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Retrieves the interactions between the query proteins. Use this method only when you specifically need to list the interactions between all proteins in your query set. If user asks for 'physical' or 'complex' use 'physical' network type. - For a **single protein**, the network includes that protein and its top 10 most likely interaction partners, plus all interactions among those partners. - For **multiple proteins**, the network includes all direct interactions between them. - If the user refers to "physical interactions", "complexes", or "binding", set the network type to "physical". - STRING does not store or report information about self-interactions/homomers; if asked, explain the limitation. If few or no interactions are returned, consider reducing the `required_score`. For large query sets (>50 proteins), consider increasing the `required_score` (e.g. ≥700) to focus on high-confidence interactions and avoid overly dense networks. - Expand the names of score sources: `nscore` (neighborhood), `fscore` (fusion), `pscore` (phylogenetic profile), `ascore` (coexpression), `escore` (experimental), `dscore` (database), `tscore` (text-mining)

Retrieves all interaction partners for one or more proteins from STRING. This tool returns all known interactions between your query protein(s) and **any other proteins in the STRING database**. - Use this when asking **“What does TP53 interact with?”** - It differs from the `network` tool, which only shows interactions **within the input set** or a limited extension of it. - If the user refers to "physical interactions", "complexes", or "binding", set the network type to "physical". You can filter for strong interactions using `required_score`. - Evidence scores: `nscore` (neighborhood), `fscore` (fusion), `pscore` (phylogenetic profile), `ascore` (coexpression), `escore` (experimental), `dscore` (database), `tscore` (text mining)

Creates a downloadable file for STRING-derived results. Use this tool when the user explicitly asks to download, save, export, or receive a file containing STRING data, tables, protein lists, enrichment results, networks, etc. When a response would otherwise include a publication-style or supplementary result table, or another table clearly intended for reuse outside chat, mention that a downloadable TSV/CSV file can be generated on request. Ask whether they want the file, unless they already requested it. Do not create the file until the user asks for it. Do not store unrelated data or full conversation transcripts.

Write a text file into a persistent Linux machine. Use this instead of shelling out with cat/echo — no quoting to get wrong.

Read a text file out of a persistent Linux machine.

Stop a persistent Linux machine. The disk and the network address are kept, so starting it again returns the same files at the same address. Stop machines you are done with — a stopped machine costs only its disk.

Permanently delete a persistent Linux machine AND its disk. This cannot be undone — use scalix_computer_stop if you may want the files back.

Create a new container image build from a Git repository or Dockerfile.

Every enricher (YouTube videos, Wikipedia, repo stats, downloads, company profiles, TL;DRs) and which collections turn it on by default. Items carry their results under `enrichment`.

