Aiden Lab plugins

Plugins from the Aiden Lab for Claude, ChatGPT and Codex. One marketplace, aidenlab/plugins, in both the Claude Code and the OpenAI Agent Plugins layouts.

Plugin

What it does

juicebot (display name Geenee)

Drive Geenee, a genome workspace holding the igv genome browser and the Juicebox Hi-C contact-map viewer side by side, by chatting: search ENCODE/4DN, load maps and tracks, navigate genes and loci, compare, share. Hosted MCP server, nothing runs locally. The skill bundles a dependency-free CLI (Python or Node) that calls the same server over HTTPS, so it works in Claude Code, Cowork and Codex even when the MCP connector is not set up.

The plugin was called JuiceBot up to version 1.3 and drove Juicebox alone. Version 2.0 is the same plugin id (juicebot), so an existing install upgrades in place and then talks to Geenee; see Upgrading from JuiceBot.

Install Geenee: paste one line

Paste this into Claude Code, Cowork, claude.ai, Codex or ChatGPT:

Set up Geenee for me: fetch https://geenee-install.3dg.io and follow its instructions for the app you are running in.

The assistant reads INSTALL-PROMPT.md, works out which app it is in, installs what it can itself (Claude Code, Codex), walks you through the three clicks it cannot do (Claude's account-level plugin page, ChatGPT's custom MCP server), then hands you the first message for a new chat: Geenee opens, Juicebox loads a GM12878 map at HOXA with the gene track, IGV goes to HOXA1 with a CTCF track. If the short link is down, use https://raw.githubusercontent.com/aidenlab/plugins/main/INSTALL-PROMPT.md instead.

Manual install

Geenee has two halves: the MCP server (the tools: open_geenee, igv_*, juicebox_*) and the skill (how the assistant uses them). The server sends its core workflow to every client on connect, so tools alone are enough to work; the plugin adds the fuller skill.

With the plugin installed but no connector, the skill falls back to skills/geenee/scripts/geenee.py (or .mjs): the same tools by name over plain HTTPS, several per shell call (call juicebox_load_map '{…}' juicebox_load_track '{"url":"genes"}'), with the Room id filled in. Only the viewers must be a real browser.

Claude — web, desktop Chat, Cowork (one account-level setup). Plugins and marketplaces live on your Claude account and follow you to every surface, Claude Code included.

1. Open https://claude.ai/new#settings/customize-plugins in a separate tab or window (in the app: Customize → Plugins, in Cowork open the Cowork tab first). Add → Add marketplace → Add from a repository → aidenlab/plugins. The Discover tab opens; find Geenee → Add.
2. On the plugin's Manage page turn on the Geenee server. If there is no switch, Customize → Connectors → enable Geenee; failing that, Settings → Connectors → Add custom connector, name Geenee, URL https://geenee-dev.3dg.io/mcp, no auth. Team/Enterprise admins can add that connector once for everyone.

Start a new conversation and the tools are there. Paid plans only (Pro, Max, Team, Enterprise).

Claude Code — picks up the account install above on next start (/login forces it). Standalone: /plugin install juicebot --marketplace aidenlab/plugins then /reload-plugins; from a terminal claude plugin install juicebot --marketplace aidenlab/plugins. The plugin bundles the server.

Codex — codex plugin marketplace add aidenlab/plugins, then codex plugin add juicebot@aidenlab. codex mcp list shows the Geenee server; start a new chat.

ChatGPT — chatgpt.com/plugins → + → Add custom MCP server, name Geenee, the URL above, authentication None. Enable it in a new chat.

Other MCP clients (Cursor, stdio-only tools) — point them at the URL; bridge stdio-only clients with npx -y mcp-remote https://geenee-dev.3dg.io/mcp.

Upgrading from JuiceBot

The plugin id did not change, so nothing has to be reinstalled.

• Claude Code: /plugin marketplace update aidenlab then /plugin update juicebot@aidenlab (or turn on auto-update for the marketplace under /plugin → Marketplaces). The bundled server is now Geenee.
• claude.ai / desktop / Cowork: on the plugin's Manage page take the update, turn on the Geenee server and turn off JuiceBot. If JuiceBot was added as a custom connector, add Geenee the same way and disable JuiceBot.
• Codex: codex plugin marketplace upgrade aidenlab.
• ChatGPT: add the Geenee custom MCP server; remove JuiceBot.

