Claude Skills by AlterLab-IEU

Query InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, and 11 other member databases. Use for protein function prediction, domain architecture analysis, evolutionary classification, and GO term mapping. Part of the AlterLab Academic Skills suite.

Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs). Search by TF name, species, or class; scan DNA sequences for TF binding sites; compare matrices; essential for regulatory genomics, motif analysis, and GWAS regulatory variant interpretation. Part of the AlterLab Academic Skills suite.

Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control. Part of the AlterLab Academic Skills suite.

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery. Part of the AlterLab Academic Skills suite.

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup. Part of the AlterLab Academic Skills suite.

Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries. Part of the AlterLab Academic Skills suite.

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification. Part of the AlterLab Academic Skills suite.

Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery. Part of the AlterLab Academic Skills suite.

Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Part of the AlterLab Academic Skills suite.

Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations. Part of the AlterLab Academic Skills suite.

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies. Part of the AlterLab Academic Skills suite.

Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology. Part of the AlterLab Academic Skills suite.

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control. Part of the AlterLab Academic Skills suite.

Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches. Part of the AlterLab Academic Skills suite.

Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery. Part of the AlterLab Academic Skills suite.

Part of the AlterLab Academic Skills suite. Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx files, inserting or replacing images in documents, performing find-and-replace in Word fi...

Part of the AlterLab Academic Skills suite. Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.

Part of the AlterLab Academic Skills suite. Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating AI-powered notes and summaries, creating multi-speaker podcasts from research, chatting with documents using context-aware AI, searching across materials with full-text and vector search, or runni...

Invoke when the user asks about accessibility, inclusive design, colorblind mode, remappable controls, screen reader support, EAA compliance, CVAA, difficulty options, motor accommodations, or one-handed mode. Triggers on: "accessibility", "inclusive design", "colorblind", "remappable controls", "screen reader", "EAA", "CVAA", "difficulty options", "motor accommodation", "one-handed". Do NOT invoke for general UX design (use game-ux-designer) or art direction (use game-art-director). Part of ...

Invoke when the user asks about art style, visual language, style guide, character design, environment art, UI art direction, asset pipeline, reference boards, color palette, or shape language. Triggers on: "art style", "visual", "style guide", "character design", "environment art", "asset pipeline", "color palette", "shape language". Do NOT invoke for UI/UX layout (use game-ux-designer) or creative vision (use game-creative-director). Part of the AlterLab GameForge collection.

Invoke when the user asks about sound design, music direction, audio identity, adaptive audio, spatial audio, SFX, sonic palette, dialogue systems, audio middleware, dynamic music, or sound bible creation. Triggers on: "sound design", "music", "audio", "SFX", "adaptive audio", "spatial audio", "sonic palette", "FMOD", "Wwise", "sound bible". Do NOT invoke for narrative dialogue writing (use game-narrative-director) or creative vision (use game-creative-director). Part of the AlterLab GameForg...

Invoke when the user asks about creative vision, game pillars, core fantasy, design direction, art style decisions, scope arbitration, or creative conflicts. Triggers on: "vision", "pillars", "creative direction", "core fantasy", "tone", "aesthetic", "creative conflict". Do NOT invoke for mechanics design (use game-designer) or technical architecture (use game-technical-director). Part of the AlterLab GameForge collection.

Invoke when the user asks about game mechanics, core loop, balance, progression, economy design, reward systems, onboarding, game feel, systems design, or GDD authoring. Triggers on: "mechanics", "core loop", "balance", "progression", "reward", "onboarding", "game feel", "systems design", "GDD". Do NOT invoke for creative vision (use game-creative-director) or economy monetization (use game-economy-designer). Part of the AlterLab GameForge collection.

Invoke when the user asks about game economy, currency design, monetization, virtual currency, inflation, sink/source balance, F2P economy, premium currency, loot boxes, season pass, battle pass economics, dual currency, or resource flow modeling. Triggers on: "economy", "currency", "monetization", "F2P", "premium", "loot box", "battle pass", "sink/source", "inflation", "resource flow". Do NOT invoke for core gameplay mechanics (use game-designer) or legal advice on gambling laws (consult leg...

Invoke when the user asks about story structure, branching narrative, dialogue systems, world-building, character design, environmental storytelling, ludonarrative coherence, writing for games, lore, theme, or character arcs. Triggers on: "story", "narrative", "dialogue", "lore", "world-building", "character arc", "branching", "ludonarrative". Do NOT invoke for creative vision (use game-creative-director) or game mechanics (use game-designer). Part of the AlterLab GameForge collection.

Invoke when the user asks about sprint planning, milestone tracking, scope management, risk assessment, scheduling, resource allocation, team velocity, or needs production coordination across the development team. Triggers on: "sprint", "milestone", "scope", "risk", "schedule", "resource", "velocity", "deadline", "crunch", "cut list". Do NOT invoke for creative vision (use game-creative-director) or architecture decisions (use game-technical-director). Part of the AlterLab GameForge collection.

