Claude Code Skills · page 62

Manage Hope Agent application settings through conversation. Use when the user wants to view or change any app configuration: theme, language, enhanced focus indicators, proxy, temperature, notifications, tool timeout, context compaction, automatic session titles, web search, GitHub issue reporting, memory, embedding, multimodal embedding, dreaming (offline memory consolidation), recap, behavior awareness, smart-mode approvals, plan mode, ask-user-question timeout, tool-result disk spill threshold, embedded server, ACP control plane, MCP subsystem (kill switch / concurrency / backoff), per-skill env vars, or any other setting visible in the Settings UI. Trigger phrases: 'change settings', 'configure proxy', 'set theme to dark', 'turn on enhanced focus indicators', 'turn off notifications', 'adjust temperature', 'show my settings', 'bind the server to all interfaces', 'enable smart mode', 'tune dreaming', 'disable mcp', 'show my channels'. Trigger even when the user doesn't explicitly say 'settings' — any intent to adjust app behavior qualifies.

Create, edit, improve, or audit Hope Agent skills. Use when the user wants to: (1) create a new skill from scratch, (2) edit or improve an existing skill, (3) review or clean up a SKILL.md file, (4) run evaluations to test skill effectiveness, (5) optimize skill descriptions for better trigger accuracy. Trigger phrases: 'create a skill', 'make a skill', 'improve this skill', 'review skill', 'audit skill'.

Hope-native test strategy for features, fixes, and refactors: select test-first, regression-first, characterization, integration, E2E, or manual evidence according to risk and repository rules.

Hope-native completion and verification discipline: map each requirement to current direct evidence, choose the smallest sufficient checks, and distinguish proven, failed, blocked, stale, or unverified claims.

Hope-native authoring and review for durable workflow.js runs: deterministic host APIs, typed child results, bounded parallel/pipeline execution, budgets, replay-safe identity, staged consumption, and honest closure.

Use when the user asks to capture, structure, or summarize meeting notes / call notes / 1:1 discussion / standup notes. Produces a standard template with attendees, agenda, decisions, action items (owner + deadline), and open questions.

Use when the user asks for a flowchart, architecture diagram, sequence diagram, ER diagram, state machine, gantt chart, or any visual that fits Mermaid syntax. Hope Agent's chat renders Mermaid blocks natively, so the diagram appears inline.

Use when the user asks to create, edit, inspect, polish, verify, or deliver Word `.docx` documents, Google Docs-targeted drafts, business briefs, forms, reports, tables, checklists, redraft-ready document sections, or PDF/Word source-to-DOCX transformations.

Use when the user asks to create, inspect, verify, polish, or deliver PowerPoint `.pptx` decks, Google Slides-targeted deck artifacts, strategy narratives, operating reviews, pitch decks, teaching decks, section slides, bullet slides, or source-to-PPTX transformations.

Use when the user asks to create, inspect, verify, analyze, format, or deliver Excel `.xlsx` workbooks, Google Sheets-targeted spreadsheet artifacts, trackers, budgets, models, tables, dashboards, formulas, CSV/TSV-to-XLSX conversions, or spreadsheet-ready data packs.

Use when the user asks for a weekly / monthly status report, project update, individual or team progress summary. Produces a tight, scannable update with what shipped, what's in flight, what's blocked, and metrics.

Use when executing implementation plans with independent tasks. Dispatches fresh subagent per task with two-stage review (spec compliance then code quality).

Use when encountering any bug, test failure, or unexpected behavior. 4-phase root cause investigation — NO fixes without understanding the problem first.

Use when implementing any feature or bugfix, before writing implementation code. Enforces RED-GREEN-REFACTOR cycle with test-first approach.

Use when you have a spec or requirements for a multi-step task. Creates comprehensive implementation plans with bite-sized tasks, exact file paths, and complete code examples.

Self-learning system that captures corrections during sessions and reminds users to run /reflect to update CLAUDE.md. Use when discussing learnings, corrections, or when the user mentions remembering something for future sessions.

Apply the standard Coding workspace workflow with explicit inspection, scoped edits, and proportionate validation.

