# Tooluniverse Synthetic Biology Parts > Look up synthetic biology genetic parts (promoters, RBS, CDS/genes, terminators, reporters, compo… Look up synthetic biology genetic parts (promoters, RBS, CDS/genes, terminators, reporters, composite devices) from the SynBioHub repository, including the iGEM Registry of Standard Biological Parts. Use when someone asks to \"find a genetic part\", \"look up a BioBrick\", \"search SynBioHub\", \"get the sequence for BBa_...\", \"browse iGEM part collections\", \"find a promoter/RBS/terminator for a genetic circuit\", or \"what parts are available for [organism/function]\". NOT for plasmid backbone/vector lookup by catalog ID (use tooluniverse-molecular-cloning's Addgene coverage), NOT for primer design once a part sequence is chosen (use tooluniverse-primer-design). Honest: SynBioHub disabled anonymous public REST access upstream — every unauthenticated call currently returns 401/HTML-login-page, verified live. This skill explains that limitation plainly and how to unlock real access (SYNBIOHUB_API_TOKEN) rather than pretending the tools work with no setup. - Page: https://ss33.ai/skills/mims-harvard/tooluniverse-synthetic-biology-parts-41362028547 - Publisher: mims-harvard - Category: [Health & Life Sciences](https://ss33.ai/skills/category/health-and-life-sciences-n8be4o) › [Misc](https://ss33.ai/skills/category/health-and-life-sciences-n8be4o/misc-dyhvin) - License: Apache-2.0 - Source: https://github.com/mims-harvard/tooluniverse/blob/265848d91a74450156f20c7a717c632a656e2ee9/plugins/tooluniverse/skills/tooluniverse-synthetic-biology-parts/SKILL.md ## Skill SKILL.md: https://ss33.ai/api/v1/ss33/download/mims-harvard/tooluniverse-synthetic-biology-parts-41362028547 # Synthetic Biology Parts Lookup (SynBioHub) Search and retrieve genetic parts — promoters, ribosome binding sites (RBS), coding sequences, terminators, reporters, and composite genetic devices — from SynBioHub, the standard synthetic-biology parts repository that hosts the iGEM Registry of Standard Biological Parts (20,000+ BioBricks), CIDAR Lab parts, Free Genes libraries, and other public SBOL collections. ## Honesty contract (read first) — verify auth status before promising results **Live-verified as of this writing: every anonymous call to all 3 tools below fails.** SynBioHub disabled anonymous access to its public REST endpoints upstream. Confirmed by actually running each tool with no token set: ``` $ tu run SynBioHub_get_collections '{}' Error: SynBioHub API HTTP error: 401 (login required). synbiohub.org now requires an authenticated session for this endpoint (no SYNBIOHUB_API_TOKEN is set). Log in at synbiohub.org, then set SYNBIOHUB_API_TOKEN to the session token to retry. $ tu run SynBioHub_search_parts '{"query": "GFP"}' Error: SynBioHub API HTTP error: 401 (login required). ... $ tu run SynBioHub_get_part '{"display_id": "BBa_E0040"}' Error: SynBioHub did not return SBOL/XML data for 'https://synbiohub.org/public/igem/BBa_E0040/1' (got non-XML content, likely an HTML login or error page). The part may not exist, or SynBioHub may now require authentication for this request. ``` **Before using this skill, always try one call first** (e.g. `SynBioHub_get_collections` with no arguments — cheapest possible check). If it returns a 401/login-required error: 1. Tell the user plainly: SynBioHub now requires authentication for these reads; this is an upstream policy change, not a bug in the request. 2. Point them to create a free account at https://synbiohub.org, log in, and retrieve a session token, then set `SYNBIOHUB_API_TOKEN` in the environment before retrying. 