Results for “pre-tool-use”

Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).

Use when serving as a peer reviewer and deciding whether and how AI may assist, when a manuscript under review must never be pasted into an external tool, or when a confidentiality-preserving review and disclosure are needed.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Build, test, inspect, install, and deploy MCP servers with FastMCP in Python. Use when creating a new MCP server, wrapping an API or database as MCP tools, exposing resources or prompts, or preparing a FastMCP server for Claude Code, Cursor, or HTTP deployment.

Build, test, inspect, install, and deploy MCP servers with FastMCP in Python. Use when creating a new MCP server, wrapping an API or database as MCP tools, exposing resources or prompts, or preparing a FastMCP server for Claude Code, Cursor, or HTTP deployment.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Search and deploy services from Railway's template marketplace. Use when user wants to add a service from a template, find templates for a specific use case, or deploy tools like Ghost, Strapi, n8n, Minio, Uptime Kuma, etc. For databases (Postgres, Redis, MySQL, MongoDB), prefer the railway-database skill.

Full architectural preferences and skill routing map for Sage/Acorn projects — complete workflow ecosystem reference, Lando command tables, design tool URL routing (Paper/Stitch/Figma/Pencil/Playwright), MCP query patterns, discover-abilities, execute-ability, WordPress MCP Adapter, plan system structure, integration with base superpowers skills. Invoke for: "which skill should I use", "architectural preferences", "design tool routing", "mcp query patterns", "full skill list", "sage ecosystem overview", "when to use Livewire vs Blade", "Acorn vs WordPress pattern decision". Skip when: the session-start routing table already covers your decision — invoke the target skill directly instead of loading this overview first.

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

Search and deploy services from Railway's template marketplace. Use when user wants to add a service from a template, find templates for a specific use case, or deploy tools like Ghost, Strapi, n8n, Minio, Uptime Kuma, etc. For databases (Postgres, Redis, MySQL, MongoDB), prefer the railway-database skill.

Self-contained code review checklist — formatting, type safety, duplication, readable conditions, logic-out-of-UI, test coverage, comment quality. Adapts to whatever tooling the project actually has (skips Prettier/TypeScript/test-runner checks if unconfigured). Use before merging, after completing a feature, or any time you want a second pass on code quality. In Claude Code, prefer the official `code-review` skill or `pr-review-toolkit`/`feature-dev` code-reviewer agents instead — both are real, installed, and go deeper than this checklist. This copy exists for Codex/Cursor portability, where those agents aren't available.

Simulates open quantum systems with QuTiP, the Quantum Toolbox in Python, solving Lindblad master equations (mesolve), Monte Carlo trajectories (mcsolve), and unitary dynamics (sesolve). Use when studying master-equation or Lindblad dynamics, decoherence, dissipation, quantum optics, cavity QED, or open-system time evolution. NOT for circuit-based quantum computing or hardware execution — for IBM Quantum circuits prefer alterlab-qiskit, for Google Quantum AI or NISQ circuits prefer alterlab-cirq, and for gradient-trained quantum ML prefer alterlab-pennylane. Part of the AlterLab Academic Skills suite.

Design privacy-aware observability for AI agents using traces, spans, structured events, metrics, cost attribution, dashboards, alerts, and investigation workflows. Use when instrumenting an agent, debugging intermittent tool or model failures, defining service-level objectives, analyzing latency or spend, auditing agent decisions, or preparing production monitoring.

Flyway database migrations for Spring Boot applications. Covers migration scripts, versioning, callbacks, and rollback strategies. Based on production patterns from castellino and gestionale-presenze projects. USE WHEN: user mentions "flyway", "database versioning", "Java migrations", "Spring Boot migrations", "V1__", "migration checksum" DO NOT USE FOR: general migration strategies - use `migrations` instead, Liquibase - use specific tool skill, Prisma/TypeORM - use respective skills

Premium product design, UX direction, conversion-aware interface strategy, and trust-focused UI guidance for Nick's apps. Use when designing or refining any UI so it feels high-end, clear, trustworthy, and shaped by the product strategy rather than generic aesthetics. Best for SaaS apps, dashboards, fintech tools, admin tools, onboarding flows, landing pages, and productized web apps where design needs to support activation, trust, buyer confidence, and monetization.

Destructive Command Guard. Installs a pre-tool-use hook that blocks unrecoverable shell commands (rm -rf /, git reset --hard, git clean -fd, rm of .env / credentials, force-pushing to main, fork bombs, shred / dd, etc.) before the agent executes them. Use when the user says "install dcg", "destructive command guard", "guard rails for destructive commands", or invokes /dcg.

VS-Enhanced Evidence Quality Appraiser - Prevents Mode Collapse with context-adaptive quality assessment Enhanced VS 3-Phase process: Avoids automatic tool application, delivers research-specific evaluation strategies Use when: appraising study quality, assessing risk of bias, grading evidence Triggers: quality appraisal, RoB, GRADE, Newcastle-Ottawa, risk of bias, methodological quality

Reviews code using pi CLI with read-only tools. Delegates the review to pi (dev/pi) with a structured review rubric, running in read-only mode to prevent accidental edits. By default reviews uncommitted working tree changes (git diff HEAD) with pi restricted to the read tool; explicit targets (--branch/--diff/@file/PR) or --explore widen pi to read,grep,find,ls. Use when the user asks to "review code with pi", "pi review", "have pi review", "let pi review", or invokes /pi:review.