Explain any topic, code, concept, or error tailored to a specific audience's level of understanding. Use this skill whenever the user says 'explain like I am', 'ELI5', 'explain this to my', 'break this down for', 'dumb it down', 'simplify this for', or asks you to explain something to a specific person or audience type (e.g., 'explain this to a manager', 'how would I explain this to my mom', 'make this understandable for a 5th grader'). Also trigger when the user mentions wanting to understand something at a particular level, or asks for an explanation targeting a non-technical audience. Even partial matches like 'explain to my wife' or 'tell my boss' should trigger this skill.

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Automatically control locally connected Android phones with OpenGUI screenshots and allowlisted actions whenever a request targets a phone, Android app, mobile game, or multiple devices. The user does not need to name OpenGUI. Use the native Codex Browser instead for browser-only work.

Launch and bootstrap OpenGUI from a plain-language user request. Use when an AI coding agent such as Claude Code, Codex, or OpenCode should install, configure, debug, and run the backend and Android client shipped in this repository while keeping manual setup to a minimum.

Control an Android phone through OpenGUI from an AI coding agent such as Claude Code, Codex, or OpenCode. Use when an agent should list online devices, run a natural-language mobile task, check execution status, pause, resume, or cancel through the local OpenGUI backend and CLI.

Install the latest stable OpenGUI release into a DeepSeek Harness web profile on macOS. Use when the user asks to download, install, update, open, or verify OpenGUI for DSH.

Generate high-converting App Store screenshots by analyzing your app's codebase, discovering core benefits, and creating ASO-optimized screenshot images using Nano Banana Pro.

Use whenever driving agent-browser against the local Relaticle app (relaticle.test and its panels) for testing, QA, business review, or UI automation. Covers Filament v5 + Livewire v4 quirks specific to this codebase: panel URL derivation (domain-routed vs path-routed, never assumed), login flows for the app and sysadmin panels, seeded credentials, Select/date-picker interaction, the $wire.mountAction gold pattern, tenant switching, Reverb/queue hazards, and session isolation. Every hard fact here is a DATED CACHED HINT. When one fails, re-derive from the running app and update this file (self-heal). Not for other sites or generic browser automation.

TRIGGER when working with ai-sdk which is Laravel official first-party AI SDK. Activate when building, editing AI agents, chatbots, text generation, image generation, audio/TTS, transcription/STT, embeddings, RAG, vector stores, reranking, structured output, streaming, conversation memory, tools, queueing, broadcasting, and provider failover across OpenAI, Anthropic, Gemini, Azure, Groq, xAI, DeepSeek, Mistral, Ollama, ElevenLabs, Cohere, Jina, and VoyageAI. Invoke when the user references ai-sdk, the `Laravel\Ai\` namespace, or this project's AI features — not for other AI packages used directly.

Use when the user asks to business-review their work (local mode default, via 'business-review' or 'review my branch'), a Relaticle pull request ('--pr <N>' or a bare PR number), or a described change (--describe). v3 is a panel-of-QAs engine. It resolves the live environment first (URLs/creds/queue/Redis/Reverb are DISCOVERED from the running app, never assumed), runs a browser-capability preflight, auto-tiers by blast radius, synthesizes journeys from the diff plus Relaticle CRM priors, walks them happy AND sad through the real browser, sweeps the regression ledger, adversarially cold-reproduces every bug, and emits a substance-gated verdict (ai-approved / ai-rejected / ai-needs-human, or blocked on a degraded channel). Browser-truth only: never tinker or hit the DB to fix or fake a result. On request ('fix all issues', --fix) enters fix mode: fix → re-verify each finding against its original repro → re-gate. Publishing to the PR is opt-in and hard-disabled on a degraded run. Does NOT do code/security/scope review; for that use /code-review, /review, /deep-review.

Handles Laravel Cashier Stripe integration including subscriptions, webhooks, Stripe Checkout, invoices, charges, refunds, trials, coupons, metered billing, and payment failure handling. Triggered when a user mentions Cashier, Billable, IncompletePayment, stripe_id, newSubscription, Stripe subscriptions, or billing. Also applies when setting up webhooks, handling SCA/3DS payment failures, testing with Stripe test cards, or troubleshooting incomplete subscriptions, CSRF webhook errors, or migration publish issues.

