Added ISO 13485 certification prep skill

docs/scientific-skills.md

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 - **UniProt** - Universal Protein Resource for protein sequences, annotations, and functional information (UniProtKB/Swiss-Prot reviewed entries, TrEMBL unreviewed entries) with REST API access for search, retrieval, ID mapping, and batch operations across 200+ databases
 - **USPTO** - United States Patent and Trademark Office data access including patent searches, trademark lookups, patent examination history (PEDS), office actions, assignments, citations, and litigation records; supports PatentSearch API (ElasticSearch-based patent search), TSDR (Trademark Status & Document Retrieval), Patent/Trademark Assignment APIs, and additional specialized APIs for comprehensive IP analysis
 - **ZINC** - Free database of commercially-available compounds for virtual screening and drug discovery maintained by UCSF. Contains 230M+ purchasable compounds from 100+ vendors in ready-to-dock 3D formats (SDF, MOL2) with pre-computed conformers. Provides compound information including chemical structures, vendor information and pricing, physicochemical properties (molecular weight, logP, H-bond donors/acceptors, rotatable bonds), drug-likeness filters (Lipinski's Rule of Five, Veber rules), and substructure search capabilities. Features multiple compound subsets (drug-like, lead-like, fragment-like, natural products), downloadable subsets for specific screening campaigns, and integration with molecular docking software (AutoDock, DOCK, Glide). Supports structure-based and ligand-based virtual screening workflows. Use cases: virtual screening campaigns, lead identification, compound library design, high-throughput docking, and drug discovery research
+- **bioRxiv** - Preprint server for the life sciences providing Python-based tools for searching and retrieving preprints. Supports comprehensive searches by keywords, authors, date ranges, and subject categories, returning structured JSON metadata including titles, abstracts, DOIs, and citation information. Features PDF downloads for full-text analysis, filtering by bioRxiv subject categories (neuroscience, bioinformatics, genomics, etc.), and integration with literature review workflows. Use cases: tracking recent preprints, conducting systematic literature reviews, analyzing research trends, monitoring publications by specific authors, and staying current with emerging research before formal peer review
 
 ## Scientific Integrations
 
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 - **NeuroKit2** - Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Key features include: automated signal processing pipelines (cleaning, peak detection, delineation, quality assessment), heart rate variability analysis across time/frequency/nonlinear domains (SDNN, RMSSD, LF/HF, DFA, entropy measures), EEG analysis (frequency band power, microstates, source localization), autonomic nervous system assessment (sympathetic indices, respiratory sinus arrhythmia), comprehensive complexity measures (25+ entropy types, 15+ fractal dimensions, Lyapunov exponents), event-related and interval-related analysis modes, epoch creation and averaging for stimulus-locked responses, multi-signal integration with unified workflows, and extensive signal processing utilities (filtering, decomposition, peak correction, spectral analysis). Includes modular reference documentation across 12 specialized domains. Use cases: heart rate variability for cardiovascular health assessment, EEG microstates for consciousness studies, electrodermal activity for emotion research, respiratory variability analysis, psychophysiology experiments, affective computing, stress monitoring, sleep staging, autonomic dysfunction assessment, biofeedback applications, and multi-modal physiological signal integration for comprehensive human state monitoring
 - **PyHealth** - Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. Provides specialized tools for electronic health records (EHR), physiological signals, medical imaging, and clinical text analysis. Key features include: 10+ healthcare datasets (MIMIC-III/IV, eICU, OMOP, sleep EEG, COVID-19 CXR), 20+ predefined clinical prediction tasks (mortality, hospital readmission, length of stay, drug recommendation, sleep staging, EEG analysis), 33+ models (Logistic Regression, MLP, CNN, RNN, Transformer, GNN, plus healthcare-specific models like RETAIN, SafeDrug, GAMENet, StageNet), comprehensive data processing (sequence processors, signal processors, medical code translation between ICD-9/10, NDC, RxNorm, ATC systems), training/evaluation utilities (Trainer class, fairness metrics, calibration, uncertainty quantification), and interpretability tools (attention visualization, SHAP, ChEFER). 3x faster than pandas for healthcare data processing. Use cases: ICU mortality prediction, hospital readmission risk assessment, safe medication recommendation with drug-drug interaction constraints, sleep disorder diagnosis from EEG signals, medical code standardization and translation, clinical text to ICD coding, length of stay estimation, and any clinical ML application requiring interpretability, fairness assessment, and calibrated predictions for healthcare deployment
 