Invoke a registered skill from the current skill listing. BLOCKING REQUIREMENT: when a skill from the listing matches the user's request, you MUST call this tool (not free-form text). Do not re-invoke a skill to repeat work already done: if a `<skill-loaded>` block for it with the same `args` is already present in the conversation, follow those instructions directly instead of calling the tool again. Do call the tool again when you need the skill with different arguments — the loaded block was expanded with the earlier `args` and will not reflect new inputs.

Design and implement CI/CD pipelines and automation — fast checks on every PR, safe releases, and repeatable workflows. Load when setting up GitHub Actions (or similar), adding pre-merge gates, automating releases, or the user asks "add CI", "set up workflows", "automate checks", "CD pipeline". Not for one-off local scripts (use task-specific tooling).

Rename Pharo methods safely through Genie's `rename_method` MCP refactoring tool. Use when a selector should be renamed while preserving behavior, updating senders and symbol references across the live image, including as one step in larger refactorings such as clarify API names, split responsibilities, or move behavior behind better messages.

Operate Firebase from the terminal with `firebase-tools`: install/auth the CLI, bootstrap `firebase.json` / `.firebaserc`, run the Emulator Suite, deploy Hosting / Functions / rules / App Hosting, manage preview channels, and handle Firebase admin tasks like auth import/export, Remote Config, App Distribution, and Extensions. Use when the job is Firebase platform/project operation through the CLI. Triggers on: firebase deploy, firebase init, firebase emulators, firebase hosting, firebase functions, firebase firestore, firebase database, firebase auth import, firebase remote config, firebase app distribution, firebase extensions, firebase apphosting, firebase dataconnect, firebase cli, firebase-tools, deploy firebase, firebase preview channel, firebase login, firebase use, firebase target apply. Route backend AI workflow orchestration to `genkit` and direct in-app SDK integration to `genkit` (`client-ai-logic` mode).

A Cursor Canvas is a live React app that the user can open beside the chat. You MUST use a canvas when the agent produces a standalone analytical artifact — quantitative analyses, billing investigations, security audits, architecture reviews, data-heavy content, timelines, charts, tables, interactive explorations, repeatable tools, or any response that benefits from visual layout. Especially prefer a canvas when presenting results from MCP tools (Datadog, Databricks, Linear, Sentry, Slack, etc.) where the data is the deliverable — render it in a rich canvas rather than dumping it into a markdown table or code block. If you catch yourself about to write a markdown table, stop and use a canvas instead. You MUST also read this skill whenever you create, edit, or debug any .canvas.tsx file.

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization, specialized fingerprint or descriptor algorithms, reaction enumeration, or conformer generation demand direct API control; for a high-level pandas-friendly wrapper over RDKit prefer alterlab-datamol, and for turning molecules into ML feature vectors prefer alterlab-molfeat. Part of the AlterLab Academic Skills suite.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

Detect-only pre-release validation sweep over the processkit content tree. Walks entity files, SKILL.md definitions, MCP server tools, and cross-references, then emits a single human-readable report with ERROR / WARN / INFO counts. Use when the user invokes `/pk-release-audit`, before tagging a release, or any time you need a comprehensive structural health check beyond what pk-doctor covers. Detect-only; never modifies any file under `context/`.

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Write concise next-agent handoff summaries across sessions, tools, and coding agents. Load when the user says handoff, next agent should know, save context, summarize where we are, switching agents, before ending a meaningful session, or when the user asks to commit, push, commit and push, create a git commit, push to origin, or publish commits — commit/push requests MUST run this skill first to prepare handoff docs, then proceed with git operations.

Port MATLAB Data Acquisition Toolbox code from the discouraged (legacy) session-based interface (daq.createSession, addAnalogInputChannel, startBackground, DataAvailable listeners, queueOutputData, wait) to the recommended DataAcquisition interface (daq("ni"), addinput, start, ScansAvailableFcn, write, preload). Use when migrating legacy DAQ scripts, converting session-API calls, working with DataAcquisition objects, writing multi-feature DAQ scripts that combine triggers, callbacks, continuous acquisition, or analog output. Also use when a user says their DAQ script "used to work" or "errors on R20XX", since modernizing legacy session-API code is a frequent fix for those failures. Trigger keywords: daq, DAQ, NI, session interface, addtrigger, addclock, ScansAvailableFcn, ScansRequiredFcn, daq.createSession, addAnalogInputChannel, startBackground, queueOutputData, DataAvailable, evt.Data, evt.TimeStamps, wait(d), preload, discouraged, legacy, modernize, R2020a.

Perform aerospace unit conversions, time conversions, coordinate frame transformations, and rotation representations using Aerospace Toolbox. Use when converting units (length, velocity, angle, acceleration, angular velocity, force, mass, pressure, temperature, density), computing Julian dates or decimal years, transforming between coordinate frames (ECEF, ECI, LLA, flat Earth, geodetic/geocentric, NED, body, wind, stability), or working with rotation representations (Euler angles, DCM, quaternion, Rodrigues vector). Also use when the user asks about aerospace coordinate systems, reference frames, or rotation conventions.

Security vulnerability scanner and OWASP compliance auditor for codebases. Dependency scanning (npm audit, pip-audit), secret detection (high-entropy strings, API keys), SAST for injection/XSS vulnerabilities, and security posture reports. Activate on 'security audit', 'vulnerability scan', 'OWASP', 'secret detection', 'dependency check', 'CVE', 'security review', 'penetration testing prep'. NOT for runtime WAF configuration (use infrastructure tools), network security/firewalls, or compliance certifications like SOC2/HIPAA (legal/organizational).