Design skills

Medicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS, Golden Triangle, Ro3), structural alerts (PAINS, NIBR, Lilly Demerits), chemical group detectors, complexity metrics, and filter composition query language. Built on RDKit/datamol. For hit-to-lead filtering, library design, ADMET pre-screening. For molecular I/O use rdkit-cheminformatics or datamol.

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Evaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, RR, NNT, Cohen's d), confounding, p-value vs clinical significance, GRADE quality assessment, reproducibility, and bias types (selection, information, confounding, reporting). Use when reading a paper or assessing claims.

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Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2. Jointly decompose omics layers (scRNA, ATAC, proteomics, methylation) into latent factors capturing major variation. Multi-group designs. AnnData views → MOFA object → train → variance explained → correlate factors with metadata → visualize/cluster → enrich top loadings.

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Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. Use for strain design, essential gene ID, flux analysis. For kinetic modeling use tellurium; for visualization use Escher.

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Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objectives and constraints; solve with NSGA-II, NSGA-III, MOEA/D, GAs, or differential evolution. Analyze Pareto fronts, visualize trade-offs, customize operators and callbacks. For engineering design, hyperparameter search, and conflicting objectives. Alternatives: scipy.optimize (single-objective, gradient), platypus, jMetalPy (Java).

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Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design rules for CRISPR experiments

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Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings. Pipeline: sequence → MFE → partition function and pair-probability matrix → dot-bracket → duplex. Use for siRNA/sgRNA targeting, ribozyme design, RNA accessibility. Use RNAfold CLI for batch use without Python.

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Best practices, design patterns, and common pitfalls for ROS1 (Robot Operating System 1) development. Use this skill when building ROS1 nodes, packages, launch files, or debugging ROS1 systems. Trigger whenever the user mentions ROS1, catkin, rospy, roscpp, roslaunch, roscore, rostopic, tf, actionlib, message types, services, or any ROS1-era robotics middleware. Also trigger for migrating ROS1 code to ROS2, maintaining legacy ROS1 systems, or building ROS1-ROS2 bridges. Covers catkin workspaces, nodelets, dynamic reconfigure, pluginlib, and the full ROS1 ecosystem.

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Foundational software design principles applied specifically to robotics module development. Use this skill when designing robot software modules, structuring codebases, making architecture decisions, reviewing robotics code, or building reusable robotics libraries. Trigger whenever the user mentions SOLID principles for robots, modular robotics software, clean architecture for robots, dependency injection in robotics, interface design for hardware, real-time design constraints, error handling strategies for robots, configuration management, separation of concerns in perception-planning- control, composability of robot behaviors, or any discussion of software craftsmanship in a robotics context. Also trigger for code reviews of robotics code, refactoring robot software, or designing APIs for robotics libraries.

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Architecture patterns, design principles, and proven recipes for building robust robotics software. Use this skill when designing robot software architectures, choosing between behavioral frameworks, structuring perception-planning-control pipelines, implementing state machines, designing safety systems, or architecting multi-robot systems. Trigger whenever the user mentions behavior trees, finite state machines, subsumption architecture, sensor fusion, robot safety, watchdogs, heartbeats, graceful degradation, hardware abstraction layers, real-time constraints, or software architecture for robots. Also applies to sim-to-real transfer, digital twins, and robot fleet management.

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Domain-Driven Design architecture for claude-flow v3. Implements modular, bounded context architecture with clean separation of concerns and microkernel pattern.

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Comprehensive guidance for building web apps with opinionated defaults for tech stack, design system, and code standards. Use when user wants to create a new web application, dashboard, or interactive interface. Provides tech choices, styling guidance, project structure, and design philosophy to get users up and running quickly with a fully functional, beautiful web app.

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Vector-clean art direction for Blender with flat fills, sharp silhouettes, and UI-like graphic clarity.

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AAA creature modeling for fantasy, aliens, monsters, and organic creature design with believable anatomy and movement. Use for creature blockouts, muscle flow, bone structure, and animation-ready creature assets in Blender via MCP.

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Frutiger Aero art direction for Blender with glossy skeuomorphism, aqua UI cues, nature-tech optimism, and mid-2000s futurism.

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Route Shift documentation, architecture notes, and tickets correctly. Use when Codex is about to create or move docs, write an architecture plan, capture a design decision, create a ticket, or update repo documentation for Shift.

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Design, implement, audit, or review Shift user interfaces and shared UI components. Use for React components, Base UI primitives, Tailwind styling or theme tokens, Figma/reference matching, accessibility, icon-only actions, tooltips, menus, popovers, dialogs, forms, layout, and visible UI regressions.

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When the user needs to identify at-risk accounts, understand why customers are leaving, reduce churn rate, build health scores, design save plays, or create win-back campaigns.

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When the user needs to design an interview process, create interview questions, build scorecards, calibrate interviewers, or evaluate candidates for a role.

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When the user needs to design or evaluate system architecture — service boundaries, data models, API contracts, infrastructure topology, database selection, or dependency analysis. Also activate for "design the system", "how should I architect this", "monolith vs microservices", or architecture decision records.

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Provides implementation patterns for Clean Architecture, Domain-Driven Design (DDD), and Hexagonal Architecture (Ports & Adapters) in NestJS/TypeScript applications. Use when structuring complex backend systems, designing domain layers with entities/value objects/aggregates, implementing ports and adapters, creating use cases, or refactoring from anemic models to rich domain models with dependency inversion.

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Provides implementation patterns for Clean Architecture, Hexagonal Architecture (Ports & Adapters), and Domain-Driven Design in PHP 8.3+ with Symfony 7.x. Use when architecting enterprise PHP applications with entities/value objects/aggregates, refactoring legacy code to modern patterns, implementing domain-driven design with Symfony, or creating testable backends with clear separation of concerns.

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Provides TypeScript patterns for DynamoDB-Toolbox v2 including schema/table/entity modeling, .build() command workflow, query/scan access patterns, batch and transaction operations, and single-table design with computed keys. Use when implementing type-safe DynamoDB access layers with DynamoDB-Toolbox v2 in TypeScript services or serverless applications.

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Provides implementation patterns for Clean Architecture, Hexagonal Architecture (Ports & Adapters), and Domain-Driven Design in Python applications with FastAPI or Flask. Use when designing maintainable backends with separation of concerns, implementing repository patterns, creating entities/value objects/aggregates, or structuring domain logic independent of frameworks for testability.

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