Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add cyanheads/protein-mcp-server --skill add-toolgit clone --depth 1 https://github.com/cyanheads/protein-mcp-serverWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/cyanheads/protein-mcp-server/add-tool)<a href="https://agentmods.dev/skills/cyanheads/protein-mcp-server/add-tool"><img src="https://agentmods.dev/badge/skills/cyanheads/protein-mcp-server/add-tool/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/cyanheads/protein-mcp-server/add-tool"><img src="https://agentmods.dev/badge/skills/cyanheads/protein-mcp-server/add-tool.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00035 | $0.17726 |
| Opus 5.5 | $0.00014 | $0.07090 |
| Sonnet 5.5 | $0.00007 | $0.03545 |
| Haiku 4.5 | $0.00003 | $0.01773 |
Grade A, and why
add-tool scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
const articles = await fetch(input.pmids); This is a copy
100% identical to add-tool — 0 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 903 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Context
Tools use the tool() builder from @cyanheads/mcp-ts-core. Each tool lives in src/mcp-server/tools/definitions/ with a .tool.ts suffix. The standard registration pattern uses a definitions/index.ts barrel that collects all tools into an allToolDefinitions array for createApp(). Fresh scaffolds from init start with direct imports in src/index.ts — the barrel is introduced as definitions grow. Match the pattern already used by the project you're editing.
Steps
- Gather the tool's name, purpose, and input/output shape from the user's request — ask only if genuinely absent
- Determine if it needs input the caller may not supply — a confirmation, a choice, the client's roots — which makes it a multi-round-trip handler (
ctx.requestInput/ctx.inputs, seeapi-context) - Create the file at
src/mcp-server/tools/definitions/{{tool-name}}.tool.ts - Register the tool in the project's existing
createApp()tool list (directly insrc/index.tsfor fresh scaffolds, or via a barrel if the repo already has one) - Run
bun run devcheckto verify — it applies Biome's formatting fixes as it runs - Smoke-test with
bun run rebuild && bun run start:stdio < /dev/null(orstart:http) — theCore services constructedlog record must list the new tool in itstoolsfield (the message text shows only counts); if it doesn't, the tool never reachedcreateApp()
Naming
Tools use lowercase snake_case with a canonical server/domain prefix, {server}_{verb}_{noun} by default. Drop the noun only when the verb is a complete action on its own (git_pull, git_status): if {server}_{verb} leaves "…what?" unanswered — search what? connect to what? — the noun is missing. The full rule is the Name row of the design-mcp-server Design table.
Examples: pubmed_search_articles, pubmed_fetch_fulltext, clinicaltrials_find_eligible.
The server prefix is judged on clarity, not length: the brand name or the plain well-known word for the domain both pass (pubmed_, patents_); an abbreviation fails only when it reads as something else out of context (loc_, ct_). A fourth segment is fine when the noun is inherently two words (openfda_search_device_clearances). When a name resists the schema — can't pick a verb, noun feels generic, the verb wants a second word — that's usually a signal the scope is fuzzy; split the tool, rename, or reconsider.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago Changed · +8 lines 9210f47a1f51
- 17d ago Changed · +13 lines 8bda9da26197
- 1mo ago Changed · +46 lines 95ce1591e082
- 1mo ago Changed 631c1b8a21c0
- 1mo ago Changed · +32 lines fd95655dd297
- 1mo ago First seen · 804 lines · 35 tokens per session scan A 5ba100b246b6
add-tool is a skill published in the GitHub repository cyanheads/protein-mcp-server (6 stars, last pushed 7d ago), licensed Apache-2.0. It adds 35 tokens to every session and 17,726 once invoked, about $0.0001 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). It is 100% identical to add-tool, differing in 0 lines, and is treated as a copy.
Other skills, from other repositories
api-context
Canonical reference for the unified Context object passed to every tool and resource handler in @cyanheads/mcp-ts-core. Covers the full interface, its RequestContext base, all sub-APIs (ctx.log, ctx.state, ctx.requestInput, ctx.inputs, ctx.clientCapabilities, ctx.enrich, ctx.content), and when to use each.
api-errors
McpError constructor, JsonRpcErrorCode reference, and error handling patterns for @cyanheads/mcp-ts-core. Use when looking up error codes, understanding where errors should be thrown vs. caught, or using ErrorHandler.tryCatch in services.
add-service
Scaffold a new service integration. Use when the user asks to add a service, integrate an external API, or create a reusable domain module with its own initialization and state.
api-workers
Cloudflare Workers deployment using createWorkerHandler from @cyanheads/mcp-ts-core/worker. Covers the full handler signature, binding types, CloudflareBindings extensibility, runtime compatibility guards, and wrangler.toml requirements.
add-app-tool
Scaffold an MCP App tool + UI resource pair. Use when the user asks to add a tool with interactive UI, create an MCP App, or build a visual/interactive tool.
api-auth
Authentication, authorization, and multi-tenancy patterns for @cyanheads/mcp-ts-core. Use when implementing auth scopes on tools/resources, configuring auth modes (none/jwt/oauth), working with JWT/OAuth env vars, or understanding how tenantId flows through ctx.state.