Connecting AI clients

Use the BioNodulo remote MCP URL for cloud account access:

https://bionodulo.com/api/mcp

Each client opens a browser sign-in when it needs your authorization. Sign in with the BioNodulo account and team you want the assistant to use. You do not need an administrator’s Clerk secret or a manually copied session token. Reading, editing, and running use separate bionodulo:read, bionodulo:write, and bionodulo:run grants. A default login may grant only read access; reconnect and request more permissions when needed.

ChatGPT

In ChatGPT, open Settings → Security and login and turn on Developer mode. Availability can depend on your account or workspace policy.
Open ChatGPT Plugins, select +, and create a connection using the BioNodulo MCP URL above.
Complete the BioNodulo sign-in and permission flow. Review the discovered tools.
In a new chat, add the connection from the tools menu and ask: “Open my BioNodulo workbench.”

This creates a personal developer-mode connection. Public directory availability requires a separate submission and review. See OpenAI’s connection guide.

Claude

In Claude, open Customize → Connectors, choose Add custom connector, and enter the BioNodulo MCP URL. Connect your BioNodulo account, then enable the connector in a conversation. For Team and Enterprise workspaces, an Owner may first need to add the custom connector in Organization settings → Connectors. See Anthropic’s custom connector guide.

Ask Claude “Open my BioNodulo workbench.” When interactive connectors are supported and enabled in that conversation, Claude can display the workbench in chat. If it does not appear, start a new conversation with the connector enabled, or use the regular BioNodulo tools. See Claude’s interactive connectors guide.

Claude Desktop can use this remote connector through your Claude account. Desktop-only BioNodulo actions require a separate local desktop extension on the same computer as the BioNodulo app.

Full cloud app and cloud runs

The open_bionodulo tool loads the full cloud app in ChatGPT and Claude when the host renders MCP Apps. It shares the hosted editor’s navigation, workflow tabs, canvas, toolbox, templates, settings, cloud workspace and run history. An MCP adapter carries the shared app’s requests to your authorized cloud account. The Workspace panel lists verified cloud uploads, and the AI panel sends your request and workflow context to the conversation’s host assistant. Saved changes made by that assistant appear in the editor; competing changes preserve your draft and offer Load latest recovery.

The regular MCP tools remain usable in Codex, Claude Code, and chats without embedded UI. The remote connection cannot access files on your computer, control the local desktop app or HPC scheduler, or change administrator settings. Cloud runs use cloud upload keys rather than local filesystem paths. The embedded app reviews your current balance and CPU/GPU cost estimate before each paid submission, then displays live progress, logs and verified outputs in the existing run UI.

Before starting a cloud run, ask the assistant to check the selected team and workflow, your credit balance, and the compute rate. A submit_run call requires bionodulo:run and an explicit confirm_credit_use: true for the specific run you authorize. A submitted run is not yet a completed run.

Codex

Add the remote server with the Codex CLI, then start browser authorization:

codex mcp add bionodulo --url https://bionodulo.com/api/mcp
codex mcp login bionodulo

Run codex mcp list to check registration. In a Codex session, use /mcp to inspect the connection. The CLI and IDE extension share the server configuration. See Codex MCP documentation.

To request the full set of permissions explicitly, run:

codex mcp login bionodulo --scopes bionodulo:read,bionodulo:write,bionodulo:run

Review the permissions in the BioNodulo authorization screen. You can grant only what you need.

Claude Code

Add the same remote server and authorize it from /mcp in Claude Code:

claude mcp add --transport http bionodulo --scope user https://bionodulo.com/api/mcp

See Claude Code’s MCP guide for scope and OAuth details.

Plugin and desktop downloads

Download the portable BioNodulo plugin (.zip) for a supported plugin host. It packages BioNodulo guidance and the remote cloud connection; its contents are also visible in the repository.
Download the Claude Desktop extension (.mcpb) and install it through Claude Desktop Settings → Extensions when you want to control a BioNodulo desktop app running on the same computer. This extension exposes only local desktop_* tools; use Claude’s remote connector above for cloud account tools.

These are GitHub release assets, separate from public ChatGPT or Claude plugin directories.

Repository marketplaces

The BioNodulo repository contains the plugin at integrations/bionodulo and marketplace catalogs for Codex and Claude Code. To add the repository as a marketplace source:

claude plugin marketplace add Classacre/BioNodulo
claude plugin install bionodulo@bionodulo-repo
 
codex plugin marketplace add Classacre/BioNodulo

For Codex, open the Plugins Directory, choose the bionodulo-repo source, and install BioNodulo. These are repository marketplace sources; the plugin is not automatically listed in a public directory. See the Claude Code marketplace guide and Codex plugin packaging guide.

Confirm the connection

Ask your client to list your BioNodulo runs or workflows. It should invoke a BioNodulo tool and show data from the team you authorized. If it reports insufficient permission, reconnect and review the requested access. Operations that start runs can consume credits; check the action and team before approving it.

Installation & Configuration Tool Reference