Use this skill whenever the user mentions Horizon by name in a Laravel context. Covers the full Horizon lifecycle: installing Horizon (horizon:install, Sail setup), configuring config/horizon.php (supervisor blocks, queue assignments, balancing strategies, minProcesses/maxProcesses), fixing the dashboard (authorization via Gate::define viewHorizon, blank metrics, horizon:snapshot scheduling), and troubleshooting production issues (worker crashes, timeout chain ordering, LongWaitDetected notifications, waits config). Also covers job tagging and silencing. Do not use for generic Laravel queues without Horizon, SQS or database drivers, standalone Redis setup, Linux supervisord, Telescope, or job batching.

Adds dynamic custom fields to Eloquent models without migrations using Filament integration. Use when adding the UsesCustomFields trait to models, integrating custom fields in Filament forms/tables/infolists, configuring field types, working with field validation, or managing feature flags for conditional visibility, encryption, and multi-tenancy.

Develops real-time broadcasting with Laravel Echo. Activates when setting up broadcasting (Reverb, Pusher, Ably); creating ShouldBroadcast events; defining broadcast channels (public, private, presence, encrypted); authorizing channels; configuring Echo; listening for events; implementing client events (whisper); setting up model broadcasting; broadcasting notifications; or when the user mentions broadcasting, Echo, WebSockets, real-time events, Reverb, or presence channels.

Builds Kanban board interfaces for Eloquent models with drag-and-drop functionality. Use when creating board pages, configuring columns and cards, implementing drag-and-drop positioning, working with Filament board pages or standalone Livewire boards, or troubleshooting position-related issues.

ACTIVATE when the user works on authentication in Laravel. This includes login, registration, password reset, email verification, two-factor authentication (2FA/TOTP/QR codes/recovery codes), passkeys, profile updates, password confirmation, or any auth-related routes and controllers. Activate when the user mentions Fortify, auth, authentication, login, register, signup, forgot password, verify email, 2FA, passkeys, WebAuthn, or references app/Actions/Fortify/, CreateNewUser, UpdateUserProfileInformation, FortifyServiceProvider, config/fortify.php, or auth guards. Fortify is the frontend-agnostic authentication backend for Laravel that registers all auth routes and controllers. Also activate when building SPA or headless authentication, customizing login redirects, overriding response contracts like LoginResponse, or configuring login throttling. Do NOT activate for Laravel Passport (OAuth2 API tokens), Socialite (OAuth social login), or non-auth Laravel features.

Use this skill to analyze how a Laravel application is actually written and record its conventions as shared rules. Trigger when the user wants to detect, infer, document, or standardize project conventions or coding style, set up or grow `.ai/rules`, resolve mixed or conflicting patterns (e.g. \"are we using Form Requests or inline validation?\"), or onboard agents and teammates to \"how we do things here\". Covers: a systematic sweep of ~49 Laravel convention dimensions (validation, models, architecture, testing, frontend, database, console), open-ended house-pattern discovery, conflict reporting, and recording rules scoped to the right paths via the Boost `record-rule` MCP tool. Do not use for one-off code review, enforcing formatting a linter already handles, or editing `.ai/rules` files by hand.

Apply this skill whenever writing, reviewing, or refactoring Laravel PHP code. This includes creating or modifying controllers, models, migrations, form requests, policies, jobs, scheduled commands, service classes, and Eloquent queries. Triggers for N+1 and query performance issues, caching strategies, authorization and security patterns, validation, error handling, queue and job configuration, route definitions, and architectural decisions. Also use for Laravel code reviews and refactoring existing Laravel code to follow best practices. Covers any task involving Laravel backend PHP code patterns.

Build filtered, sorted, and included API endpoints using spatie/laravel-query-builder. Activates when working with QueryBuilder, AllowedFilter, AllowedSort, AllowedInclude, or when the user mentions query parameters, API filtering, sorting, includes, or spatie/laravel-query-builder.

Use for any task or question involving Livewire. Activate if user mentions Livewire, wire: directives, or Livewire-specific concepts like wire:model, wire:click, wire:sort, or islands, invoke this skill. Covers building new components, debugging reactivity issues, real-time form validation, drag-and-drop, loading states, migrating from Livewire 3 to 4, converting component formats (SFC/MFC/class-based), and performance optimization. Do not use for non-Livewire reactive UI (React, Vue, Alpine-only, Inertia.js) or standard Laravel forms without Livewire.

