Calculate portfolio risk metrics including VaR, CVaR, Sharpe, Sortino, and drawdown analysis. Use when measuring portfolio risk, implementing risk limits, or building risk monitoring systems.

Master defensive Bash programming techniques for production-grade scripts. Use when writing robust shell scripts, CI/CD pipelines, or system utilities requiring fault tolerance and safety.

Step-by-step cookbook for setting up cryptographically signed audit trails on Claude Code tool calls. Use when explaining, evaluating, or demonstrating the pattern before committing to the protect-mcp runtime hooks. Covers Cedar policy, Ed25519 receipts, offline verification, tamper detection, CI/CD integration, and SLSA composition.

Build scalable design systems with design tokens, theming infrastructure, and component architecture patterns. Use when creating design tokens, implementing theme switching, building component libraries, or establishing design system foundations.

Design and implement microinteractions, motion design, transitions, and user feedback patterns. Use when adding polish to UI interactions, implementing loading states, or creating delightful user experiences.

Add Atomic Chat MCP server so the container agent can call local models served by the Atomic Chat desktop app via its OpenAI-compatible API.

Add a monitoring dashboard to NanoClaw. Installs @nanoco/nanoclaw-dashboard and a pusher that sends periodic JSON snapshots.

Add Ollama MCP server so the container agent can call local models and optionally manage the Ollama model library.

Install the claw CLI tool — run NanoClaw agent containers from the command line without opening a chat app.

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.

Cloud computing platform for running Python on GPUs and serverless infrastructure. Use when deploying AI/ML models, running GPU-accelerated workloads, serving web endpoints, scheduling batch jobs, or scaling Python code to the cloud. Use this skill whenever the user mentions Modal, serverless GPU compute, deploying ML models to the cloud, serving inference endpoints, running batch processing in the cloud, or needs to scale Python workloads beyond their local machine. Also use when the user wants to run code on H100s, A100s, or other cloud GPUs, or needs to create a web API for a model.

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.

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU infrastructure.

Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.

Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.

Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use scientific-visualization.

Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.

Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify RAM/GPU before first use.

Guide for building Graph Neural Networks with PyTorch Geometric (PyG). Use this skill whenever the user asks about graph neural networks, GNNs, node classification, link prediction, graph classification, message passing networks, heterogeneous graphs, neighbor sampling, or any task involving torch_geometric / PyG. Also trigger when you see imports from torch_geometric, or the user mentions graph convolutions (GCN, GAT, GraphSAGE, GIN), graph data structures, or working with relational/network data. Even if the user just says 'graph learning' or 'geometric deep learning', use this skill.

UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.

Query the U.S. Treasury Fiscal Data API for federal financial data including national debt, government spending, revenue, interest rates, exchange rates, and savings bonds. Access 54 datasets and 182 data tables with no API key required. Use when working with U.S. federal fiscal data, national debt tracking (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates on Treasury securities, foreign exchange rates, savings bonds, or any U.S. government financial statistics.

Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.

Converts X content to markdown:

Transform content into professional slide deck images. The deck is designed for **reading and sharing** (self-explanatory slides, logical scroll flow, social-media-friendly) rather than live presentat

Use when you need to ask questions about a codebase or understand code using a knowledge graph

Launch the interactive web dashboard to visualize a codebase's knowledge graph

Analyze a codebase to produce an interactive knowledge graph for understanding architecture, components, and relationships

Designs and implements production-grade RAG systems by chunking documents, generating embeddings, configuring vector stores, building hybrid search pipelines, applying reranking, and evaluating retrieval quality. Use when building RAG systems, vector databases, or knowledge-grounded AI applications requiring semantic search, document retrieval, context augmentation, similarity search, or embedding-based indexing.

State-space model with O(n) complexity vs Transformers' O(n²). 5× faster inference, million-token sequences, no KV cache. Selective SSM with hardware-aware design. Mamba-1 (d_state=16) and Mamba-2 (d_state=128, multi-head). Models 130M-2.8B on HuggingFace.

RNN+Transformer hybrid with O(n) inference. Linear time, infinite context, no KV cache. Train like GPT (parallel), infer like RNN (sequential). Linux Foundation AI project. Production at Windows, Office, NeMo. RWKV-7 (March 2025). Models up to 14B parameters.

Fine-tune LLMs using reinforcement learning with TRL - SFT for instruction tuning, DPO for preference alignment, PPO/GRPO for reward optimization, and reward model training. Use when need RLHF, align model with preferences, or train from human feedback. Works with HuggingFace Transformers.

Trains large language models (2B-462B parameters) using NVIDIA Megatron-Core with advanced parallelism strategies. Use when training models >1B parameters, need maximum GPU efficiency (47% MFU on H100), or require tensor/pipeline/sequence/context/expert parallelism. Production-ready framework used for Nemotron, LLaMA, DeepSeek.

Serverless GPU cloud platform for running ML workloads. Use when you need on-demand GPU access without infrastructure management, deploying ML models as APIs, or running batch jobs with automatic scaling.

Provides guidance for experiment tracking with SwanLab. Use when you need open-source run tracking, local or self-hosted dashboards, and lightweight media logging for ML workflows.

Agentic Workflow Pattern

Guide to the math cognitive stack - what tools exist and when to use each

Deterministic router for math cognitive stack - maps user intent to exact CLI commands

Unified math capabilities - computation, solving, and explanation. I route to the right tool.

Problem-solving strategies for modular arithmetic in graph number theory

Develops mathematical understanding through examples, visualization, and analogy

Routes problems to appropriate mathematical frameworks using expert heuristics

Metacognitive check-ins during problem solving - detects when to pivot or persist

Problem-solving strategies for predicate logic in mathematical logic

Problem-solving strategies for proof theory in mathematical logic

Problem-solving strategies for propositional logic in mathematical logic