+### Clinical Documentation & Decision Support
+- **Clinical Decision Support** - Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings. Includes patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Features GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration (genomic alterations, gene expression signatures, IHC markers), and regulatory compliance. Use cases: pharmaceutical cohort reporting, clinical guideline development, comparative effectiveness analyses, treatment algorithm creation, and evidence synthesis for drug development
+- **Clinical Reports** - Write comprehensive clinical reports following established guidelines and standards. Covers case reports (CARE guidelines), diagnostic reports (radiology, pathology, laboratory), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP notes, H&P, discharge summaries). Includes templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools. Use cases: journal case reports, diagnostic findings documentation, clinical trial reporting, patient progress notes, and regulatory submissions
+- **Treatment Plans** - Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Features SMART goal frameworks, evidence-based interventions, HIPAA compliance, and professional formatting. Use cases: individualized patient care plans, rehabilitation programs, psychiatric treatment plans, surgical care pathways, and pain management protocols
+
 ### Neuroscience & Electrophysiology
 - **Neuropixels-Analysis** - Comprehensive toolkit for analyzing Neuropixels high-density neural recordings using SpikeInterface, Allen Institute, and International Brain Laboratory (IBL) best practices. Supports the full workflow from raw data to publication-ready curated units. Key features include: data loading from SpikeGLX, Open Ephys, and NWB formats, preprocessing pipelines (highpass filtering, phase shift correction for Neuropixels 1.0, bad channel detection, common average referencing), motion/drift estimation and correction (kilosort_like and nonrigid_accurate presets), spike sorting integration (Kilosort4 GPU, SpykingCircus2, Mountainsort5 CPU), comprehensive postprocessing (waveform extraction, template computation, spike amplitudes, correlograms, unit locations), quality metrics computation (SNR, ISI violations, presence ratio, amplitude cutoff, drift metrics), automated curation using Allen Institute and IBL criteria with configurable thresholds, AI-assisted visual curation for uncertain units using Claude API, and export to Phy for manual review or NWB for sharing. Supports Neuropixels 1.0 (960 electrodes, 384 channels) and Neuropixels 2.0 (single and 4-shank configurations). Use cases: extracellular electrophysiology analysis, spike sorting from silicon probes, neural population recordings, systems neuroscience research, unit quality assessment, publication-ready neural data processing, and integration of AI-assisted curation for borderline units
 
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 - **HypoGeniC** - Automated hypothesis generation and testing using large language models to accelerate scientific discovery. Provides three frameworks: HypoGeniC (data-driven hypothesis generation from observational data), HypoRefine (synergistic approach combining literature insights with empirical patterns through an agentic system), and Union methods (mechanistic combination of literature and data-driven hypotheses). Features iterative refinement that improves hypotheses by learning from challenging examples, Redis caching for API cost reduction, and customizable YAML-based prompt templates. Includes command-line tools for generation (hypogenic_generation) and testing (hypogenic_inference). Research applications have demonstrated 14.19% accuracy improvement in AI-content detection and 7.44% in deception detection. Use cases: deception detection in reviews, AI-generated content identification, mental stress detection, exploratory research without existing literature, hypothesis-driven analysis in novel domains, and systematic exploration of competing explanations
 
