Philipp J. Thoss

Develop a high-performance liquid chromatography method: define separation goals, select column chemistry and mobile phase, optimize gradient and flow conditions, choose the appropriate detector, and evaluate initial method performance for target analytes in solution or complex matrices.

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Develop a gas chromatography method from scratch: define analytical objectives, select column chemistry, optimize temperature programming, choose carrier gas and detector, and validate initial system performance for target analytes in a given matrix.

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Implement AI-powered anomaly detection for operational metrics using time series analysis (Isolation Forest, Prophet, LSTM), alert correlation, and root cause analysis. Reduce alert fatigue by intelligently identifying true anomalies in system metrics, logs, and traces. Use when operations teams are overwhelmed by alert volume, when detecting complex multi-metric anomalies beyond static thresholds, when seasonal patterns make thresholds ineffective, or when needing to predict issues proactively before they impact users.

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Design a GxP training programme covering training needs analysis by role, curriculum design (regulatory awareness, system-specific, data integrity), competency assessment criteria, training record retention, and retraining triggers for SOP revisions and incidents. Use when a new validated system requires user training before go-live, an audit finding cites inadequate training, organisational changes introduce new roles, a periodic programme review is due, or inspection preparation requires demonstrating training adequacy.

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Design serialization schemas using JSON Schema, Protocol Buffer definitions, or Apache Avro. Covers schema versioning, backwards compatibility, validation rules, and evolution strategies for long-lived data formats. Use when defining a new API contract or data interchange format, adding fields to an existing schema without breaking consumers, migrating between schema versions, choosing between schema systems, or documenting data validation rules for automated enforcement.

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Design sustainable on-call rotations with balanced schedules, clear escalation policies, fatigue management, and handoff procedures. Minimize burnout while maintaining incident response coverage. Use when setting up on-call for the first time, scaling a team from 2-3 to 5+ engineers, addressing on-call burnout or alert fatigue, improving incident response times, or after a post-mortem identifies handoff issues.

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Design practical electromagnetic devices including electromagnets, DC and brushless motors, generators, and transformers by bridging theory to application. Use when sizing a solenoid or toroidal electromagnet for a target field or force, selecting motor topology and computing torque and efficiency, designing a transformer for a given voltage ratio and power rating, or analyzing losses from copper resistance, core hysteresis, and eddy currents.

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Design a compliance architecture that maps applicable regulations to computerized systems. Covers system inventory, criticality classification (GxP-critical, GxP-supporting, non-GxP), GAMP 5 category assignment, regulatory requirements traceability, and governance structure definition. Use when establishing a new regulated facility, formalising compliance across multiple systems, addressing a regulatory gap analysis, harmonising compliance after mergers or reorganisations, or preparing a site master file that references computerized systems.

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Create interactive maps, elevation profiles, and spatial visualizations from GPX tracks, waypoints, or route data using R (sf, leaflet, tmap) or Observable (D3, deck.gl). Covers data import, coordinate system handling, map styling, and export to HTML or image formats. Use when visualizing a planned or completed tour route on an interactive map, creating elevation profiles for hiking or cycling routes, overlaying waypoints and POIs on a basemap, or building a web-based trip dashboard.

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Configure MCP (Model Context Protocol) servers for Claude Code and Claude Desktop. Covers mcptools setup, Hugging Face integration, WSL path handling, and multi-client configuration. Use when setting up Claude Code to connect to R via mcptools, configuring Claude Desktop with MCP servers, adding Hugging Face or other remote MCP servers, or troubleshooting MCP connectivity between clients and servers.

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Create a new agent definition file following the agent-almanac agent template and registry conventions. Covers persona design, tool selection, skill assignment, model choice, frontmatter schema, required sections, registry integration, and discovery symlink verification. Use when adding a new specialized agent to the library, defining a persona for a Claude Code subagent, or creating a domain-specific assistant with curated skills and tools.

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Author a new agent-almanac workflow — a self-contained `.mjs` orchestration script run by Claude Code's Workflow tool. Covers choosing a workflow over a team, copying the template, the triple-name discovery contract, the pure-literal meta and sidecar frontmatter, building the body with the injected primitives, the advisory/implementing capability contract, the adversarial-verification fail-safes, validation, and manual installation. Use when you have a repeatable, parameterized procedure that coordinates several agents and want it captured as a reusable, auditable artifact whose control flow is fixed in code.