Use immediately after finishing any code change in Relaticle (implementation, fix, refactor, migration) before reporting work as complete. The skill itself decides whether to run; do not skip on 'small' changes. Triggers an adversarial post-task QA pass: reads the diff, scores risk, generates an SBTM charter, drives a real browser through a pairwise-reduced test matrix across Filament/Livewire/REST/MCP surfaces, classifies findings by severity, auto-fixes High findings within strict guardrails, and promotes High+ findings to permanent Pest browser regression tests. Reports land in .context/testing/reports/. Skip with [skip-qa] in the user message or MANUAL_TESTING_SKIP=1.

Use this skill for Laravel MCP development. Trigger when creating or editing MCP tools, resources, prompts, servers, or UI apps in Laravel projects. Covers: artisan make:mcp-* generators, routes/ai.php, Tool/Resource/Prompt/AppResource classes, schema validation, shouldRegister(), OAuth setup, URI templates, read-only attributes, MCP debugging, MCP UI apps, the x-mcp::app Blade component, createMcpApp(), default AppResource handle() auto-infers view from class name, Response::view(), AppMeta/Csp/Permissions/appMeta() configuration, #[RendersApp] attribute, Library enum for CDN libraries (Tailwind, Alpine), and host theming via CSS variables. Use this whenever the user mentions MCP apps, MCP UI, interactive MCP resources, styling MCP apps with Tailwind or Alpine, or building visual interfaces for AI agents.

Build and work with spatie/laravel-medialibrary features including associating files with Eloquent models, defining media collections and conversions, generating responsive images, and retrieving media URLs and paths.

Develops OAuth2 API authentication with Laravel Passport. Activates when installing or configuring Passport; setting up OAuth2 grants (authorization code, client credentials, personal access tokens, device authorization); managing OAuth clients; protecting API routes with token authentication; defining or checking token scopes; configuring SPA cookie authentication; handling token lifetimes and refresh tokens; or when the user mentions Passport, OAuth2, API tokens, bearer tokens, or API authentication. Make sure to use this skill whenever the user works with OAuth2, API tokens, or third-party API access, even if they don't explicitly mention Passport.

Use when working with Laravel Pennant the official Laravel feature flag package. Trigger whenever the query mentions Pennant by name or involves feature flags or feature toggles in a Laravel project. Tasks include defining feature flags checking whether features are active creating class based features in `app/Features` using Blade `@feature` directives scoping flags to users or teams building custom Pennant storage drivers protecting routes with feature flags testing feature flags with Pest or PHPUnit and implementing A B testing or gradual rollouts with feature flags. Do not trigger for generic Laravel configuration authorization policies authentication or non Pennant feature management systems.

Mandatory point-of-use sequence for capturing annotated screenshots that go into deliverables (ClickUp reviews, bug repros, internal evidence, end-user docs). Invoke this BEFORE every screenshot capture, not once per session, so the rules are fresh in context at the moment you actually shoot. Covers the annotate → verify-crop → shoot → read-back flow, the helper JS files (annotate.js, verify-crop.js), and the audience-specific annotation rules (label vs. no label). If you are about to type `agent-browser screenshot file.png` for any reason other than throwaway debugging, invoke this skill first.

Manages OAuth social authentication with Laravel Socialite. Activate when adding social login providers; configuring OAuth redirect/callback flows; retrieving authenticated user details; customizing scopes or parameters; setting up community providers; testing with Socialite fakes; or when the user mentions social login, OAuth, Socialite, or third-party authentication.

Apply Spatie's JavaScript coding standards for any task that creates, edits, reviews, refactors, or formats JavaScript or TypeScript code; use for variable declarations, comparisons, functions, destructuring, and Prettier configuration to align with Spatie's JS conventions.

Apply Spatie's Laravel and PHP coding standards for any task that creates, edits, reviews, refactors, or formats Laravel/PHP code or Blade templates; use for controllers, Eloquent models, routes, config, validation, migrations, tests, and related files to align with Laravel conventions and PSR-12.

Apply Spatie's security guidelines when configuring applications, databases, servers, credentials, or signed Git commits, or when reviewing code for security concerns; use for SSL setup, CSRF protection, password hashing, database permissions, and server hardening.