 ### Scientific Communication & Publishing
+- **Citation Management** - Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata from multiple sources (CrossRef, PubMed, arXiv), validate citations, and generate properly formatted BibTeX entries. Features include converting DOIs, PMIDs, or arXiv IDs to BibTeX, cleaning and formatting bibliography files, finding highly cited papers, checking for duplicates, and ensuring consistent citation formatting. Use cases: building bibliographies for manuscripts, verifying citation accuracy, citation deduplication, and maintaining reference databases
 - **Generate Image** - AI-powered image generation and editing for scientific illustrations, schematics, and visualizations using OpenRouter's image generation models. Supports multiple models including google/gemini-3-pro-image-preview (high quality, recommended default) and black-forest-labs/flux.2-pro (fast, high quality). Key features include: text-to-image generation from detailed prompts, image editing capabilities (modify existing images with natural language instructions), automatic base64 encoding/decoding, PNG output with configurable paths, and comprehensive error handling. Requires OpenRouter API key (via .env file or environment variable). Use cases: generating scientific diagrams and illustrations, creating publication-quality figures, editing existing images (changing colors, adding elements, removing backgrounds), producing schematics for papers and presentations, visualizing experimental setups, creating graphical abstracts, and generating conceptual illustrations for scientific communication
+- **LaTeX Posters** - Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication with layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices. Features compliance with conference size requirements (A0, A1, 36×48"), complex multi-column layouts, and integration of figures, tables, equations, and citations. Use cases: conference poster sessions, thesis defenses, symposia presentations, and research group templates
+- **Market Research Reports** - Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter's Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix. Use cases: investment decisions, strategic planning, competitive landscape analysis, market sizing, and market entry evaluation
 - **Paper-2-Web** - Autonomous pipeline for transforming academic papers into multiple promotional formats using the Paper2All system. Converts LaTeX or PDF papers into: (1) Paper2Web - interactive, layout-aware academic homepages with responsive design, interactive figures, and mobile support; (2) Paper2Video - professional presentation videos with slides, narration, cursor movements, and optional talking-head generation using Hallo2; (3) Paper2Poster - print-ready conference posters with custom dimensions, professional layouts, and institution branding. Supports GPT-4/GPT-4.1 models, batch processing, QR code generation, multi-language content, and quality assessment metrics. Use cases: conference materials, video abstracts, preprint enhancement, research promotion, poster sessions, and academic website creation
 - **Perplexity Search** - AI-powered web search using Perplexity models via LiteLLM and OpenRouter for real-time, web-grounded answers with source citations. Provides access to multiple Perplexity models: Sonar Pro (general-purpose, best cost-quality balance), Sonar Pro Search (most advanced agentic search with multi-step reasoning), Sonar (cost-effective for simple queries), Sonar Reasoning Pro (advanced step-by-step analysis), and Sonar Reasoning (basic reasoning). Key features include: single OpenRouter API key setup (no separate Perplexity account), real-time access to current information beyond training data cutoff, comprehensive query design guidance (domain-specific patterns, time constraints, source preferences), cost optimization strategies with usage monitoring, programmatic and CLI interfaces, batch processing support, and integration with other scientific skills. Installation uses uv pip for LiteLLM, with detailed setup, troubleshooting, and security documentation. Use cases: finding recent scientific publications and research, conducting literature searches across domains, verifying facts with source citations, accessing current developments in any field, comparing technologies and approaches, performing domain-specific research (biomedical, clinical, technical), supplementing PubMed searches with real-time web results, and discovering latest developments post-database indexing
+- **PPTX Posters** - Create professional research posters using PowerPoint/HTML formats for researchers who prefer WYSIWYG tools over LaTeX. Features design principles, layout templates, quality checklists, and export guidance for poster sessions. Use cases: conference posters when LaTeX is not preferred, quick poster creation, and collaborative poster design
+- **Scientific Schematics** - Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review with document-type-specific thresholds (journal: 8.5/10, conference: 8.0/10, poster: 7.0/10). Specializes in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations. Features natural language input, automatic quality assessment, and publication-ready output. Use cases: creating figures for papers, generating workflow diagrams, visualizing experimental designs, and producing graphical abstracts
+- **Scientific Slides** - Build slide decks and presentations for research talks using PowerPoint and LaTeX Beamer. Features slide structure, design templates, timing guidance, and visual validation. Emphasizes visual engagement with minimal text, research-backed content with proper citations, and story-driven narrative. Use cases: conference presentations, academic seminars, thesis defenses, grant pitches, and professional talks
+- **Venue Templates** - Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). Provides ready-to-use templates and detailed specifications for successful academic submissions. Use cases: manuscript preparation, conference papers, research posters, and grant proposals with venue-specific formatting
 
