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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.
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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.
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Add moments of joy, personality, and unexpected touches that make interfaces memorable and enjoyable to use. Elevates functional to delightful. Use when the user asks to add polish, personality, animations, micro-interactions, delight, or make an interface feel fun or memorable.
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Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.
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Astropy is the core Python package for astronomy, providing essential functionality for astronomical research and data analysis.
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Edit EcoSIM PFT-parameter NetCDF files such as ecosim_pftpar_20260303.nc with the ParEditor class from applications/notebooks/scripts/ParamEditor.py. Use when asked to modify, scale, copy, compare, or delete PFT parameter records for a plant functional type (six-character pfts code such as gr3s43 or ndlf34), update microbe parameter NetCDF values, or maintain the JSONL change log that records past parameter changes. Never modify plant_trait.*.desc files; they are read-only references.
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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.
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Space/aerospace mission monitoring: dark command center, amber telemetry on navy, monospace precision. Functional clarity above all. For ops dashboards, build/deploy status, and real-time monitoring.
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Raw, anti-design aesthetic inspired by concrete architecture with unadorned elements, jarring layouts, and functional minimalism.
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Use before any creative work - creating a feature, building a component, adding functionality, or changing behavior - to explore intent and design before implementation
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Design precise, production-grade enterprise UI — dashboards, admin panels, SaaS interfaces, and data-heavy applications. Use this skill for professional software interfaces that need Jony Ive-level craft: clean, minimal, functional, with intentional personality. Do NOT use for creative landing pages, marketing sites, or experimental/artistic frontends.
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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.
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Guide for testing code changes in AEM Edge Delivery projects including blocks, scripts, and styles. Use this skill after making code changes and before opening a pull request to validate functionality. Covers unit testing for utilities and logic, browser testing with Playwright, linting, and guidance on what to test and how
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Apply a Content Driven Development process to AEM Edge Delivery Services development. Use for ALL code changes - new blocks, block modifications, CSS styling, bug fixes, core functionality (scripts.js, styles, etc.), or any JavaScript/CSS work that needs validation.
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Guide for implementing code changes in AEM Edge Delivery Services. Handles block development (new or modified), core functionality changes (scripts.js, styles, delayed.js, etc.), or both. Use this skill for all implementation work guided by the content-driven-development workflow.
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Refactor code to improve quality while maintaining functionality. Use when you need to improve code structure, eliminate duplication, optimize performance, or enhance maintainability without changing behavior.
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Upgrades existing websites and apps to premium quality. Audits current design, identifies generic AI patterns, and applies high-end design standards without breaking functionality. Works with any CSS framework or vanilla CSS.
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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.
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Create a new command file following repo conventions. Use when you need to add a new slash command, create automation workflows, or extend the command library with new functionality.
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Fix broken or failing functionality through structured reproduction, root-cause analysis, minimal fix, and verification. Load when the user asks to fix a bug, debug an error, resolve an issue, or work on a Linear ticket. Also triggers on "this is broken", "fix this bug", "why is this failing", "debug this", "resolve this error", "what went wrong", or any request to diagnose and fix a problem.
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Write the executable feature specification — the WHAT and WHY artifact that agents and reviewers treat as source of truth. Owns both /specify and /clarify modes. Load when the user asks to write a feature spec, write a specification, write an executable spec, define functional requirements, capture acceptance criteria as Given/When/Then, or when the spec-driven-development orchestrator routes here. Also triggers on "feature spec", "executable spec", "/specify", "/clarify", "write the spec for this feature", "specification for", "spec-driven", "machine-readable spec". Output: docs/specs/YYYY-MM-DD-<slug>-feature-spec.md. Hard gate: cannot Approve while [NEEDS CLARIFICATION] markers remain.
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Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.
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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.
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Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.
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