Motif

Motif for Claude Science

Website · [Installation](docs/CLAUDESCIENCE_QUICKSTART.md) · [Capabilities](docs/CAPABILITIES.md) · [Examples](examples/README.md) · [Security](SECURITY.md)

Motif is an AI-native molecular biology workbench for Claude Science. It combines sequence records and analysis results in a self-contained HTML workspace that opens locally or in Claude Science. You can inspect and edit records, review maps and alignments, save checkpoints, and export a workspace ZIP.

Claude Science can use motif_open_workbench to open the MCP App. If the host does not display the App, motif_create_workbench_artifact returns a self-contained HTML workbench that opens in the right pane.

Motif in Claude Science with two sequence records, annotated sequence detail, a linear map, and restriction-digest results.

This repository contains the source for the workbench, Claude plugin, standalone skill, and local connector. The connector builds and runs from this checkout.

Motif is an independent hackathon project and is not an Anthropic product or an official Claude Science integration.

Install with a coding agent

Give Claude Code, Codex, or another local coding agent with terminal access this repository and the following request:

Install the latest released version of Motif for Claude Science from
https://github.com/jvogan/motif.

Follow docs/CLAUDE_SCIENCE_QUICKSTART.md. Place the checkout in a stable local
folder, run npm ci and npm run claude-science:setup, and use only the bundled
examples/motif-demo.gb file for the first test. Verify any downloaded release
assets against the published checksums. Preserve unrelated local connectors.
Tell me when I need to grant folder access, restart Claude Science, or
reconnect motif-local.

For manual installation, follow the [Claude Science quickstart](docs/CLAUDESCIENCEQUICKSTART.md).

What is included

• DNA, RNA, and protein records with annotations, tags, notes, and editing

tools

• Standard and per-base Detail sequence views with selection and editing
• Circular and linear maps with features, coordinates, restriction sites,

selection, labels, and pan/zoom

• Restriction digest prediction, fragment records, and a qualitative gel
• Primer/PCR design, Gibson, Golden Gate, GoldenBraid, and traditional ligation

workflows

• In-browser MSA for 2–10 compatible records of up to 3,000 residues each,

plus import and review of aligned FASTA/CLUSTAL

• An external MSA runner for MAFFT, MUSCLE, and Clustal Omega that invokes one

selected executable without a command shell and records its version, arguments, and hashes

• AB1/ABI Sanger import and chromatogram review using existing base calls
• ORF and translation analysis, plus PAM-based CRISPR guide candidates
• Workflow history, typed analysis results, and plain-text or JSON attachments

that Motif stores and displays without executing

• Database JSON checkpoint and restore, plus workspace ZIP export
• A deterministic Claude plugin bundle, standalone skill, and local MCP

connector with a full-workbench ui:// App and embedded HTML fallback

Develop from source

Requires Git and Node.js 22.12 or newer. From a source checkout:

git clone https://github.com/jvogan/motif.git
cd motif
npm ci
npm run preview:motif

Open preview/motif-artifact.html, or start an editable Vite session with:

npm run dev

First success in Claude Science

Install the local connector from the checkout you intend to keep:

npm run claude-science:setup

Setup registers this checkout's path. Moving the folder later requires running setup again. Grant Claude Science access to the exact folder, fully quit and reopen the app, then reconnect motif-local. The connector exposes exactly motif_open_workbench and motif_create_workbench_artifact.

For the most reliable first visual result, attach the bundled synthetic [examples/motif-demo.gb](examples/motif-demo.gb) and ask Claude Science:

Read the complete text of motif-demo.gb, including ORIGIN. Call motif-local's
motif_create_workbench_artifact exactly once with filename "motif-demo.gb",
the complete content, title "Motif demo — MOTIFDEMO", and outputFilename
"motif-demo-workbench.html". Preserve the exact returned HTML as a Claude
Science artifact and open it in the right pane. Report the record name,
topology, and residue count.

Click the generated HTML to open the interactive workbench. The file contains a snapshot of the input and Motif build used to create it; later source or build changes do not update it. Export a new checkpoint to preserve edits made in the workbench. See the [Claude Science quickstart](docs/CLAUDESCIENCEQUICKSTART.md) for permission, verification, and optional live-App steps.

