the data from Table 1 in results.pdf and create a summary ``` Claude will use the PDF skill to extract data and potentially the XLSX skill to organize it. ### Using MarkItDown Skill ``` > Convert all PDFs in the literature folder to Markdown ``` Claude will use the markitdown skill to batch convert files. ``` > Convert this PowerPoint presentation to Markdown with AI-generated descriptions ``` Claude will use markitdown with AI enhancement for detailed image descriptions. ### Using Peer Review Skill ``` > Review my discussion section for logical flow and adherence to reporting standards ``` Claude will use the peer-review skill to provide constructive feedback. ### Using Scholar Evaluation Skill ``` > Evaluate this paper using the ScholarEval framework ``` Claude will use the scholar-evaluation skill to provide systematic quantitative evaluation across 8 dimensions. ``` > Assess publication readiness for Nature Machine Intelligence ``` Claude will evaluate the paper and provide scores and recommendations for submission readiness. ### Using Research Grants Skill ``` > Help me write an NSF proposal for my computational neuroscience research ``` Claude will use the research-grants skill to provide NSF-specific guidance. ``` > I need to draft NIH Specific Aims for my cancer immunotherapy R01 ``` Claude will help structure your 1-page specific aims using NIH best practices. ``` > What should I include in broader impacts for an NSF Materials Research proposal? ``` Claude will provide substantive broader impacts strategies aligned with NSF criteria. ### Using Scientific Schematics Skill ``` > Create a CONSORT flowchart for my clinical trial showing participant flow from screening (n=500) through randomization to final analysis ``` Claude will generate a methodology flowchart following CONSORT guidelines. ``` > Generate a circuit diagram for an RC low-pass filter ``` Claude will create an electrical circuit schematic using CircuitikZ or Schemdraw. ``` > Create a biological pathway diagram showing the MAPK signaling cascade from receptor to gene expression ``` Claude will visualize the signaling pathway with properly styled proteins and activation arrows. ``` > Design a block diagram showing the architecture of my data acquisition system with sensor, ADC, microcontroller, and wireless transmission ``` Claude will create a system architecture diagram with labeled components and data flow. ### 11. Venue Templates **Location**: `.claude/skills/venue-templates/` **Capabilities**: - Query LaTeX templates for 50+ major journals and conferences - Access grant proposal templates (NSF, NIH, DOE, DARPA) - Retrieve poster templates for academic conferences - View formatting requirements and submission guidelines - Customize templates with author and project information - Validate document formatting against venue requirements **References**: - `journals_formatting.md`: Requirements for Nature, Science, PLOS, IEEE, ACM, Cell Press, and other major journals - `conferences_formatting.md`: ML, CS, biology conference paper formats (NeurIPS, ICML, ICLR, CVPR, CHI, ISMB, etc.) - `posters_guidelines.md`: Poster design, sizes, layout principles, and best practices - `grants_requirements.md`: Federal and private grant proposal formats (NSF, NIH, DOE, DARPA) **Scripts**: - `query_template.py`: Search and retrieve templates by venue name or keywords - `customize_template.py`: Customize templates with author information - `validate_format.py`: Check document compliance with venue requirements **Assets**: - `journals/`: LaTeX templates for Nature, Science, PLOS ONE, NeurIPS, and other major venues - `posters/`: Academic poster templates (beamerposter, tikzposter, baposter) - `grants/`: Grant proposal templates (NSF, NIH Specific Aims, DOE, DARPA) **Features**: - Comprehensive formatting guidelines for major publication venues - Ready-to-use LaTeX templates with proper structure - Helper scripts for template discovery and customization - Formatting validation tools - Integration with scientific writing workflow **Use Cases**: - **Journal submission**: Get proper formatting for Nature, Science, PLOS, IEEE, ACM journals - **Conference papers**: Templates for NeurIPS, ICML, CVPR, CHI, and other major conferences - **Research posters**: Professional poster templates for A0, A1, and US sizes - **Grant proposals**: NSF, NIH R01, DOE, DARPA proposal templates with requirements - **Format validation**: Check if your document meets venue specifications **Example Usage**: ### Query Template for a Journal ``` > I need to submit to Nature ``` Claude will provide the Nature article template and formatting requirements. ### Get Conference Paper Template ``` > Show me the NeurIPS paper template ``` Claude will provide the NeurIPS conference paper template with anonymization guidelines. ### Grant Proposal Template ``` > I need an NSF proposal template ``` Claude will provide the NSF proposal template with all required sections and formatting. ### Conference Poster ``` > Create a research poster for ISMB conference ``` Claude will provide poster template and size specifications for the conference. ### Format Validation ``` > Check if my paper meets Nature's requirements ``` Claude can guide you through using the validation script to check formatting compliance. --- ## Adding Custom Skills To add your own skills: 1. …(truncated)