AlterLab-IEU

Part of the AlterLab Academic Skills suite. Meta-skill for auditing and repairing Markdown link health across a skills repo. Runs a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of previously-passing links. Designed for lychee-based GitHub Actions link checkers, but the methodology generalizes to markdown-link-check and similar tools. Triggers on: link audit, dead links, link health, lychee, broken links, link checker, markdown link audit, link-health audit, 404 audit, check-links failing, CI link-check, 連結健檢, 死鏈, 失效連結, 斷鏈檢查.

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.

Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design. Part of the AlterLab Academic Skills suite.

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation. Part of the AlterLab Academic Skills suite.

Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler. Part of the AlterLab Academic Skills suite.

RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference. Part of the AlterLab Academic Skills suite.

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics. Part of the AlterLab Academic Skills suite.

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction. Part of the AlterLab Academic Skills suite.

This skill should be used when the user asks about "digital campaign", "social impact campaign", "digital activism", "civic tech", "awareness campaign", "advocacy campaign", "act as a digital campaign planner", "digital campaign mode", "hashtag campaign", "change.org petition", "awareness-to-action funnel", "online mobilization", "cause marketing", "social change campaign", "petition strategy", or needs expertise in designing and executing digital campaigns for social impact and civic engagement. Part of the AlterLab FC Skills collection (New Media & Communication department).

This skill should be used when the user asks about "media theory", "critical theory", "academic writing", "Foucault", "Habermas", "McLuhan", "Baudrillard", "Stuart Hall", "act as a media theory companion", "media theory mode", "theoretical framework", "literature review", "discourse analysis", "semiotics", "cultural studies", "political economy", or needs expertise in applying media and communication theory to academic writing and critical analysis. Part of the AlterLab FC Skills collection (New Media & Communication department).

This skill should be used when the user asks about "newsletter", "email newsletter", "email content strategy", "subject lines", "newsletter structure", "email marketing", "act as a newsletter designer", "newsletter mode", "Substack", "Mailchimp", "CTA optimization", "open rate", "email design", "subscriber growth", "Beehiiv", or needs expertise in planning, writing, and optimizing email newsletters. Part of the AlterLab FC Skills collection (New Media & Communication department).

This skill should be used when the user asks about "digital portfolio", "portfolio website", "project description", "case study", "portfolio curation", "creative portfolio", "act as a portfolio curator", "portfolio curator mode", "portfolio review", "professional presentation", "portfolio architecture", "work samples", "portfolio bio", or needs expertise in building, structuring, and writing professional digital portfolios. Part of the AlterLab FC Skills collection (New Media & Communication department).

This skill should be used when the user asks about "social media analytics", "platform analytics", "audience insights", "engagement rate", "social media strategy report", "competitive benchmarking", "act as a social media analyst", "social analyst mode", "social media metrics", "content performance", "follower growth", "social media audit", "social listening", or needs expertise in analyzing social media data and translating it into actionable strategy reports. Part of the AlterLab FC Skills collection (New Media & Communication department).

This skill should be used when the user asks about "video essay", "visual essay", "narration script", "essay film", "argument-driven editing", "video analysis", "act as a video essay creator", "video essay mode", "YouTube essay", "voiceover script", "visual argument", "essay film structure", "film criticism video", or needs expertise in writing, structuring, and producing argument-driven video essays. Part of the AlterLab FC Skills collection (New Media & Communication department).

This skill should be used when the user asks about "web content strategy", "SEO writing", "UX writing", "information architecture", "content architecture", "website structure", "act as a web content strategist", "web strategist mode", "site map", "content audit", "microcopy", "meta descriptions", "content hierarchy", "content governance", or needs expertise in planning, structuring, and writing content for websites and digital platforms. Part of the AlterLab FC Skills collection (New Media & Communication department).

This skill should be used when the user asks about "writing an abstract", "abstract format", "structured abstract", "IMRAD abstract", "conference abstract", "thesis abstract", "dissertation abstract", "abstract submission", "keyword selection", "research summary", "act as an abstract writer", "abstract writer mode", "executive summary", "abstract optimization", "abstract for publication", "paper abstract", "how to write an abstract", "abstract word limit", "abstract discoverability", "journal abstract", "poster abstract", "abstract revision", or needs expertise in crafting compelling academic abstracts, structured summaries, and keyword strategies. Part of the AlterLab FC Skills collection (Research Methods & Academic Writing department).

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 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 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 wants to start a new game project, set up project scaffolding, onboard into an existing codebase, or initialize GameForge session state. Triggers on: "start a game", "new game project", "set up project", "project onboarding", "initialize project". Do NOT invoke for brainstorming ideas (use game-brainstorm) or prototyping mechanics (use game-prototype). Part of the AlterLab GameForge collection.

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 the AlterLab GameForge collection.