Connect Mass Dynamics to the AI tool you already use. It works on your live data, where it already is, with the same validation and the same record as everything else you do in Mass Dynamics.
Nothing to export. Nothing to install. No terminal.
Ask in plain language and it does the work in Mass Dynamics for you. This is about getting data in and analyses running faster. It is not doing the science for you.
Point it at your files and it uploads and processes them. Validation runs as the data goes in, so anything wrong surfaces immediately rather than after the job has run.
Group your samples, name the conditions and set the metadata by asking. This is the step that decides what your analysis compares, so always check this work.
Normalization, pairwise comparisons and the other analyses Mass Dynamics runs. Start one, then ask where it got to.
You do not need to know the file spec or the exact parameters. It asks when it is unsure, checks as it goes, and corrects course rather than stopping.
You need a Mass Dynamics account. Everything else happens inside the AI tool you already use. Any tool that lets you add a custom MCP server by URL can connect to Mass Dynamics.
https://mcp-app.massdynamics.com/mcp
In your AI tool's connector settings, add the URL above as a custom connector. Exact wording varies by tool.
If it asks how to authorize, choose OAuth. You sign in with your normal Mass Dynamics login. No API key to copy or store.
Paste this in: “Run a health check on Mass Dynamics.” If it comes back, you are connected. Then try one of the prompts.
You can disconnect at any time, in your AI tool's own settings. Managing the connection to your AI Tool covers how, and what happens to work already done.
AI tools change often and without notice, so we keep this current as they do. If a connection stops working, contact support.
| AI tool | Integration with Mass Dynamics | Setup notes |
|---|---|---|
| Claude Desktop | Supported | Settings, then Connectors, then add a custom connector with the server URL. For uploads, allow *.amazonaws.com in the connector's network access. Steps here. |
| Claude Code | Supported | Add the server URL. It asks permission for network access at the moment it needs it, so there is nothing to set up in advance. |
| Claude Cowork | Supported | Add our plugin file, which carries the server URL for you. Steps here. |
| Codex | Supported | Add the server URL. No additional configuration. |
| ChatGPT (work) | Supported | Set up once through ChatGPT in a browser, with developer mode on. Enable the plugin's actions after you add it or it will connect but do nothing. If you have a work or business license, use this one. |
| ChatGPT (personal) | Not recommended | It connects, however network access is blocked and it gets confused, causing issues with uploads. Use a work license if you have one. |
| Microsoft 365 Copilot | Coming soon | Adding Mass Dynamics as an M365 connector is not working yet. If you are on Copilot, use Copilot Studio, or tell us and we will work on it with you. |
| Copilot Studio | Supported | You can build an agent, add Mass Dynamics to it as a tool, and publish it. This is likely a job your systems admin may need to do, rather than a two-minute setup. |
| Cursor | Coming soon |
The exact clicks for each tool, including Claude, ChatGPT, Codex and Copilot Studio, are in Connect your AI tool.
Not listed does not mean it will not work. Any AI tool that lets you add a custom MCP server by URL can connect. This list is what we have run and tested ourselves. Contact support with the tool you use and we will work through it with you.
Five prompts covering the path from connected to a finished analysis. Say them in your own words.
Tell me what you can do with Mass Dynamics.
Upload the files in this folder to Mass Dynamics. Before you create anything, show me the sample names and conditions you worked out, and where you got them from.
Build a dataset from that upload and set the metadata. Ask me if anything is ambiguous rather than guessing.
Normalize it, then run a pairwise comparison between treated and control.
That upload failed. Work out why and fix it.
When you upload, your AI tool works out the sample names and conditions, often from your file names. It will usually ask you to confirm. Confirm it properly. An experiment design can pass every validation rule and still not be the comparison you meant, and the analysis on top of it will be wrong with it. Prompt 2 is written to make it show its working first.
The questions that come up most. Anything you need to forward to IT or security is in the help center.
No. That is what this path is for. You add a connector once, then ask for what you need in plain language. If you would rather drive it programmatically, the API is the better route.
This is the production version of what the Agent Pack was testing, so the Agent Pack has been retired. If your old setup has stopped working it is inert and you can leave it.
One thing does need doing. The old installer saved a Mass Dynamics API token to your disk, and deleting the files does not revoke it. Removing the Agent Pack has the steps, including retiring that token.
Your AI tool runs on the API, so these are not two separate systems. The real question is whether a person is in the loop.
Use an AI tool when you are exploring and the next step depends on what the last one showed. Day-to-day work, following the science.
Use the API on its own for routine processing: the same workflow every time, on a schedule or triggered by your own systems, with nobody watching. Instrument and vendor output formats belong here too.
Plenty of teams run both, against the same workspace.
Connecting does not change your Mass Dynamics plan.
Your AI tool is a separate subscription with whoever provides it, at your own cost. Whatever plan you hold with them is what you are using.
The list covers the AI tools we have run ourselves. It is not a limit on what can connect, and any tool that lets you add a custom MCP server by URL will often work already. Contact support with the tool you use and we will confirm it and add it to the list.
More detail lives in the help center. Security and data when using an AI tool is the one to forward to whoever reviews this in your organization. Managing the connection to your AI Tool covers disconnecting and what happens to work already done.
Thank you for testing it. What you found is why this version is better: it's hosted, so there's nothing to install, and the error handling that used to leave you stuck now lives in the server. The Agent Pack has done its job and we've retired it.
You may not need to do anything. If the old setup has stopped working it is inert and you can leave it. You only need to act if your AI tool starts offering two sets of Mass Dynamics operations and picking the wrong one — switching the old connector off fixes that in a second.
There is one loose end worth closing. The old installer put a Mass Dynamics API token on your disk. It stays valid until you retire it, whatever else you delete.
Most people are connected in a couple of minutes using the steps above. If yours is not one of those, an unusual setup, an AI tool that is not on the list yet, or something that just will not behave, there are two ways to reach us.
Send us a message using the form, and tell us which tool you are using and where it got stuck. Or book a session and we will work through it with you live.
Which tool you're using and where it got stuck. That's usually enough for us to know the answer. Takes about two minutes.