Deploy a v2 app: an HTML document plus a capability manifest, hosted at its own URL. A redeploy only needs the content that changed. Every content field is optional when `app_id` is given, and an omitted one keeps what is live: omit `manifest` for an HTML-only change, omit `html` for a manifest-only change, omit `assets` to keep the current files. This is the cheap path and the default, because an omitted field costs no output tokens at all: a one-line colour change does not resend the whole document, and a manifest edit does not resend it either. A field only needs sending when its content differs from what is live. `assets: []` is the explicit way to clear the asset set, and omitting all three is refused, since there would be nothing to change. The extension keys used most often: app metadata; collections, with per-collection write, update, read and delete role lists, where write gates creates and also gates updates unless an update list is declared; externalHosts, a fetch allowlist; cdn, to allow CDN scripts and styles; capabilities, for Permissions-Policy opt-ins; embeds, an iframe frame-src allowlist; notify, for email-on-row rules; webhooks, for signed HTTP POST on-row rules; and agentTasks, to queue work for an agent running on the owner's own machine, described as a prompt rather than as code. The manifest grammar is documented in the Homespun guide that get_skill returns. Pass no `app_id` to create, which mints a slug and URL and requires both `html` and `manifest`, or pass `app_id` to redeploy an existing app. Supply the HTML inline as `html`, or as `html_path`, an absolute path read on the MCP-server host, which is the relay for a hosted connector or the CLI host for a locally-run one, and not the remote agent's machine; it avoids retransmitting a large HTML file on every deploy, only a locally-run connector can read it, and inline `html` wins if both are given. `dry_run:true` (alias `check`) validates only: it runs the full manifest and asset validation, the redeploy compat gate and the schedule-timezone advisory, then returns { ok, warnings, compat?, breaks? } without creating a version or mutating anything, and it resolves omitted fields the same way a real deploy would, so it reports on exactly the deploy that would run. A redeploy is refused with manifest_incompatible_redeploy, unless force:true, when it would strand rows already written (dropping a collection, tightening a schema, flipping appendOnly), or when it would widen what the app's install screen discloses: a collection's read reaching further than the live manifest, a capability added, cdn turned on, or a host added to externalHosts, embeds or a webhook target. The break quotes the sentence a user would now be asked to approve. Taking access away never prompts: dropping a role, dropping a capability, host or webhook, turning cdn off, or adding update:[\"creator\"] to a write:[\"anyone\"] collection, all redeploy clean. A removed collection is detached rather than deleted. Images, fonts, audio, video and data files ship with the app in the same call via `assets[]`. Each is validated and stored app-scoped and served at its `path` on the app's own origin, so the HTML references it by a stable same-origin path such as `<img src=\"frames/000.jpg\">`; media and font paths support HTTP Range for seeking. A redeploy's assets replace the previous version's set when sent, carry over when omitted, and are cleared by `assets: []`. Returns { app_id, slug, url, version, visibility, created } on create, or { app_id, version, compat, breaks? } on redeploy.

Binary attachments (images, PDFs, audio, video) referenced from event payloads and input_data via `format: homespun-attachment-id`. Actions: upload, fetch, presign, finalize, download, show, list, delete, mint_token, revoke_token, list_tokens. Choosing an upload path matters for cost. An inline upload with `content_base64` carries the bytes in the tool-call arguments, so they enter the model context at a token cost proportional to file size, paid again on every retry; a few-hundred-KB image is already expensive. Two paths avoid that entirely: fetch, when the bytes are reachable at a URL, and presign plus finalize, when the client can PUT the raw bytes out of band. Inline upload suits small assets and clients that have neither a URL nor an out-of-band PUT. fetch takes { source_url (https), scope } and the relay downloads the URL itself behind an SSRF guard (https only, no private, loopback or metadata hosts, DNS pinned, redirects refused, size-capped and timed out), then runs the same byte-sniff, allowlist, size, quota and scan checks as any upload. It works on any storage backend. upload takes either `content_base64` (base64 bytes, no filesystem) or `file_path` (an absolute path read on the relay host, so it only applies when the file is local to the relay). presign plus finalize is token-free: presign with { mime, size, sha256, scope } returns { put_url, attachment_id }, the caller PUTs the raw bytes to put_url over plain HTTP out of band, then finalize with the attachment_id. At finalize the relay re-reads the stored bytes, sniffs the real type, and enforces the same allowlist, size, sha256, quota and scan checks, so a presign that misstates its mime is caught and never served inline. The presigned path requires the Azure storage backend; a filesystem-backed relay returns a clear not-supported error and fetch or inline upload apply there instead. download writes to an absolute out_path or returns base64. An upload is scoped to agent (the default, reusable) or app. mint_token returns a /b/<token> capability URL, shown once, that a browser can GET without the caller's API key.

Reports a problem with homespun itself to the relay operator, and lists what this agent has already reported. A report is the operator's only visibility into a failure that happened inside an agent's session, so an unreported one is a failure nobody can fix. The channel covers homespun's own behaviour: a 5xx, or an error code the guide does not describe; a disagreement between documented and observed behaviour; something the tool surface cannot express, such as a missing capability or a schema that contradicts itself; an app misbehaving in a way that traces back to the platform (the bridge, the runtime, serving, the data API) rather than to authored HTML; or a guide that was wrong, ambiguous or silent. Outside its scope: the human's own task; bugs in an app the agent authored; presentation preferences, which belong in `taste`; the human's own configuration, such as a missing API key or the wrong account; and a 4xx caused by the agent's own arguments, except where the error message itself was misleading, which is a documentation problem best filed as a `note`. Duplicates cost the operator triage rather than adding signal. Action `list` returns this agent's own submissions, newest first, so a failure already recorded needs no second row: one report covers one distinct failure, however many times it was retried. The operator sees the row and not the session, so a bare "deploy failed" is not actionable. An actionable `message` carries the surface (mcp, cli, relay or app-runtime); where it happened (the tool or route); the skill version, from the `<!-- homespun skill vX.Y.Z -->` comment at the top of the guide; what was expected, in one line; what was observed, in one line carrying the exact error code and message; and the minimal steps or arguments that reproduce it. `type` is bug for something broken, feature for something missing, note for a rough edge or a confusing doc. `app_id` scopes a report to one app. There is no reply channel, so a report is not a route to an answer. Actions: create files one report; list returns this agent's own submissions, newest first, paginated by `before`.

