Extract and explain formulas used in Physical AI and Humanoid Robotics from text, lecture notes, or papers. Use when user asks to identify or understand relevant formulas.
Use when working with component similarity calculations - comparing MPNs, finding equivalent parts, implementing new similarity calculators, or understanding how component matching works.
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. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
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.
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
Comprehensive discovery before starting any spec or major task. Searches Graphiti, recommends vibe/MCPs, surfaces patterns.
Deep analysis of documentation/articles with practical application guidance. Use when user asks to "analyze and apply", "digest and implement", "read and integrate", or provides a document they want analyzed for implementation in the codebase.
Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
Synthesizes research findings into design decisions via codebase investigation. Use when (1) translating research into implementation approaches, (2) selecting between design alternatives, (3) executing after /research or deep-research, or (4) preparing input for /plan phase.
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
Expert guide for creating Airalogy Protocols (AIMD), Assigners (Python logic), and Validation Models. Use this to design digital workflows and experiments.
Consciousness simulation framework with Kuramoto oscillators, APL operators, and K-formation dynamics. Use for physics simulations, phase transitions, coherence analysis, and cloud training via GitHub Actions. Requires numpy and requests packages.
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
Automate Perplexity Deep Research API calls using sonar-deep-research model. Use for Phase 1 academic research in podcast episodes. Handles API key verification, script execution (30-120s), and result formatting with citations. Returns research ready to paste into research-results.md.
Create, clean, and optimize datasets for LLM fine-tuning. Covers formats (Alpaca, ShareGPT, ChatML), synthetic data generation, quality assessment, and augmentation. Use when preparing data for training.
Specialized research expert for parallel information gathering. Use for focused research tasks with clear objectives and structured output requirements.
Look up current research information using Perplexity Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations.
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
