Get set up before the hands-on.

In 2.4 you analyze a real RNA-Seq table by talking to an AI assistant. Do this page before Friday: pick where you will work, set it up, and check that it can run code for you.

Set up

Pick where you will work

You can do this exercise in any of the places below. Open the section for the one you pick and follow it; you can ignore the rest. Wherever you work, do the whole exercise in one conversation, so the assistant remembers the data and every step you have taken. The hands-on pages say “Claude” throughout: if you use ChatGPT or Codex, read it as your assistant, and the tasks, hints, and checkpoints stay the same.

BROWSER Claude in your web browser (easiest: nothing to install)

Go to claude.ai, sign in, and start a new chat. Claude writes Python, runs it in its own sandbox, and shows tables and plots right in the chat. The 2.4 checkpoints were written against this.

If Claude says it cannot run code or make files, open Settings, find the code execution and file creation option, and turn it on.

DESKTOP The Claude desktop app

Download it for Windows or macOS from claude.com/download, install it, sign in with your Claude account, and start a new chat. It works the same way as the browser version.

SCIENCE Claude Science

Claude Science is Anthropic’s workbench for research, with common analysis packages and databases built in. It is a desktop app for macOS and Linux only, in beta, and needs a Claude Pro, Max, Team, or Enterprise plan (on Team and Enterprise, your admin has to turn it on).

Download it from claude.com/science, sign in, and start a new analysis. It runs code on your own computer or on machines you connect to it, so, as in VS Code, ask it to save plots as files and tell you where they are.

CHATGPT ChatGPT or Codex

In the browser: go to chatgpt.com, sign in, and start a new chat. ChatGPT also writes and runs Python and shows plots in the chat.

Desktop app: download the ChatGPT app for Windows or macOS from chatgpt.com/download and sign in. Choose ChatGPT or Codex from the menu at the top left. Codex works with files on your own computer, so, as in VS Code, it needs Python installed; ask it to check that first.

VS CODE VS Code with Claude or Codex

Claude and Codex both run inside VS Code, a free code editor. Open the steps below in order, ideally before the session, and skip anything you already have.

STEP A Install VS Code, if you have not yet

Download it free for Windows or macOS from code.visualstudio.com/download, and run the installer with the default options.

STEP B Install Python, if you have not yet

Download Python 3 free from python.org/downloads.

Windows: tick Add python.exe to PATH on the first installer screen. If you miss it, the assistant cannot find Python. macOS: run the downloaded installer as usual.

STEP C Add Claude to VS Code

Open the Extensions view (Ctrl+Shift+X on Windows, Cmd+Shift+X on macOS), search for Claude Code, and install Claude Code for VS Code by Anthropic. Click the Claude icon that appears, sign in with your Claude account, and approve the request in the browser window that opens. Then start a new conversation in the Claude panel.

The extension may need a paid Claude plan. Check this before the session, not during it.

STEP C Or add Codex to VS Code

Open the Extensions view (Ctrl+Shift+X on Windows, Cmd+Shift+X on macOS), search for Codex, and install Codex – OpenAI’s coding agent by OpenAI. Open the Codex panel, sign in with your ChatGPT account, and approve the request in the browser window that opens.

The extension may need a paid ChatGPT plan. Check this before the session, not during it.

STEP D What changes when you work in VS Code

Make a new folder for today, for example session2-handson, and open it with File, Open Folder. Everything the assistant makes (data, plots, scripts, the report) lands in that folder.

The assistant runs code on your own computer, so your first message should also ask it to check that Python and the packages it needs (pandas, matplotlib, seaborn, scipy, scikit-learn) are installed, and to help you install anything missing.

Plots are saved as image files rather than shown in the chat. Ask it to save each plot as a PNG and tell you the file name, then click the file in VS Code to see it.

It asks your permission before it runs commands or edits files. Read what it wants to do before you approve.

Later in the bootcamp we will run this kind of analysis on the UMass Chan cluster through Foundry Connect. The way you talk to Claude stays the same.

Check that it works

In a new conversation, ask your assistant to run a line of Python and draw a small plot of anything, for example a line through a few points. If you see the plot (or, in VS Code, Claude Science, or Codex, a saved PNG file you can open), you are ready for 2.4.

No plot? Tell the assistant exactly what happened and ask it what to do. That is already practice for the hands-on. If you are still stuck, bring your laptop on Friday and we will sort it out at the start.