Use when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports and PDF visualization in a single output directory. NOT for: differential expression, single-cell analysis, enrichment analysis, or workflows without a key gene list.

Routes and links multilingual Astro sites with the built-in `i18n` config and `astro:i18n`. Use when adding locale folders or `prefixDefaultLocale`, building links with `getRelativeLocaleUrl` or reading `Astro.currentLocale`, falling back to an untranslated locale, translating content per locale, or emitting hreflang alternates.

Configures Astro deploy adapters for Cloudflare Workers, Vercel, Netlify, and Node. Use when adding or switching an adapter, wiring platform bindings, running middleware at the edge, caching on-demand pages, or fixing a failing deploy build.

Use when correcting batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and generating before-and-after QC plots. NOT for: single-cell integration, raw FASTQ processing, differential expression without batch labels, or datasets without biological groups.

Migrates Astro projects off the removed `@astrojs/db` package and wires up a replacement SQL database. Use when a project still imports `astro:db`, or when choosing and querying a SQL database on Astro 7 — node:sqlite, Drizzle, or a platform database.

Use when building XGBoost models on tabular data and returning feature importance ranking outputs. Supports binary classification and regression with automatic task detection, train-test split, performance tables, feature importance ranking tables, and PNG importance plots.

Project rules for building Astro sites with coding agents. Use when scaffolding, adding integrations, running astro dev, or choosing how to install packages in an Astro repo.

Builds Astro content collections in `src/content.config.ts`. Use when adding a collection, writing a loader or schema, querying or rendering entries, configuring Markdown or MDX plugins, or migrating a legacy `src/content/config.ts`.

Use when training a LightGBM model on tabular data in R and returning model metrics, feature importance ranking tables, and feature importance plots.

Optimizes images and loads fonts in Astro. Use when adding local or remote images, choosing between `<Image />`, `<Picture />`, and `getImage()`, making images responsive, or registering a font family.

Optimizes manuscript titles and abstracts for information density, factual accuracy, and submission fit in biomedical research writing.

Builds type-safe Astro server functions with `defineAction`. Use when handling an HTML form POST, calling a server mutation from client JavaScript, or choosing between an action and an API endpoint.

Matches your study to appropriate journals based on topic, design, and evidence strength. Use when deciding where to submit a manuscript, comparing journal options by impact factor vs scope fit vs method tolerance, or finding a realistic submission target after a rejection. Also triggers on "where should I submit this paper", "which journal is best for my study", "find journals for my manuscript", "is this a good fit for [journal]", or "I need a journal with IF around X".

Configures Astro 7 routing, output modes, middleware, and upgrades from Astro 5 or 6. Use when choosing static or server output, adding middleware, creating pages or endpoints, or migrating to Astro 7.

Converts biomedical table content into clear manuscript or presentation narrative by prioritizing meaningful patterns, contrasts, and interpretation boundaries rather than restating every number.

Register Model Context Protocol servers on the host with sbx mcp and expose them to sandboxes through the built-in MCP gateway — registration, OAuth, static vs dynamic mode, and Cedar MCP policy. Use when adding an MCP server to a sandbox, deciding between --static-mcp and dynamic discovery, wiring OAuth credentials for a remote server, or writing a governance policy for MCP tool calls.

Structures research progress into focused and actionable slides for lab meetings or project reviews without inventing missing content.

Run and operate Docker Sandboxes — choosing an agent, passing it flags, git workspace modes, ports, secrets, network policy, and sharing host skills into a sandbox. Use when starting or re-attaching to a sandbox, picking between the built-in agents, signing in from CI, copying files in or out, or reaching for the right sbx command.

Administer Docker Sandbox governance — local versus organization policy, filesystem and network access rules, audit logging, and sign-in enforcement across a fleet of developer machines. Use when creating or scoping an organization policy, diagnosing why an allow rule has no effect, writing filesystem mount rules, configuring audit delivery or SIEM forwarding, or deploying MDM sign-in enforcement. This is the administrator's view; route a single developer's blocked request to diagnosing-sbx-sandboxes instead.

Builds prioritized manuscript revision plans for major or minor revisions by separating comments that require experiments, analyses, clarification, restructuring, or wording changes.