delphine-l

Token optimization best practices for cost-effective Claude Code usage. Automatically applies efficient file reading, command execution, and output handling strategies. Includes model selection guidance (Opus for learning, Sonnet for development/debugging). Prefers bash commands over reading files.

Core bioinformatics concepts including SAM/BAM format, AGP genome assembly format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, pairing issues, and AGP coordinate validation.

Integration with Obsidian vault for managing notes, tasks, and knowledge when working with Claude. Supports adding notes, creating tasks, and organizing project documentation. Updated with 2025-2026 best practices including MOCs, properties, practical organization patterns, and Obsidian CLI (1.12+).

Best practices for creating comprehensive Jupyter notebook data analyses with statistical rigor, outlier handling, and publication-quality visualizations. Includes Claude API image size helpers.

Best practices for managing development environments including Python venv and conda. Always check environment status before installations and confirm with user before proceeding.

Best practices for using Claude Code in team environments. Covers skill management, knowledge capture, version control, and collaborative workflows.

Expert guide for managing Claude Code global skills and commands. Use when creating new skills, symlinking to projects, updating existing skills, or organizing the centralized skill repository.

Expert in building and testing conda/bioconda recipes, including recipe creation, linting, dependency management, and debugging common build errors

BioBlend and Planemo expertise for Galaxy workflow automation. Galaxy API usage, workflow invocation, status checking, error handling, batch processing, and dataset management. Essential for any Galaxy automation project.

Prepare organized packages of project files for sharing at different levels - from summary PDFs to fully reproducible archives. Creates copies with cleaned notebooks, documentation, and appropriate file selection. After creating sharing package, all work continues in the main project directory.

Best practices for iterative refinement of publication-quality scientific figures. Covers systematic improvement workflows, layout optimization, and ensuring all figure elements are publication-ready.

Expert in Galaxy tool wrapper development, XML schemas, Planemo testing, and best practices for creating Galaxy tools