Motif plugin
A molecular biology workbench for Codex and Claude Science that opens DNA, RNA and protein sequences, alignments and results.
- 51 ★ on the repository
- Last commit
- MIT
Extended access
Why this level
- The plugin runs a local MCP server and reads sequence files you provide.
- Generated HTML holds the data in plain text.
Install
- Works in
Manual install
codex plugin add motif-for-claude-science@motif-localFirst build the local marketplace: `npm ci --ignore-scripts`, `npm run build:codex-marketplace`, then `codex plugin marketplace add "$PWD/.motif/codex-marketplace"`.
Access and checks
How we reviewExtended accessThe tool runs code or makes network calls and only reads external data.
- The plugin runs a local MCP server and reads sequence files you provide.
- Generated HTML holds the data in plain text.
This is third-party code. Review the repository files before installing.
What it does
Motif opens and analyzes DNA, RNA and protein records, annotations, alignments, comparisons and cloning inside an agent session. The core is a self-contained HTML workspace that runs on its own or opens through an AI host. It supports maps and annotations, Sanger traces, provenance, checkpoints and portable export. There are three ways to use it. A portable HTML workbench serves local viewing and sharing with no integration. The skills-only Codex plugin creates such workbenches from Codex. The full local Codex plugin and the Claude Science adapter open the interactive app through a local MCP server. The `motif_open_workbench` and `motif_create_workbench_artifact` tools open the workbench or return portable HTML.
Who it is for. Biologists and bioinformaticians who work with sequences alongside an agent and want to browse results interactively.
Good fit when
- An agent should open a FASTA or GenBank file and show records with annotations.
- You need to align and compare sequences and share the result as portable HTML.
- You want to check a cloning construct, such as a Golden Gate assembly.
- You want to view Sanger traces next to the sequence.
Not a fit when
- You need a laboratory or clinical conclusion with guaranteed accuracy.
- The data cannot go into an unencrypted HTML file.
- The required Node.js version is unavailable for building the plugin.
Example request
Open plasmid.gb in Motif, show the annotations and align it with the reference sequence.Limitations
The full Codex plugin needs Codex Desktop or a CLI with `codex plugin` support, Node.js 22.13 or newer on the 22 line or Node.js 24, and a trusted repository copy in a stable folder. The plugin is built locally and installation uses separate commands that change configuration. The generated HTML file is unencrypted and holds the supplied records, so share it only on purpose. Analysis results need review by a specialist.
How to disable. Remove the plugin with the Codex plugin commands and delete the local `.motif/codex-marketplace` folder. Generated HTML files are deleted manually.
FAQ
How do I install the full plugin in Codex?
Build the marketplace with `npm run build:codex-marketplace`, then run `codex plugin marketplace add` with the path to `.motif/codex-marketplace` and `codex plugin add motif-for-claude-science@motif-local`.
Why does the identifier contain Claude Science?
The `motif-for-claude-science` identifier is kept for compatibility while the plugin displays as Motif.
How does the skills-only edition differ?
It creates a self-contained HTML workbench with no local connector or MCP app. The full plugin also opens the interactive workbench.
What does the doctor command check?
`npm run codex:doctor:marketplace` verifies package integrity, performs a real MCP handshake and sends a small synthetic FASTA request.
What data goes into the generated HTML?
The supplied records in full. The file is unencrypted, so share it only with people allowed to see that data.
Discussion
No questions or reviews yet.
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README in short
The repository holds a portable HTML workbench, two Codex plugins and a Claude Science adapter. Documentation includes guides on quick start, capabilities and security.