Helical Platform plugin

A plugin for Claude Code and Codex that gives you metered access to the Helical platform from the chat you're already in: compute embeddings for a single-cell dataset with a foundation model, and fine-tune a model on your own labelled data.

Runs execute on Helical's GPUs and are paid for with the credits in your Helical account. Nothing starts on its own: every run is priced first and only launches after you approve it.

Skills

Skill	What it does
compute-embeddings	dataset → model → quote → approve → run → outputs
fine-tune-model	labelled dataset → trained, registered model
in-silico-perturbation	edit genes locally → upload → embed → rank shifts toward a target state
check-credits	reads your balance, explains what a run costs and when you're charged
reconnect-helical	connects the plugin, relays the authorization link, or reconnects a refused sign-in

In Claude Code, skills are namespaced by plugin: /helical-platform:compute-embeddings and so on.

Installing it in Claude Code

From GitHub:

claude plugin marketplace add helicalAI/heli-plugin#main   # reads .claude-plugin/marketplace.json
claude plugin install helical-platform@helical-marketplace

#main pins the released branch; the default branch, develop, holds unreleased work. From a local checkout, use claude plugin marketplace add ./ instead (a bare . is rejected). The same commands work inside a session as /plugin marketplace add … and /plugin install ….

Then run /mcp to sign in. Claude Code registers the server as plugin:helical-platform:helical, so from the shell it is claude mcp login plugin:helical-platform:helical.

Installing it in Codex CLI

From GitHub, pinned to the released branch:

codex plugin marketplace add helicalAI/heli-plugin --ref main
codex plugin add helical-platform@helical-marketplace

From a local checkout:

codex plugin marketplace add .   # reads ./.agents/plugins/marketplace.json
codex plugin add helical-platform@helical-marketplace

Signing in

The plugin holds no credentials. mcp.json names the remote endpoint (https://api.helical.bio/mcp), and your MCP client signs you in through the browser using OAuth (Authorization Code + PKCE). Installing does not sign you in: until you connect, the plugin shows as enabled with none of its tools.

claude mcp login plugin:helical-platform:helical   # Claude Code; or /mcp → helical → Authenticate
codex mcp login helical                            # Codex CLI, IDE extension, ChatGPT desktop

Both take --no-browser on a machine without one. ChatGPT's directory install signs in with Connect after Install plugin, or later under Settings → Plugins.

Your account, credits and usage history live at console.helical.bio.

Layout

.agents/plugins/marketplace.json  # Codex marketplace
.claude-plugin/marketplace.json   # Claude Code marketplace
scripts/release.py                # release zips and the version gate (see DEVELOPING.md)
tests/test_release.py             # its tests
plugins/helical-platform/
├── plugin.json                 # OpenAI / Codex manifest (Agent Plugins format; listing under extensions.com.openai)
├── .claude-plugin/plugin.json  # Claude Code plugin manifest (same metadata; tests keep them in sync)
├── mcp.json                    # the remote MCP endpoint the plugin connects to (shared)
├── assets/icon.png             # listing icon for both directories
├── skills/
│   ├── check-credits/
│   ├── compute-embeddings/
│   ├── fine-tune-model/
│   ├── in-silico-perturbation/
│   └── reconnect-helical/
└── tests/                      # test_plugin_manifest.py

Validate

make check                         # unit tests, strict manifest validation, install through both loaders
make check TMP_DIR=/tmp/heli       # keep the throwaway Codex / Claude Code config homes there
make package                       # dist/<name>-<version>.zip per plugin, for OpenAI submission

Needs uv, jq, codex and claude on the PATH. The installs go into a throwaway config home, never your own ~/.codex or ~/.claude.

CI runs make check.

Releases go through main. See DEVELOPING.md for the branch model, the version bump and the OpenAI upload.

License

AGPL-3.0-or-later, matching the open-source helical package.