 ### Document Processing & Conversion
 - **MarkItDown** - Python utility for converting 20+ file formats to Markdown optimized for LLM processing. Converts Office documents (PDF, DOCX, PPTX, XLSX), images with OCR, audio with transcription, web content (HTML, YouTube transcripts, EPUB), and structured data (CSV, JSON, XML) while preserving document structure (headings, lists, tables, hyperlinks). Key features include: Azure Document Intelligence integration for enhanced PDF table extraction, LLM-powered image descriptions using GPT-4o, batch processing with ZIP archive support, modular installation for specific formats, streaming approach without temporary files, and plugin system for custom converters. Supports Python 3.10+. Use cases: preparing documents for RAG systems, extracting text from PDFs and Office files, transcribing audio to text, performing OCR on images and scanned documents, converting YouTube videos to searchable text, processing HTML and EPUB books, converting structured data to readable format, document analysis pipelines, and LLM training data preparation
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 - **PyLabRobot** - Hardware-agnostic, pure Python SDK for automated and autonomous laboratories. Provides unified interface for controlling liquid handling robots (Hamilton STAR/STARlet, Opentrons OT-2, Tecan EVO), plate readers (BMG CLARIOstar), heater shakers, incubators, centrifuges, pumps, and scales. Key features include: modular resource management system for plates, tips, and containers with hierarchical deck layouts and JSON serialization; comprehensive liquid handling operations (aspirate, dispense, transfer, serial dilutions, plate replication) with automatic tip and volume tracking; backend abstraction enabling hardware-agnostic protocols that work across different robots; ChatterboxBackend for protocol simulation and testing without hardware; browser-based visualizer for real-time 3D deck state visualization; cross-platform support (Windows, macOS, Linux, Raspberry Pi); and integration capabilities for multi-device workflows combining liquid handlers, analytical equipment, and material handling devices. Use cases: automated sample preparation, high-throughput screening, serial dilution protocols, plate reading workflows, laboratory protocol development and validation, robotic liquid handling automation, and reproducible laboratory automation with state tracking and persistence
 
 ### Tool Discovery & Research Platforms
+- **Get Available Resources** - Detect available computational resources and generate strategic recommendations for scientific computing tasks at the start of any computationally intensive scientific task. Automatically identifies CPU capabilities, GPU availability (NVIDIA CUDA, AMD ROCm, Apple Silicon Metal), memory constraints, and disk space. Creates JSON file with resource information and recommendations for parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use cases: determining optimal computational approaches before data analysis, model training, or large file operations
 - **ToolUniverse** - Unified ecosystem providing standardized access to 600+ scientific tools, models, datasets, and APIs across bioinformatics, cheminformatics, genomics, structural biology, and proteomics. Enables AI agents to function as research scientists through: (1) Tool Discovery - natural language, semantic, and keyword-based search for finding relevant scientific tools (Tool_Finder, Tool_Finder_LLM, Tool_Finder_Keyword); (2) Tool Execution - standardized AI-Tool Interaction Protocol for running tools with consistent interfaces; (3) Tool Composition - sequential and parallel workflow chaining for multi-step research pipelines; (4) Model Context Protocol (MCP) integration for Claude Desktop/Code. Supports drug discovery workflows (disease→targets→structures→screening→candidates), genomics analysis (expression→differential analysis→pathways), clinical genomics (variants→annotation→pathogenicity→disease associations), and cross-domain research. Use cases: accessing scientific databases (OpenTargets, PubChem, UniProt, PDB, ChEMBL, KEGG), protein structure prediction (AlphaFold), molecular docking, pathway enrichment, variant annotation, literature searches, and automated scientific workflows
 
+### Research Methodology & Proposal Writing
+- **Research Grants** - Write competitive research proposals for NSF, NIH, DOE, and DARPA. Features agency-specific formatting, review criteria understanding, budget preparation, broader impacts statements, significance narratives, innovation sections, and compliance with submission requirements. Covers project descriptions, specific aims, technical narratives, milestone plans, budget justifications, and biosketches. Use cases: federal grant applications, resubmissions with reviewer response, multi-institutional collaborations, and preliminary data sections
+- **Research Lookup** - Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Intelligently selects models based on query complexity. Provides access to current academic literature, recent studies, technical documentation, and general research information with proper citations. Use cases: finding latest research, literature verification, gathering background research, finding citation sources, and staying current with emerging trends
+- **Scholar Evaluation** - Apply the ScholarEval framework to systematically evaluate scholarly and research work. Provides structured evaluation methodology based on peer-reviewed research assessment criteria for analyzing academic papers, research proposals, literature reviews, and scholarly writing across multiple quality dimensions. Use cases: evaluating research papers for quality and rigor, assessing methodology design, scoring data analysis approaches, benchmarking research quality, and assessing publication readiness
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+### Regulatory & Standards Compliance
+- **ISO 13485 Certification** - Comprehensive toolkit for preparing ISO 13485:2016 certification documentation for medical device Quality Management Systems. Provides gap analysis of existing documentation, templates for all mandatory documents, compliance checklists, and step-by-step documentation creation. Covers 31 required procedures including Quality Manuals, Medical Device Files, and work instructions. Use cases: starting ISO 13485 certification process, conducting gap analysis, creating or updating QMS documentation, preparing for certification audits, transitioning from FDA QSR to QMSR, and harmonizing with EU MDR requirements
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 ## Scientific Thinking & Analysis
 
 ### Analysis & Methodology