pur3-pkb-codebase

Implement optimal chunking strategies in RAG systems and document processing pipelines. Use when building retrieval-augmented generation systems, vector databases, or processing large documents that require breaking into semantically meaningful segments for embeddings and search.

Senior Quality Documentation Manager for comprehensive documentation control and regulatory document review. Provides document management system design, change control, configuration management, and regulatory documentation oversight. Use for document control system implementation, regulatory document review, change management, and documentation compliance verification.

Senior Quality Manager Responsible Person (QMR) for HealthTech and MedTech companies. Provides overall quality system responsibility, regulatory compliance oversight, management accountability, and strategic quality leadership. Use for quality system governance, regulatory compliance oversight, management responsibility, and quality strategic planning.

Build Retrieval-Augmented Generation (RAG) systems for AI applications with vector databases and semantic search. Use when implementing knowledge-grounded AI, building document Q&A systems, or integrating LLMs with external knowledge bases.

This skill should be used when creating, optimizing, or implementing advanced prompt patterns including few-shot learning, chain-of-thought reasoning, prompt optimization workflows, template systems, and system prompt design. It provides comprehensive frameworks for building production-ready prompts with measurable performance improvements.

Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.

Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, 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.

Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model's knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.

Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.

Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.

Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.

Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.

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. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.

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). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.

Expert on Anthropic Claude API, models, prompt engineering, function calling, vision, and best practices. Triggers on anthropic, claude, api, prompt, function calling, vision, messages api, embeddings

Expert on Claude Code CLI, skills, commands, hooks, plugins, MCP, settings, and workflows. Triggers on claude code, cli, skill, command, hook, plugin, mcp, slash command, settings

Interactive slash command creator for Claude Code. Triggers when user mentions creating commands, slash commands, command templates, command arguments, or wants to build a new command workflow.

Interactive hook creator for Claude Code. Triggers when user mentions creating hooks, PreToolUse, PostToolUse, hook validation, hook configuration, settings.json hooks, or wants to automate tool execution workflows.

Expert on Model Context Protocol (MCP) integration, MCP servers, installation, configuration, and authentication. Triggers when user mentions MCP, MCP servers, installing MCP, connecting tools, MCP resources, MCP prompts, or remote/local MCP servers.

Expert on Claude Code settings.json configuration, permissions, sandbox, environment variables, and settings hierarchy. Triggers when user mentions settings.json, permissions, allow rules, deny rules, sandbox, hooks configuration, or settings precedence.

Interactive skill creator for Claude Code. Triggers when user mentions creating skills, building skills, skill templates, skill frontmatter, allowed-tools, or wants to scaffold a new skill.