Apply Spatie's version control conventions when creating commits, branches, pull requests, or managing Git repositories; use for naming repos, writing commit messages, choosing branch strategies, and merging code.

Always invoke when the user's message includes 'tailwind' in any form. Also invoke for: building responsive grid layouts (multi-column card grids, product grids), flex/grid page structures (dashboards with sidebars, fixed topbars, mobile-toggle navs), styling UI components (cards, tables, navbars, pricing sections, forms, inputs, badges), adding dark mode variants, fixing spacing or typography, and Tailwind v3/v4 work. The core use case: writing or fixing Tailwind utility classes in HTML templates (Blade, JSX, Vue). Skip for backend PHP logic, database queries, API routes, JavaScript with no HTML/CSS component, CSS file audits, build tool configuration, and vanilla CSS.

Laravel test design and review. Use when selecting coverage, naming or structuring tests, choosing assertions or test data, isolating dependencies, testing HTTP or security boundaries, improving suite performance, or reviewing test value. Use framework guidance or search-docs for Pest and PHPUnit syntax.

Check OSWorld tasks. Validate the evaluation function, verify that the instruction is feasible given the task setup and agent-visible files, inspect setup artifacts when needed, and produce both markdown and structured JSON reports.

Analyze OSWorld-V2 agent trajectory logs and task results to produce actionable insights. Use this skill whenever the user wants to understand agent performance on OSWorld tasks — including analyzing trajectories, reviewing task results, finding error patterns, comparing code vs GUI strategies, identifying which tools/commands the agent used, or deciding which task types to scale up in the benchmark.

Migrate an agent from upstream OSWorld into this OSWorld-V2 repository, add matching evaluation entrypoints, and verify the integration.

Provision and verify an OSWorld-V2 checkout after clone. Use when the user asks for OSWorld-V2 setup, installation, onboarding, AWS provider setup, Docker provider setup, mocked website server setup, GitLab server setup, gated task download, CUA-Harness hybrid experiment setup, or a final runnable export block. The skill should install/configure the selected supported infrastructure where possible, ask for user confirmation or credentials when required, and report what is fully configured versus still blocked.

Reproduce CUA-Harness experiments on WeaveBench from a GitHub checkout. Use when the user wants an AI coding agent to set up dependencies, download WeaveBench assets, prepare the 120G VM, configure Qwen/Anthropic-compatible APIs, run smoke tests, launch full or subset evaluations, inspect logs, or summarize scores for this repository.

Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+ AI clients (Cursor, Claude Desktop, Windsurf, VS Code, Codex, Gemini CLI, Trae, Cline, etc.), full CLI reference (tu list/grep/find/info/run/test/status/build/serve), Coding API quickstart, agentic tools, code executor, API key walkthrough, skill installation, and upgrading. Use when user asks how to set up ToolUniverse, which access mode to use (MCP vs CLI vs SDK), configuring MCP servers, using the CLI, troubleshooting installation, upgrading, or mentions installing ToolUniverse or setting up scientific tools. Also triggers for "how do I use ToolUniverse", "what's the best way to access tools", "command line", "tu command", "coding API", "tu build".

Systematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) for clinical significance. Produces 5-tier verdict (Pathogenic / Likely Pathogenic / VUS / Likely Benign / Benign) with cited evidence per criterion. Use for variant interpretation, VUS resolution, and pathogenicity assessment. Combines ClinVar, gnomAD, computational predictors, and gene-mechanism context.

Comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling for drug candidates. Integrates ADMET-AI predictions, SwissADME drug-likeness, PubChemTox experimental toxicity, ChEMBL clinical data, Lipinski rule-of-five, and CYP interaction data. Use for drug-likeness assessment, BBB penetration, bioavailability, hepatotoxicity prediction, ADME/PK profiling, or screening compound libraries before lab testing.

Detect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC). Generates quantitative safety signal scores (0-100) with evidence grading. Use for post-market surveillance, pharmacovigilance, drug safety assessment, regulatory submissions, and detecting rare AE signals not visible in clinical trials.

