# Motif > An AI-native molecular biology workbench for Claude Science: Claude opens sequence files and prepares analyses on request; you annotate, align, and review them in an interactive workspace. - **Type:** MCP server - **Install:** `agentstack add mcp-jvogan-motif` - **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior - **Seller:** [jvogan](https://agentstack.voostack.com/s/jvogan) - **Installs:** 0 - **Category:** [Integrations](https://agentstack.voostack.com/c/integrations) - **Latest version:** 0.1.0 - **License:** MIT - **Upstream author:** [jvogan](https://github.com/jvogan) - **Source:** https://github.com/jvogan/motif - **Website:** https://jvogan.github.io/motif-site/ ## Install ```sh agentstack add mcp-jvogan-motif ``` Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent. ## About # Motif for Claude Science [Website](https://jvogan.github.io/motif-site/) · [Installation](docs/CLAUDE_SCIENCE_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: ```text 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/CLAUDE_SCIENCE_QUICKSTART.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: ```bash 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: ```bash npm run dev ``` ## First success in Claude Science Install the local connector from the checkout you intend to keep: ```bash 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: ```text 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/CLAUDE_SCIENCE_QUICKSTART.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: ```text 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 ```bash npm run build:motif ``` The build writes: ```text 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: ```bash 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 ```bash 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/CLAUDE_SCIENCE_QUICKSTART.md). Build, check, and register the connector: ```bash 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/CLAUDE_SCIENCE_INTEGRATION.md). Known host errors, reload boundaries, and visual acceptance steps are in the [Motif + Claude Science troubleshooting guide](docs/CLAUDE_SCIENCE_TROUBLESHOOTING.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 [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.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](https://github.com/jvogan) - **Source:** [jvogan/motif](https://github.com/jvogan/motif) - **License:** MIT - **Homepage:** https://jvogan.github.io/motif-site/ Install and usage instructions live in the source repository linked above. ## Pricing - **Free** — Free ## Security capabilities Automated source analysis of v0.1.0 — what this tool can access: - **Network access:** no - **Filesystem access:** no - **Shell / process execution:** no - **Environment & secrets:** no - **Dynamic code execution:** no *"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.* ## Versions - **0.1.0** — security scan: passed — Imported from the upstream source. ## Links - Listing page: https://agentstack.voostack.com/l/mcp-jvogan-motif - Seller: https://agentstack.voostack.com/s/jvogan - Browse the marketplace: https://agentstack.voostack.com/browse --- Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.