Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

Use when users need to debug, modify, or extend the code-forge application's CLI commands, argument parsing, or CLI behavior. This includes adding new commands, fixing CLI bugs, updating command options, or troubleshooting CLI-related issues.

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.

Package entire code repositories into single AI-friendly files using Repomix. Capabilities include pack codebases with customizable include/exclude patterns, generate multiple output formats (XML, Markdown, plain text), preserve file structure and context, optimize for AI consumption with token counting, filter by file types and directories, add custom headers and summaries. Use when packaging codebases for AI analysis, creating repository snapshots for LLM context, analyzing third-party libraries, preparing for security audits, generating documentation context, or evaluating unfamiliar codebases.

Capture solved problems as categorized documentation with YAML frontmatter for fast lookup

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.

Retrieval-augmented generation (RAG) skill for the D&D 5e System Reference Document (SRD). Use when answering questions about D&D 5e core rules, spells, combat, equipment, conditions, monsters, and other SRD content. This skill provides agentic search-based access to the SRD split into page-range markdown files.

Query and analyze SEC filings and financial statements using EdgarTools. Get company data, filings, XBRL financials, and perform multi-company analysis.

Generate structured task lists from specs or requirements. IMPORTANT: After completing ANY spec via ExitSpecMode, ALWAYS ask the user: "Would you like me to generate a task list for this spec?" Use when user confirms or explicitly requests task generation from a plan/spec/PRD.

PDF generation toolkit. Create invoices, reports, certificates, forms, charts, tables, barcodes, QR codes, Canvas/Platypus APIs, for professional document automation.

Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields

Execute Codex CLI for code analysis, refactoring, and automated code changes. Use when you need to delegate complex code tasks to Codex AI with file references (@syntax) and structured output.

Write automated tests for features, validate functionality against acceptance criteria, and ensure code coverage. Use when writing test code, verifying functionality, or adding test coverage to existing code.

Review code using Linus Torvalds' "good taste" philosophy. Eliminates defensive code, special cases, and deep nesting. Use when reviewing code quality, refactoring, or checking for code smells.

Tauri framework for building cross-platform desktop and mobile apps. Use for desktop app development, native integrations, Rust backend, and web-based UIs.

Use when design is complete and you need detailed implementation tasks for engineers with zero codebase context - creates comprehensive implementation plans with exact file paths, complete code examples, and verification steps assuming engineer has minimal domain knowledge