Map environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-level toxicity. Uses AOPWiki, GHS classification, IARC carcinogen status, and LD50 data. Use for environmental/industrial chemical risk assessment, regulatory-grade hazard characterization, and AOP stressor mapping. Distinct from drug-safety analysis (use tooluniverse-pharmacovigilance for drugs).

Aging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug discovery (dasatinib+quercetin, fisetin, navitoclax), epigenetic clocks, telomere biology, and longevity GWAS. Use for senescence-pathway analysis, age-related disease genetics, senolytic-target discovery, and centenarian-genetics queries. Distinguishes correlative vs causal evidence (knockout, intervention).

Therapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity maturation, developability (aggregation, stability, PTMs), structure modeling (AlphaFold/PDB CDR analysis), immunogenicity prediction, and manufacturing feasibility. Use for biologic-drug optimization, mAb design review, biosimilar engineering, and clinical-precedent comparison.

Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on Google Antigravity (AGY / Antigravity IDE / Antigravity 2.0). ALWAYS consult this skill for any of those — don't answer from memory, because the exact CLI name (agy), the "agy plugin install <path>" flow, the uvx tooluniverse MCP server, and the API-key env vars are easy to get wrong. Use it whenever someone wants to get ToolUniverse (or "the 1000+ scientific tools" / "the harvard tools") working on Antigravity, says the Antigravity plugin or its tools/skills won't load, hits a uvx or MCP-server startup error, asks how Antigravity updates it, wants to pin or remove it, or finds it running an old tool version. Not for the Codex plugin (use tooluniverse-codex-plugin) or Claude Code plugin (use tooluniverse-claude-code-plugin), for running research with the tools, or for authoring new tools or skills.

Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem.

Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory. Triggers on any 'which gene/drug/variant/disease/pathway/miRNA/TF...' lookup, any question phrased 'according to <database>' (DisGeNet, OMIM, MSigDB, miRDB, GTRD, MGI, Ensembl, ClinVar, ChEMBL, OpenTargets, Reactome, GtoPdb, UniProt...), and multiple-choice biology/medicine knowledge questions where one option must be verified against an authoritative source. NOT for analyzing user-supplied data files (CSV/VCF/h5ad → use the data-analysis router) and NOT for open-ended literature synthesis. Use whenever a single correct answer exists in a public biomedical database and could be looked up rather than guessed.

Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring consistent terminology across cancer-genomics pipelines.

TCGA/GDC cancer genomics analysis — cohort construction, clinical metadata retrieval, somatic mutation frequencies, survival analysis, and multi-omics integration. Use for TCGA-BRCA-style cohort studies, mutation prevalence by cancer type, survival-by-mutation analysis, and pan-cancer driver discovery. Always cancer-type-specific (don't use pan-cancer counts without cohort context).

Clinical interpretation of somatic cancer mutations for precision oncology. Transforms a gene + variant + cancer-type input into an actionable report: clinical evidence tier (CIViC, OncoKB), therapeutic options (FDA-approved + investigational), resistance mechanisms, prognosis, and matching clinical trials. Use for tumor-board variant calls, somatic-mutation actionability assessment, and treatment selection. Always cancer-type-specific.

Cancer cell-line selection and profiling for experimental model choice. Cross-references DepMap, Cellosaurus, COSMIC, PharmacoDB to deliver identity verification, mutation/CNV profile, gene dependencies, drug sensitivities, and druggable targets. Use to answer 'which cell line should I use for studying gene X?' or 'is this cell line a good model for cancer Y?'. Outputs ranked recommendations with rationale, growth characteristics, and known pitfalls.

Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing), fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity across databases. Always use English compound names; flags ambiguous queries (e.g., Vitamin D has multiple forms).

Chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experimental data, GHS/IARC hazard classification, and exposure-context analysis. Use for chemical hazard identification, occupational/consumer-product toxicity, dose-response evaluation, and acute (LD50) vs chronic toxicity assessment. Distinguishes drug toxicity from environmental chemical toxicity.

Find commercial sources for chemical compounds — PubChem/ChEMBL identity resolution then vendor catalog search across ZINC, Enamine, eMolecules, Mcule. Compares pricing, availability, and identifies purchasable analogs when an exact compound is not in stock. Use for chemical procurement, virtual library curation, and 'where can I buy X' questions for synthesis planning.