The old server (juicebot-mcp.3dg.io) keeps running: Geenee forwards Juicebox commands to it.

First run

Open Geenee. In Juicebox, load the ENCODE GM12878 in situ Hi-C map at the HOXA cluster and add the gene track. In IGV, go to HOXA1 and add the GM12878 CTCF ChIP-seq track.

You get a Geenee link. Open it in a browser tab: the page has an IGV tab and a Juicebox tab, and the assistant drives both. Every later command updates that tab; the page switches to the viewer that was last driven. The Geenee link is live and shared (everyone in the Room follows along); "create a link I can share" makes a snapshot of one viewer that preserves the current view.

Directory listing (one-click install, no marketplace)

Plugins listed in Anthropic's community directory appear in Cowork's Discover tab and in the claude.ai plugin catalog, so any Cowork session can offer an install card and nobody has to add a marketplace. Submit at claude.ai/admin-settings/directory/submissions/plugins/new (Team/Enterprise owner) or platform.claude.com/plugins/submit; run claude plugin validate ./plugins/juicebot first. ChatGPT has the equivalent "With MCP" submission for the remote server. Until listed, users add the aidenlab/plugins marketplace once as above.

For the whole organization (admins)

1. Connector: add https://geenee-dev.3dg.io/mcp as an organization connector named Geenee (Claude Team/Enterprise; ChatGPT workspace admins can publish the plugin to the workspace). Members get the tools with no setup.
2. Plugin: Claude: Organization settings → Plugins & skills → Marketplaces → Add plugins → Sync from GitHub (needs a private or internal mirror with the Claude GitHub App) or upload the release's juicebot.plugin as a ZIP. See Manage plugins for your organization.

Layout and maintenance

.claude-plugin/marketplace.json     Claude Code marketplace catalog
.agents/plugins/marketplace.json    OpenAI (ChatGPT/Codex) marketplace catalog
plugins/juicebot/                   the Geenee plugin (id kept as juicebot, see above)
  .claude-plugin/plugin.json        Claude manifest
  .mcp.json                         Claude MCP server (type: http)
  plugin.json                       portable Agent Plugins manifest (ChatGPT/Codex)
  mcp.json                          portable MCP server (type: streamable-http)
  skills/geenee/SKILL.md            the skill, shared by all
  skills/geenee/scripts/            geenee.py / geenee.mjs: the connector-free CLI
  skills/geenee/references/         tools.md (generated from tools/list), cli.md
  assets/                           icon.svg (source: make_icon.py), icon.png 512, icon-128.png — used by the OpenAI
                                    manifest and the directory submission form; claude.ai strips an `icon` key from plugin.json
INSTALL-PROMPT.md                   what the one-line prompt fetches
install-worker/                     Cloudflare Worker serving it at geenee-install.3dg.io (and juicebot-install.3dg.io)
scripts/gen-tools-md.py             regenerates references/tools.md from the live server
scripts/package.sh                  builds dist/juicebot.plugin
scripts/make-dev.sh                 turns a checkout of main into the dev branch

• Change the server URL in both plugins/juicebot/.mcp.json and plugins/juicebot/mcp.json, in SERVERS of both CLI scripts, and in the docs.
• Bump version in all four manifests when anything changes; users on an older version stay there until they update (/plugin marketplace update aidenlab + /plugin update juicebot@aidenlab in Claude Code; codex plugin marketplace upgrade aidenlab in Codex). Never change the plugin name: it is the install id, and a rename breaks every existing install.
• Validate: claude plugin validate . && claude plugin validate ./plugins/juicebot; codex plugin marketplace add ./ && codex plugin add juicebot@aidenlab.
• CLI smoke test against the live server: scripts/test-cli.sh. Regenerate references/tools.md after a tool change: scripts/gen-tools-md.py.
• The MCP endpoint is https://geenee-dev.3dg.io/mcp, Geenee's development deployment (it forwards to the igv-bot and Juicebox dev servers). It will move to a production hostname without changing anything but the URL here.
• Tagging v* runs the release workflow, which attaches juicebot.plugin to the GitHub release.

Server source: aidenlab/geenee (forwarding to aidenlab/igvjs-mcp and weiszd/juicebox-mcp). License: MIT.