3. **Never fabricate a part record, sequence, or collection list** to work around the error. If the token isn't available, say the lookup cannot be completed right now — do not guess a BioBrick's sequence from training-data memory and present it as a live SynBioHub result. If a valid `SYNBIOHUB_API_TOKEN` is set and the call succeeds, proceed with the workflow below using the real returned data. ## When to Use This Skill Apply when users: - Want to find a genetic part by function (promoter, RBS, terminator, CDS, reporter) or by keyword (gene name, biological description) - Have a BioBrick ID (e.g. `BBa_E0040`) or a SynBioHub part URI and want its sequence, role, and provenance - Want to browse what part collections/libraries exist on SynBioHub before searching (iGEM Registry, CIDAR Lab, Free Genes, organism-specific sets) - Are assembling a genetic circuit and need to identify candidate parts (promoter + RBS + CDS + terminator) before moving to cloning/plasmid design **NOT for** (route elsewhere): - Plasmid backbone/vector catalog lookup by Addgene ID — the registry has `Addgene_search_plasmids`, `Addgene_get_plasmid`, `Addgene_search_depositors` (`src/tooluniverse/data/addgene_tools.json`) for this. These only appear in `tu list` once an `ADDGENE_API_KEY` environment variable is set (ToolUniverse deliberately hides any tool with unmet `required_api_keys` until the key is present — verified, not a bug); register for a free key at https://developers.addgene.org/ if it's missing. - Cloning workflow steps (restriction sites, Gibson/Golden Gate assembly planning) once parts are chosen -> `tooluniverse-molecular-cloning` - Primer design for amplifying a chosen part/sequence -> `tooluniverse-primer-design` ## Workflow ### 1. Browse available collections (optional starting point) ``` SynBioHub_get_collections {} ``` No parameters. Returns collection `name`, `description`, `display_id`, `uri`, `version`, and `member_count` for every public collection (iGEM Registry, CIDAR Lab parts, Free Genes, organism-specific sets, etc.) — useful when the user wants to know what's searchable before committing to a query. ### 2. Search for a part by keyword ``` SynBioHub_search_parts {"query": "", "limit": <1-50, default 10>, "offset": } ``` `query` accepts gene names, functional descriptions, or BioBrick IDs — e.g. `"GFP"`, `"lac promoter"`, `"BBa_E0040"`, `"terminator"`, `"riboswitch"`, `"CRISPR"`, `"T7 promoter"`. Returns an array of candidate parts, each with `display_id`, `name`, `description`, `uri` (feed this into step 3), `version`, `sbol_type` (e.g. `ComponentDefinition`), and `role` (`promoter`, `CDS`, `terminator`, `RBS`, etc.). When narrowing a search (e.g. by organism or exact function), refine the query text itself — there is no separate organism/role filter parameter. If the first query is too broad, tighten the keyword and re-search rather than trying to filter client-side on an incomplete result page. ### 3. Get full detail for one part ``` SynBioHub_get_part {"display_id": ""} # or, for parts outside the iGEM collection: SynBioHub_get_part {"part_uri": ""} ``` Exactly one of `display_id` or `part_uri` should be supplied (`display_id` for iGEM BioBricks like `BBa_E0040`, `part_uri` for anything else — take the `uri` field straight from a `SynBioHub_search_parts` result). Returns `title`, `description`, `type` (SBOL biological type, e.g. `DnaRegion`), `role` (array of SO terms / iGEM part types), `sequence` (first 500 bp — note this is truncated, not the full sequence, for long parts), `sequence_length` (the true full length), `created`/`modified` dates, and `derived_from` (original source URI, e.g. the iGEM registry page). **`sequence` is capped at 500 characters.** For a part longer than that, report `sequence_length` honestly and say the returned `sequence` field is a prefix, not the complete sequence — do not imply completeness. ## Downstream Handoff Once parts are identified: move to `tooluniverse-molecular-cloning` for assembly planning (Gibson/Golden Gate/restriction-based cloning of the chosen parts into a vector) and `tooluniverse-primer-design` for amplification primers. ## Reference - `references/synbiohub_tool_reference.md` — full parameter/response tables for all 3 tools, plus the exact live error text observed when testing this skill (for future maintainers to recognize the same failure mode).