Install the ToolUniverse Claude Code plugin in one step — provides MCP server with 1000+ scientific tools, 120+ research skills, slash commands, hooks, and the research agent. Use for first-time plugin install, troubleshooting plugin not loading, verifying MCP server connection, listing API key requirements, or configuring auto-update.

End-to-end drug safety review integrating FDA labels, FAERS adverse event reports, PRR/ROR disproportionality, pharmacogenomic biomarkers, clinical trial data, and published literature. Use for regulatory drug safety reviews, comprehensive pharmacovigilance reports, label-vs-real-world AE comparison, and clinical decision support for drug safety.

Search and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, USPSTF, IDSA, NIH consensus, ESMO/ESC/EASL European societies, and US specialty associations. Use for evidence-graded treatment recommendations, dosing protocols, screening guidance, and authoritative-source-prioritized clinical guidance (NICE/WHO ranked above society guidelines).

Compute and interpret validated bedside clinical risk scores and pretest probabilities for an INDIVIDUAL patient — pick the right score for the scenario, gather inputs, run the deterministic calculator tool, and read the result against an interpretation table. Covers CHA2DS2-VASc (AF stroke risk), HAS-BLED (bleeding on anticoagulation), CURB-65 (pneumonia severity / admit decision), qSOFA (sepsis screen), Child-Pugh + MELD-Na (cirrhosis severity / transplant priority), Wells DVT and Wells PE (VTE pretest probability), ASCVD (10-year cardiovascular risk / statin decision), and eGFR CKD-EPI (kidney function / drug dosing). Use when asked things like "stroke risk for this AF patient", "should this patient be anticoagulated", "pneumonia severity — admit or not?", "sepsis screen this patient", "DVT/PE pretest probability", "10-year cardiovascular risk", "cirrhosis severity / MELD score", or "eGFR / kidney function". Pairs CHA2DS2-VASc with HAS-BLED to weigh anticoagulation. NOT for polygenic/genetic risk (use tooluniverse-polygenic-risk-score), NOT for population-level epidemiology/incidence (use tooluniverse-epidemiological-analysis), and NOT for diagnostic test sensitivity/specificity/likelihood-ratio math (use tooluniverse-diagnostic-test-evaluation).

Strategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory pathway) using precedent trials and FDA guidance. Produces enrollment projections, endpoint recommendations, and approval-pathway analysis. Use for trial-protocol design, power/sample-size estimation, comparator selection, and FDA submission strategy. Driven by precedent-based reasoning rather than first-principles math.

AI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient's molecular profile (mutations, biomarkers, expression) and clinical state into ranked clinical-trial recommendations with evidence tiers. Searches ClinicalTrials.gov, the EU CTIS register (European/EEA trials), AND the ISRCTN registry (UK/international) plus cross-references CIViC, OpenTargets, ChEMBL, and FDA labels. Use for matching patients to trials by genotype, biomarker-driven trial selection, trial-eligibility scoring, and finding trials across the US, Europe, and the UK.

Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses. Use for phylogenetic gene tracing, model-organism mapping, and evolutionary-genomics queries.

Solve quantitative problems in biophysics — pharmacokinetics (PK volume of distribution, clearance, half-life), epidemiology (R0, attack rate), toxicology (LD50, NOAEL), population genetics (Hardy-Weinberg, Fst), enzyme kinetics (Michaelis-Menten), thermodynamics. Use for first-principles quantitative biology calculations, dose calculations, exposure assessment, and biophysical-property estimation.

Analyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritization, and pathway GSEA on screen output. Use for genome-wide essentiality screens, synthetic-lethality discovery, dropout vs positive-selection screen analysis, target identification, and resistance-screen interpretation. Includes screen-QC and statistical thresholds.

Add custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL APIs, computational logic), and best-practices for return schemas. Use for wrapping new APIs, adding domain-specific computations, or contributing tools to the registry.

Integrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse databases (UniProt, GO, Reactome, ClinVar, OpenTargets). Use for adding gene function/pathway/disease annotations to a result list, building biological narrative around statistical findings, and going beyond p-values to mechanism.

Universal data access patterns for downloading and parsing scientific data when ToolUniverse tools don't cover the source, only return metadata, or you need bulk records. Use for VCF/h5ad/BAM/SDF/GCT parsing, multi-step API workflows (search to filter to download to parse), thousands of records at once, or sources with no dedicated tool. Write Python code via Bash for every step.