Invoke when the user asks about testing strategy, bug tracking, playtest methodology, regression testing, release certification, QA automation, or bug triage. Triggers on: "testing", "bug", "QA", "regression", "certification", "playtest methodology", "test plan", "release gate". Do NOT invoke for usability testing (use game-ux-designer) or balance validation (use game-balance-check). Part of the AlterLab GameForge collection.

Invoke when the user asks about game architecture, engine selection, performance budgets, technical debt, build pipeline, cross-platform, rendering pipeline, or CI/CD for games. Triggers on: "architecture", "engine selection", "performance budget", "tech debt", "build pipeline", "cross-platform", "rendering", "CI/CD". Do NOT invoke for creative vision (use game-creative-director) or engine-specific code (use engine specialists). Part of the AlterLab GameForge collection.

Invoke when the user asks about game UI, onboarding, HUD design, controller navigation, player feedback, usability testing, colorblind modes, or game-specific UX patterns. Triggers on: "UI", "UX", "onboarding", "HUD", "controller nav", "usability", "colorblind", "player feedback", "menu design". Do NOT invoke for deep accessibility audits (use game-accessibility-specialist) or art style (use game-art-director). Part of the AlterLab GameForge collection.

Invoke when the user works with Godot Engine or asks about GDScript, scene composition, signals, resources, shaders, GDExtension, physics, or Godot UI. Triggers on: "Godot", "GDScript", "scene tree", "signals", ".tscn", ".tres", "GDExtension", "project.godot". Do NOT invoke for engine-agnostic architecture (use game-technical-director) or Unity/Unreal questions (use the appropriate engine specialist). Part of the AlterLab GameForge collection.

Invoke when the user works with Unity or asks about C#, MonoBehaviour, DOTS/ECS, Shader Graph, Addressables, UI Toolkit, URP/HDRP, or ScriptableObjects. Triggers on: "Unity", "MonoBehaviour", "DOTS", "ECS", "Shader Graph", "Addressables", "UI Toolkit", "URP", "HDRP", "ScriptableObject", ".unity", ".cs". Do NOT invoke for engine-agnostic architecture (use game-technical-director) or Godot/Unreal questions. Part of the AlterLab GameForge collection.

Invoke when the user works with Unreal Engine 5 or asks about C++/Blueprints, GAS, replication, Nanite, Lumen, CommonUI, Enhanced Input, or World Partition. Triggers on: "Unreal", "UE5", "Blueprint", "GAS", "Nanite", "Lumen", "CommonUI", "Enhanced Input", "World Partition", ".uproject". Do NOT invoke for engine-agnostic architecture (use game-technical-director) or Godot/Unity questions. Part of the AlterLab GameForge collection.

Invoke when the user needs to set up analytics, define telemetry events, establish KPIs, build dashboards, configure A/B testing, or implement data-driven design capabilities. Triggers on: "analytics", "telemetry", "KPIs", "metrics", "player data", "retention", "DAU", "dashboard", "A/B testing", "funnel analysis". Do NOT invoke for balance tuning (use game-balance-check) or economy design (use game-economy-designer). Part of the AlterLab GameForge collection.

Invoke when the user needs to validate game balance, tune economy systems, analyze progression curves, evaluate difficulty scaling, or check reward pacing. Includes Monte Carlo simulation and statistical validation. Triggers on: "balance", "economy tuning", "progression curve", "difficulty scaling", "reward pacing", "Monte Carlo", "fairness check". Do NOT invoke for economy/monetization design (use game-economy-designer) or code review (use game-code-review). Part of the AlterLab GameForge co...

Invoke when the user wants to brainstorm game ideas, explore concepts, run structured ideation, or develop a new game concept from scratch. Triggers on: "game idea", "brainstorm", "concept", "ideation", "what if", "game concept", "pitch". Do NOT invoke for reviewing existing designs (use game-design-review) or market analysis (use game-market-research). Part of the AlterLab GameForge collection.

Invoke to set up CI/CD pipelines for game builds -- automated testing, build pipelines, and deployment to Steam, itch.io, or Epic. Triggers on: "CI", "CD", "pipeline", "automated build", "deploy", "Steam deploy", "itch.io butler", "GitHub Actions game", "build automation". Do NOT invoke for general code review (use game-code-review) or manual testing guidance (use game-qa-lead). Part of the AlterLab GameForge collection.

Invoke when the user wants a game-specific code review, architecture check, or technical analysis of game code. Covers frame independence, hot path performance, state machine integrity, and resource lifecycle. Triggers on: "code review", "review my code", "check architecture", "game code quality". Do NOT invoke for design document review (use game-design-review) or general sprint planning (use game-sprint-plan). Part of the AlterLab GameForge collection.