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Create a new team composition file following the agent-almanac team template and registry conventions. Covers team purpose definition, member selection, coordination pattern choice, task decomposition design, machine-readable configuration block, registry integration, and README automation. Use when defining a multi-agent workflow, composing agents for a complex review process, or creating a coordinated group for recurring collaborative tasks.

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Create a new SKILL.md file following the Agent Skills open standard (agentskills.io). Covers frontmatter schema, section structure, writing effective procedures with Expected/On failure pairs, validation checklists, cross-referencing, and registry integration. Use when codifying a repeatable procedure for agents, adding a new capability to the skills library, converting a guide or runbook into agent-consumable format, or standardizing a workflow across projects or teams.

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Scaffold a new R package with complete structure including DESCRIPTION, NAMESPACE, testthat, roxygen2, renv, Git, GitHub Actions CI, and development configuration files (.Rprofile, .Renviron.example, CLAUDE.md). Follows usethis conventions and tidyverse style. Use when starting a new R package from scratch, converting loose R scripts into a structured package, or setting up a package skeleton for collaborative development.

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Create a Dockerfile for R projects using rocker base images. Covers system dependency installation, R package installation, renv integration, and optimized layer ordering for fast rebuilds. Use when containerizing an R application or analysis, creating reproducible R environments, deploying R-based services (Shiny, Plumber, MCP server), or setting up consistent development environments across machines.

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Create a Quarto document for reproducible reports, presentations, or websites. Covers YAML configuration, code chunk options, output formats, cross-references, and rendering. Use when creating a reproducible analysis report, building a presentation with embedded code, generating HTML, PDF, or Word documents from code, or migrating an existing R Markdown document to Quarto.

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Create and manage pull requests using GitHub CLI. Covers branch preparation, writing PR titles and descriptions, creating PRs, handling review feedback, and merge/cleanup workflows. Use when proposing changes from a feature or fix branch for review, merging completed work into the main branch, requesting code review from collaborators, or documenting the purpose and scope of a set of changes.

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Create multi-stage Dockerfiles that separate build and runtime environments for minimal production images. Covers builder/runtime stage separation, artifact copying, scratch/distroless/alpine targets, and size comparison. Use when production images are too large, when build tools are included in the final image, when you need separate dev and prod images from one Dockerfile, or when deploying to constrained environments like edge or serverless.

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Create R-based pictogram glyphs for skill, agent, or team icons in the visualization layer. Covers concept sketching, ggplot2 layer composition using the primitives library, color strategy, registration in the appropriate glyph mapping file and manifest, rendering via the build pipeline, and visual verification of the neon-glow output. Use when a new entity has been added and needs a visual icon for the force-graph visualization, an existing glyph needs replacement, or when batch-creating glyphs for a new domain.

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Create a GitHub release with proper tagging, release notes, and optional build artifacts. Covers semantic versioning, changelog generation, and GitHub CLI usage. Use when marking a stable version of software for distribution, publishing a new library or application version, creating release notes for stakeholders, or distributing build artifacts (binaries, tarballs).

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Structured GitHub issue creation from review findings or task breakdowns. Groups related findings into logical issues, applies labels, and produces issues with standard templates including summary, findings, and acceptance criteria. Designed to consume output from review-codebase or similar review skills.

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Create general-purpose Dockerfiles for Node.js, Python, Go, Rust, and Java projects. Covers base image selection, dependency installation, user permissions, COPY patterns, ENTRYPOINT vs CMD, and .dockerignore. Use when containerizing an application for the first time, creating a consistent build/runtime environment, preparing an app for cloud deployment or Docker Compose, or when no existing Dockerfile is present in the project.

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Set up a Blender scene programmatically via Python (bpy) with objects, materials, lighting, camera, and environment configuration. Use when creating reproducible 3D visualization scenes, automating product or architectural rendering setup, generating multiple scene variations programmatically, building template scenes for batch rendering workflows, or integrating 3D visualization into data pipelines.

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