To have Claude prepare a workbench with colored annotations, replace the bracketed text in this prompt:

Read the complete attached sequence file. Build a Motif payload that preserves
the source sequences, record names, molecule types, topology, coordinates, and
existing annotations. Add only these annotations: [names, types, coordinates,
and directions]. Give new annotation types distinct, readable colors; use the
same color for annotations with the same type and keep adjacent features easy
to distinguish. Call motif_create_workbench_artifact with the payload, preserve
the exact returned HTML as a Claude Science artifact, and open it in the right
pane.

The [public examples](examples/README.md) also include synthetic FASTA, aligned CLUSTAL, and complete workspace JSON inputs with expected identities.

Build the distributable

npm run build:motif

The build writes:

dist-motif/
├── claude-science/
│   ├── motif-mcp-app.html
│   └── motif-mcp-server.mjs
├── motif-template.html
├── motif-artifact.html
├── motif-for-claude-science/
├── motif-for-claude-science.zip
├── motif-for-claude-science.checksums.json
└── motif-for-claude-science-skill/SKILL.md

The HTML and MCP App are self-contained: Vite's JavaScript and CSS assets are inlined, and the plugin contains its compiled connector, App, standalone template, and artifact resource. The ZIP is deterministic and its file/archive SHA-256 values are recorded beside it.

The plugin ZIP is for Claude/plugin hosts. It does not install the Claude Science local connector. Run npm run claude-science:setup from a source checkout instead.

To generate an additional repo-local artifact with preloaded data:

npm run build:motif -- \
  --payload ./inventory.json \
  --out ./preview/my-motif-workspace.html

Use --handoff /explicit/path/motif-artifact.html only to write a copy outside the repository. By default, the build writes nothing outside it.

Validate

npm run typecheck
npm run lint
npm test
npm run test:plugin
npm run test:connector
npm run check:css-tokens
npm run check:aria-controls
npm run build:motif
npm run test:e2e
npm run test:e2e:msa

npm run validate:plugin adds strict validation through the Claude CLI when it is installed.

Claude Science local connector

For a fresh installation, follow the [public Claude Science quickstart](docs/CLAUDESCIENCEQUICKSTART.md).

Build, check, and register the connector:

npm run claude-science:setup

Setup builds the connector and checks its protocol before changing Claude Science's configuration. It then adds exactly one motif-local entry, preserves unrelated entries, and writes a private backup before installing a changed configuration. Grant the Motif checkout read access in Claude Science, fully quit and reopen the app, then reconnect motif-local.

The connector exposes motif_open_workbench for bounded Motif payload, FASTA, GenBank, raw-sequence, or Motif JSON review. Pass the complete text and its exact filename. A successful result means Motif parsed the input; only a visible Motif frame confirms that Claude Science mounted the MCP App. Some local/custom connector builds do not list Motif in the artifact viewer chooser; use that path only when Motif appears there.

If no workbench appears, use motif_create_workbench_artifact. Save the exact returned HTML resource, then open it in Claude Science's right pane. The file contains a snapshot of the input and Motif build used to create it; later source or build changes do not update it.

The connector does not write a database or run external executables. It uses Motif's bounded page-local workspace API and does not expose a generic DOM, evaluation, shell, or filesystem bridge. Setup, verification, rollback, and host limitations are documented in [Claude Science integration](docs/CLAUDESCIENCEINTEGRATION.md). Known host errors, reload boundaries, and visual acceptance steps are in the [Motif + Claude Science troubleshooting guide](docs/CLAUDESCIENCETROUBLESHOOTING.md).

Data safety

Motif has no hosted backend. The standalone HTML does not upload sequence data to a Motif service. External MSA tools run only when explicitly invoked outside the HTML. Data supplied through Claude Science remains subject to your Claude and organization data policies. Do not use sensitive or unpublished sequences without authorization. Workspace exports are unencrypted files; store and back them up according to their sensitivity.

See the plugin [README](src/artifacts/motif-for-claude-science-plugin/README.md) for payload, MSA, Sanger, installation, and security details. The public [capability reference](docs/CAPABILITIES.md) distinguishes built-in analysis from externally produced results that Motif can store and display.

For project support and release information, see [SUPPORT.md](SUPPORT.md), [SECURITY.md](SECURITY.md), [CHANGELOG.md](CHANGELOG.md), and [THIRDPARTYNOTICES.md](THIRDPARTYNOTICES.md).

License

MIT. Redistributed plugin bundles must retain LICENSE, THIRD_PARTY_NOTICES.md, and record-level reference provenance.

Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: jvogan
• Source: jvogan/motif
• License: MIT
• Homepage: https://jvogan.github.io/motif-site/

Install and usage instructions live in the source repository linked above.