Invoke when the user wants feedback on a game design document, GDD review, design evaluation, or consistency check on an existing design. Triggers on: "review my GDD", "design feedback", "evaluate design", "design document review", "GDD critique". Do NOT invoke for brainstorming new ideas (use game-brainstorm) or balance tuning (use game-balance-check). Part of the AlterLab GameForge collection.

Invoke for guided game design document authoring -- section-by-section GDD creation with validation, pillar alignment, and scope tier marking. Triggers on: "write GDD", "create GDD", "game design document", "document my game", "GDD authoring", "fill in GDD". Do NOT invoke for reviewing an existing GDD (use game-design-review) or designing specific game systems (use game-designer). Part of the AlterLab GameForge collection.

Invoke for game jam participation -- 48-72 hour compressed development workflow. Triggers on: "game jam", "jam mode", "Ludum Dare", "GMTK Jam", "Global Game Jam", "Brackeys Jam", "48 hours", "jam submission". Do NOT invoke for normal development timelines (use game-start). Part of the AlterLab GameForge collection.

Invoke when the user is preparing for game release, needs a launch checklist, store submission guidance, go/no-go decision framework, or day-one patch planning. Covers Steam, itch.io, Epic, and console submission pipelines. Triggers on: "launch", "release", "store submission", "go/no-go", "day-one patch", "launch readiness". Do NOT invoke for sprint planning (use game-sprint-plan) or code review (use game-code-review). Part of the AlterLab GameForge collection.

Invoke when the user asks about localization, translation, i18n, internationalization, string extraction, cultural adaptation, RTL support, CJK text, or EFIGS preparation. Triggers on: "localization", "translation", "i18n", "internationalization", "string extraction", "cultural adaptation", "RTL", "CJK", "EFIGS". Do NOT invoke for narrative writing (use game-narrative-director) or accessibility (use game-accessibility-specialist). Part of the AlterLab GameForge collection.

Conduct market research for a game concept -- competitive landscape, market sizing, audience analysis, trend detection, and positioning strategy. Triggers on: "market research", "competitive analysis", "market sizing", "audience analysis", "is this game viable", "similar games", "market validation". Do NOT invoke for brainstorming ideas (use game-brainstorm) or economy monetization design (use game-economy-designer). Part of the AlterLab GameForge collection.

Invoke when the user wants to plan, execute, or analyze a structured playtest session with behavioral observation. Covers protocol design, observer guides, and data synthesis. Triggers on: "playtest", "player feedback", "usability test", "observation session", "playtest analysis". Do NOT invoke for QA bug testing (use game-qa-lead) or balance tuning (use game-balance-check). Part of the AlterLab GameForge collection.

Run a structured post-mortem analyzing what went well, what went wrong, and extractable lessons. Pulls git history, milestone data, and retrospective notes automatically. Triggers on: "post-mortem", "project review", "what did we learn", "lessons learned", or when a major milestone or project is complete. Do NOT invoke for sprint-level retrospectives (use game-retrospective) or design reviews (use game-design-review). Part of the AlterLab GameForge collection.

Invoke when the user wants to rapidly prototype a mechanic, test a proof of concept, run hypothesis-driven development, or validate a game idea before full production. Triggers on: "prototype", "proof of concept", "test this mechanic", "validate idea", "rapid prototype", "bake-off". Do NOT invoke for starting a full project (use game-start) or brainstorming concepts (use game-brainstorm). Part of the AlterLab GameForge collection.

Run a game development post-mortem rooted in the GDC tradition. Triggers on: "retrospective", "retro", "post-mortem", "lessons learned", "what went right", "what went wrong", "kill list review". Do NOT invoke for design document review (use game-design-review) or playtesting (use game-playtest). Part of the AlterLab GameForge collection.

Generate documentation from existing code or prototypes. Triggers on: "document this", "reverse document", "generate docs from code", "onboard to codebase", "document existing system". Do NOT invoke for writing new design docs from scratch (use game-brainstorm or game-design-review). Part of the AlterLab GameForge collection.

Evaluate project scope against timeline and resources. Triggers on: "scope creep", "feature list", "can we fit this in", "timeline pressure", "resource constraints", "cut list", "scope evaluation". Do NOT invoke for sprint planning (use game-sprint-plan) or general project status (use game-producer). Part of the AlterLab GameForge collection.

Invoke when the user needs to plan a development sprint, break down tasks, schedule game work, or organize a sprint with cross-discipline dependencies. Triggers on: "sprint plan", "task breakdown", "development planning", "scheduling", "sprint backlog". Do NOT invoke for scope evaluation (use game-scope-check) or retrospectives (use game-retrospective). Part of the AlterLab GameForge collection.