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Bootcamp / Session 1 / 1.0

Session 1.0 · Pre-work · About 30 minutes

Four green lights before Session 2.

Everything hands-on in this bootcamp runs on the UMass Chan HPC cluster through Foundry Connect, with Claude as the assistant. These steps connect the pieces once, so class time goes to the science.

Do these first

  1. Request your HPC cluster account now. Use the request form or email hpc@umassmed.edu. Your PI has to approve it, which can take days. You can do Steps 1 and 4 while you wait.
  2. Log in to Foundry Connect once at viafoundry.umassmed.edu with your UMass Chan email and email password.
  3. Off campus? The cluster only answers from the UMass Chan network or VPN.
  4. Bring a charged laptop with Chrome or Firefox to every session.

Where things run

Your data and the heavy compute live on the cluster. Foundry Connect runs pipelines there for you and collects the results. Your laptop is a window onto both. Claude never touches the cluster directly: it sees what the Foundry Connect connector exposes, which is your runs, their parameters, and their result files.

ConnectionWhat proves it is youWhere you revoke it
Foundry Connect to clusterAn SSH key that Foundry Connect creates for you, added to your HPC accountHPC portal, Public Keys
Claude to Foundry ConnectA browser sign-in, with no key or password to copyClaude connector settings, or Foundry Connect

Each connection is a trust you grant and can take back.

The last one lets an AI read your runs and results, and anything it reads is sent to the AI provider. Grant it knowingly, and know where to revoke it. Part 1.4 comes back to this.

The four steps

Create an SSH key in Foundry Connect

  1. Go to viafoundry.umassmed.edu, click Log in (top right), and sign in with your UMass Chan email address and email password.
  2. Click your profile avatar (top right), then the Credentials tab, then Create Credential.
  3. Set the credential type to SSH and enter any name.
  4. Click Generate Keys for Me, then Save.
  5. Next to your new key, open the … menu, choose View, then Copy to copy the public key. You paste it in the next step.

Add the public key to the HPC portal

  1. No cluster account yet? Request one first (see above) and come back once it is approved.
  2. Go to hpcportal.umassmed.edu/PublicKeys/Create and paste your public key. Sign in with your UMass Chan email address and email password.

Set up your HPC run environment in Foundry Connect

Click your profile avatar, then the Run Environments tab. Your run environment is already listed; you only add your key.

  1. Open the existing run environment.
  2. Select your SSH key.
  3. Click Test Connection, then Save Changes.

Add Foundry Connect to Claude as a connector

With this connection you can ask Claude in plain language to find pipelines, launch and track runs, open processed samples, and explore, plot, and summarize your results, without leaving the chat.

  1. In claude.ai (or Claude for Science), go to Settings, then Connectors.
  2. Click Add custom connector.
  3. Enter the Foundry Connect connector URL: https://viafoundry.umassmed.edu/mcp
  4. Click Connect and authorize in the browser.

More detail: using Foundry Connect with Claude.

Check your four green lights

  1. You can log in to Foundry Connect.Step 1
  2. Your public key is listed in the HPC portal.Step 2
  3. Test Connection succeeds on your run environment.Step 3
  4. Asking Claude “list my Foundry Connect runs” returns an answer, not an error. An empty list is fine.Step 4

Stuck on a step? Bring your laptop to the break on Sep 18 or to the start of Session 2, or email biocore@umassmed.edu with the step number and a screenshot. Never include a password or private key in the email.

General help: Foundry Connect getting-started guide.