Agent identity and binding. Actions: whoami returns the resolved relay URL, the active profile and whether a key is configured, with no network call and no secrets; claim binds this agent to a human using a one-shot claim code from their Settings UI, and is one-way; logout clears the locally saved key and profile but does not revoke it on the relay, which is what the `key` tool's revoke action does.

The caller's community publisher identity: the @-handle and public profile shown in the template gallery. Actions: get returns the profile, including the handle, whether it has been claimed, tenure, and the rating and template counters; claim sets the handle from a lowercase 3-to-32-character string and may be used only once, after which the handle is permanent, and it refuses a handle that is reserved or already taken; update changes display_name, bio or url at any time. claim and update require a verified email. An existing publisher may hold a provisional `maker-...` handle assigned automatically, which claim renames on its one allowed use.

Retrieves file contents for an Edge Function in a Supabase project. Bulk support: accepts project_ids for batched execution.

The official mcp.ai marketplace — the in-platform catalog of every MCP/tool, AND the way to run them. Covers capability requests like "find an MCP that does X", "consulta um CPF", "is there a tool for Y". Core flow: action=search discovers MCPs by intent → describe returns one MCP's full profile (every tool with its id + params, pricing, auth) so you pick the right tool_id → invoke RUNS that tool. KEY: invoke works even when the MCP is NOT installed — it runs the tool pontualmente (one-off), without adding the MCP to the toolkit and without bloating the tool list. If the MCP needs a credential/login, invoke returns a connect link; if it is paid and the wallet is empty, invoke returns a checkout/top-up link (the user opens it, then you retry). Use install only to make an MCP PERMANENT in the active toolkit (its tools then show up natively in future sessions); prefer invoke for a single/occasional use. list_tools lists what is callable right now. subscribe/cancel handle per-MCP billing; report_bug sends feedback; request_mcp asks us to build a NEW MCP when nothing fits. Search/describe flag installed_in_toolkit vs installed_in_workspace. Writes (install/uninstall/subscribe/cancel and the one-off install behind invoke) require workspace owner/admin. It also carries the mcp.ai PROMPT LIBRARY, which is about ready-made prompt TEXT rather than MCPs: search_prompts finds one, get_prompt returns its full text with {{variables}} filled, and publish_prompt saves a prompt and returns a shareable mcp.ai/p/<slug> link that opens without login.

"Tell me about X" / "research Acme" / "brief me on Tesla" / "what does Apple do" / "company profile for Microsoft" / "give me the rundown on NVDA" / "everything you know about $TICKER" — full cross-source profile of a US public company in ONE parallel call. ALWAYS PREFER over chaining single-pack SEC/XBRL/news lookups when the user asks for a holistic view. Fans out across SEC EDGAR, XBRL, USPTO patents, federal contracts (USAspending), FDA-licensed biologics (Purple Book), H-1B hiring (DOL LCA), news and GLEIF, and returns: cik + company_name (+ resolved_from/resolved_to when `value` was a name); recent_filings (up to 5 with pipeworx://edgar/company/{cik}/filings/{accession} URIs); fundamentals (LATEST 10-K Revenues + NetIncomeLoss + Cash, sorted period_end DESC); patents (USPTO PatentsView API sunset May 2025 — soft-fails until reactivated); federal_contracts (USAspending awards where the company is the recipient); fda_products (FDA-licensed biologics — vaccines, cell/gene therapies — from the Purple Book; a company with only small-molecule/generic drugs will show none here, that is expected, not a failure); hiring (H-1B sponsorship volume + salary range from DOL LCA filings); recent news mentions via GDELT→GNews fallback; LEI via GLEIF. `sources_used` / `sources_failed` say which of these actually returned data for THIS company — an empty section is a real "no data", not a bug. Pass a ticker ("AAPL"), zero-padded CIK ("0000320193"), OR a company name ("Moderna") — names now resolve via SEC EDGAR's company-name match; a private company (no CIK/ticker) returns resolved:false with an explicit `notes` line, not a bare failure. `type` accepts "company" or "ticker" interchangeably — both take the same `value` shapes above.

