AI and MCP connectors
Connect your AI
Every Anaphase product works without AI. When you want it, there are three routes, and you can use any, all or none.
- An assistant inside the product, with your own key. You pay your AI provider directly. Available in all four products today.
- An assistant inside the product, hosted by Anaphase. Not yet funded. The products say so and ask you to use your own key.
- An MCP connector. Your own assistant, such as Claude or ChatGPT, uses the product's tools from outside the product.
AI suggestions are drafts for you to check. Nothing here is statistical, clinical or scientific advice. Do not send patient-identifiable or confidential material to an AI provider unless your organisation has approved it.
Connector status by product
Status on 22 Oct 2026. MCP, the Model Context Protocol, is an open standard that lets an AI assistant call a program's tools.
| Product | Claude | ChatGPT | What exists today |
|---|---|---|---|
| BioPlot | Available as a custom connector through the BioPlot relay. A Claude Desktop extension and a Claude Code plugin are in preparation. | Available in developer mode through the same relay. | A connector built into the app, reached through a relay, with 27 tools. The BioPlot tab must be open and connected. Risky commands wait for a Yes in the tab. |
| SideScatter | In development. | In development. | A local MCP server for FCS files, parameters, saved gate trees, population statistics and CSV export is being built. It is not published yet. |
| BioSmith | Claude Desktop and Claude Code, as a local server you install. Not yet published. | Not available yet. | A local MCP server that reads and edits plasmid files in a folder you choose. Six design tools need a separate design component. Not on npm yet. |
| BioGlyph | Claude Desktop and Claude Code, as a local server, for invited beta users. | Not available yet. | A local MCP server with 15 tools. A hosted connector exists in code and is not deployed. The local server edits figures directly, without the in-app review step, so keep a copy of the original. |
Install files, tool lists and instructions for each connector will be published in the Anaphase plugins repository: https://github.com/paulmacdad/anaphase-plugins. The repository is being prepared; if the link does not open yet, contact us and we will send setup details.
Claude
In Claude (web, desktop or mobile), add a custom connector in Settings under Connectors, using the product name and the connector address from the product's connector page. A custom connector gets the public read-only tools. For the full tool set in Claude Desktop, install the product's extension file and paste your access token when asked.
In Claude Code, once the repository is published:
claude plugin marketplace add paulmacdad/anaphase-plugins
claude plugin install bioplot@anaphaseReplace bioplot with sidescatter, biosmith or bioglyph when that connector is listed as available.
ChatGPT
ChatGPT needs a plan that offers developer mode. Turn on developer mode in ChatGPT's settings, create a connector with the product name and connector address, and choose no authentication. ChatGPT gets the public read-only tools.
Menu names in Claude and ChatGPT change between versions. If a name differs, search their settings for "connectors".
Your own key
Create an API key in your own provider account and paste it into the product's AI settings. A chat subscription such as Claude Pro or ChatGPT Plus is not an API key. Set a monthly spend limit at your provider, and use a key just for this tool so you can revoke it without breaking anything else.
| Product | Where your key is held | What a request carries |
|---|---|---|
| BioPlot | This browser tab for the session; remembering it on this device is an option, off by default, in unencrypted browser storage. Requests pass through BioPlot's server, which relays them and does not store the key. | Table names, column titles, a bounded sample of values from the selected table, analysis and graph settings. |
| SideScatter | This browser tab for the session; remembering it on this device is an explicit option, in unencrypted browser storage. | Channel and marker names, gate names, counts and statistics shown on screen. Never event data. |
| BioSmith | The app's key vault on your device. Not on an Anaphase server. | The selected sequence region or feature list, construct name and your question. |
| BioGlyph | The BioGlyph server, encrypted for your account. Server operators can reach stored data. | Object IDs, types, names, labels, positions and lock state for the scope you choose. Not image pixels or hidden objects. |
Access tokens
During the beta, access tokens for the full tool set are issued by hand. Email paul@anaphasescience.com with your product and use. Keep the token private and never paste it into a chat, an issue or a repository.
More detail: AI disclosure.