Find and evaluate research datasets for any scientific question. Maps research questions to required study designs (longitudinal vs cross-sectional, observational vs experimental, single-cohort vs multi-cohort). Use when the user asks 'find data about X', 'where can I get data on Y', or needs a specific cohort/survey/repository. Covers GEO, ArrayExpress, dbGaP, NHANES, UK Biobank, ClinicalTrials.gov, GWAS Catalog, and 30+ scientific repositories.

Diagnostic test / biomarker accuracy — sensitivity, specificity, PPV, NPV, likelihood ratios, accuracy from a 2x2 table; ROC curve, AUC, and the optimal cutoff (Youden) for a continuous biomarker; and post-test probability via Bayes. Use when you have test results vs a gold standard (binary 2x2, or a continuous score + true labels) and need to judge how good the test is, pick a threshold, or compute the probability of disease given a result. Emphasizes the prevalence-dependence of PPV/NPV.

Generate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies, repurposing candidates), clinical trials, epidemiology (prevalence, incidence), and phenotypes (HPO). Use for full disease overviews, comprehensive disease characterization, and orphan/rare-disease profiling.

Dose-response / concentration-response curve fitting — IC50, EC50, Hill slope, Emax/Emin efficacy, and relative potency from paired concentration vs response data (enzyme/cell assays, drug screening, agonist/antagonist pharmacology). Fits the 4-parameter logistic (Hill sigmoidal) model. Use when you have concentrations + responses and need a potency value, to compare two compounds' potency, or to judge curve quality. NOT for image-derived dose-response (use tooluniverse-image-analysis) and NOT for survival/regression (use tooluniverse-statistical-modeling).

Assess drug-drug interactions — CYP metabolic interactions (substrate/inhibitor/inducer), transporter (P-gp, BCRP, OATP) effects, pharmacodynamic synergy/antagonism, clinical significance scoring, and management recommendations. Use for polypharmacy review, prescribing decision support, and safety analysis when adding or switching drugs.

Trace drug mechanism of action — primary target → downstream signaling → pathway perturbation → tissue/organ effect → clinical outcome. Uses DrugBank, ChEMBL, KEGG, Reactome, STRING. Use for understanding how a drug works, identifying off-target effects, mechanism-based combination therapy design, and writing mechanism sections of reports.

Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity, NDA/BLA pathways. Use for jurisdiction-aware approval status (FDA vs EMA), generic vs brand availability, exclusivity expiry tracking, and regulatory pathway selection. Always specifies the market when reporting status.

Identify drug repurposing candidates via target-based, compound-based, and disease-based strategies. Combines drug-target-disease network reasoning with mechanism rationale, clinical-trial precedent, and patent/regulatory feasibility. Use for hypothesis-generating repurposing for orphan diseases, finding existing drugs for new indications, and prioritizing candidates by evidence and feasibility.

Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researchers, or regulatory work.

Drug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic using the standard reference models (Bliss independence, HSA / highest single agent, Loewe additivity, ZIP, and the Chou-Talalay Combination Index). Use when you have measured single-drug and combination effects (inhibition/viability) and need a synergy score. Explains which model to use, what data each one needs, and how to read the score. NOT for looking up pre-computed synergy in a database (use the SYNERGxDB tool / cell-line-profiling skill).

Quantitative drug-target validation pipeline. Scores druggability, selectivity, safety profile, ADMET feasibility, and structural tractability with a composite Target Validation Score (0-100) and GO/NO-GO recommendation. Use for go/no-go decisions on a target before commit-to-medchem, target prioritization across a list, and target-deselection rationale.

Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamics, conservation status (IUCN), niche ecology. Use for biodiversity questions, species comparison, invasion biology, conservation prioritization, and ecology-related literature search.

Search and analyze electron microscopy data — cryo-EM density maps (EMDB), fitted atomic models (PDB), raw micrograph datasets (EMPIAR), and cryo-electron tomography volumes (CryoET Data Portal). Use for finding 3D structural data on a protein/complex, comparing experimental EM resolution to AlphaFold confidence, and accessing raw EM data for re-processing.