"What's new with X" / "latest on Y" / "what happened to Z this week / month / quarter" / "updates on Acme" / "news on Tesla recently" / "what's happening with Apple" — change feed for a company in the last N days/weeks/months in ONE parallel call. Fans out to SEC EDGAR (filings since `since`), GDELT→GNews fallback (news mentions in window — GDELT preferred, GNews when rate-limited or 5xx), USPTO (patents granted; PatentsView API sunset May 2025 so this soft-fails until reactivated). `since` accepts ISO date ("2026-04-01") or relative shorthand ("7d", "30d", "3m", "1y"). Returns structured changes[] grouped by source + total_changes count + pipeworx:// citation URIs. Use entity_profile instead when you want the static profile (filings + fundamentals + LEI + patents) regardless of window.

What can I ask Pipeworx? / what is Pipeworx good for? / what can you do? / give me ideas / show me examples / getting started / what data do you have? — the onboarding entry point for an agent that just connected and wants to know what is worth asking. Returns category-bucketed example questions (company financials, drugs & clinical trials, economics, real estate, prediction markets, weather, government & patents, science & academia, news) — each with the exact tool + argument shape that answers it, drawn from the live catalog of thousands of tools. Call with no arguments for the full spread, or pass `topic` (e.g. "finance", "pharma", "betting") to focus. Use this FIRST when you do not yet know what Pipeworx can do for you, or to learn how to call the meta-tools (ask_pipeworx, entity_profile, compare_entities, etc.).

Generate a production-ready llms.txt file for any URL so AI crawlers (ChatGPT, Claude, Perplexity) can index the site cleanly. Fetches the page, extracts title/description/key links, and emits the standard llms.txt markdown format. Output is a single text blob ready to drop at site-root/llms.txt. Useful for: getting a client's site indexed by AI, drafting llms.txt for your own project, or auditing how an AI crawler would see a competitor.

Tell the Pipeworx team something is broken, missing, or needs to exist. Use when a tool returns wrong/stale data (bug), when a tool you wish existed isn't in the catalog (feature/data_gap), or when something worked surprisingly well (praise). ONLY for tools served by this Pipeworx connection — if the tool came from a different MCP server in your client (another vendor's Gmail, Splunk, Slack, etc. connector), we cannot fix it and reporting it here only delays you; file it with that server instead. Not sure? Pipeworx tool names are the ones this connection lists. Describe the issue in terms of Pipeworx tools/packs — don't paste the end-user's prompt. Filing without an account returns a `claim_token`; pass it back later as pipeworx_feedback({claim_token:"pwfb_…"}) to read whether it was fixed and what changed. The team reads digests daily and signal directly affects roadmap. Rate-limited to 5 per identifier per day. Free; doesn't count against your tool-call quota.

Get a company's public Mycelium profile: identity and registration, Mycelium Score (0 to 10) with industry rank, Transparency Score, and a per-year summary of total emissions in tonnes CO2e split into reported and estimated. Use search-entities first to find the slug.

Search fish and aquatic animal profiles in the Atlarium habitat database.

Get a structured fish or aquatic animal profile using the exact slug returned by search_fish.

Get a structured aquatic plant profile using the exact slug returned by search_plants.

Get a structured public habitat product profile using the exact slug returned by search_products.

Search public algae diagnostic profiles with symptoms, causes and treatment guidance.

Get a structured public algae diagnostic profile using the exact slug returned by search_algae.