Applied Module 12 · AI-Powered Bioinformatics Tools

Pick Your Runtime: Browser, CLI, or Both

What you'll learn

~5 min
  • Pick the runtime that fits your situation today
  • Run the same applied-lesson prompt in any of 5 environments
  • Switch runtimes mid-clinic without rewriting the prompt

Why this exists

Day 2 small groups have a mixed bag of tooling. Some of you are happy in the browser. Some of you have UW Copilot or UW Gemini accounts and are curious about CLI. A few of you already have Claude Code installed from Day 1. You should not have to wait for a tool install to participate in your facility clinic.

Every applied-lesson prompt in this module is runtime-agnostic. The same prompt block works in 5 different environments. The only thing that changes is where the file lands — browser tools return an artifact you save manually, CLIs write a file directly to your folder.

This page is your facilitator + learner cheat sheet for today.


Decision tree: pick your runtime in 30 seconds

💡Start here
  1. Already have Claude Code installed and working from Day 1? → use Claude Code.
  2. Have a UW Microsoft account (you do)? → try Copilot CLI if you want CLI today, otherwise copilot.microsoft.com in the browser.
  3. Have a UW Google account (you do)? → try Gemini CLI if you want CLI today (verify it works for your account first — see note below), otherwise gemini.google.com in the browser.
  4. Don’t want to install anything?claude.ai or chatgpt.com in the browser. This is the default and it works for everything in this module.

If you’re stuck for more than 2 minutes on any of the CLI options, fall back to browser. Don’t burn your clinic time on tool setup.


The portability rule

Every applied-lesson prompt in this curriculum is a single block of plain text. That block does not change between runtimes. Only the invocation changes.

RuntimeHow you feed the prompt inWhere the file lands
claude.ai (browser)Paste prompt into chat → click “Save as artifact” or copy code into a .html fileYour Downloads folder
ChatGPT (browser)Paste prompt into chat → copy code into a .html fileWherever you saved it
Copilot Chat (browser)copilot.microsoft.com → paste → copy codeWherever you saved it
Claude Code (CLI)claude "$(cat prompt.txt)" or paste into the claude REPLCurrent working directory
Copilot CLI (CLI)gh copilot suggest "$(cat prompt.txt)" (limited) — for full code generation use copilot CLI in agent modeCurrent working directory
Gemini CLI (CLI)gemini -p "$(cat prompt.txt)" or paste into the gemini REPLCurrent working directory
Verify before your clinic: Gemini CLI with UW NetID

We have not yet confirmed that Gemini CLI authenticates cleanly with UW NetID Google accounts. If you want to try the Gemini CLI path, take 2 minutes before your clinic to run gemini in a terminal and sign in. If it works, great — use it. If it errors out or asks for billing setup, fall back to the browser (gemini.google.com) or to one of the other CLIs. Do not let this block your clinic participation.


Facilitator swap card

If a learner is mid-clinic and wants to switch tracks, here’s the 1-line equivalent. The prompt body stays the same — only the wrapper changes.

If they’re in……and they want to switch to…tell them this
claude.ai browserClaude Code CLISave the prompt to prompt.txt, then claude "$(cat prompt.txt)" in a clean folder
claude.ai browserCopilot CLISave to prompt.txt, then copilot --prompt-file prompt.txt (or paste into copilot REPL)
claude.ai browserGemini CLISave to prompt.txt, then gemini -p "$(cat prompt.txt)"
Any CLIclaude.ai browserOpen claude.ai, paste the prompt body, save the artifact as .html
ChatGPT browserCopilot Chat browserOpen copilot.microsoft.com, paste the same prompt — it’s free with your UW NetID
Stuck on any setupBrowser, anythingOpen claude.ai. It’s the lowest-friction path. You’ll catch up faster than fighting the tool.

Three things that are the same across all runtimes

  1. The prompt body is the prompt body. The 50–150 line applied-lesson prompts in this module are written to be runtime-agnostic. Don’t rewrite them per runtime.
  2. The 9 hardening clauses from the Patch Kit (Lesson 00c) work everywhere. Append them to any prompt in any runtime to close the “almost right” gaps.
  3. The output is the output. Whether the file lands in your Downloads or your ~/projects/biotech folder, double-clicking it opens it the same way in your browser.

Three things that change between runtimes

  1. Where the file lands. Browser = manual save. CLI = automatic file write.
  2. Iteration speed. CLI lets you say “now add a clear button” and the file updates in place. In browser, you copy-paste a fresh artifact each iteration.
  3. Cost / quotas. UW Copilot and UW Gemini are free with your NetID. claude.ai free tier has message limits. Claude Code Pro is $20/month. Pick what fits.

What you do not need to decide today

  • Which runtime is “best.” None of them are. They are interchangeable for the work in this module.
  • Whether to install a CLI permanently. You can try a CLI for one clinic and abandon it. The browser path is always there.
  • Whether your facility has standardized. It hasn’t. That’s fine.
💬The point of this page

We don’t want the runtime question to slow down your clinic. If you spend 10 minutes picking the perfect tool, you’ve already lost a quarter of your facility’s session. Pick one in 30 seconds, ship a working tool, swap runtimes later if you want.


Quick reference: copy-pasteable invocations

For learners who want to run a saved prompt from prompt.txt:

Terminal window
# Claude Code
claude "$(cat prompt.txt)"
# Gemini CLI (verify auth first)
gemini -p "$(cat prompt.txt)"
# Copilot CLI (if installed via gh extension)
gh copilot suggest "$(cat prompt.txt)"
# All browser tools: just paste prompt.txt content into the chat box

For Windows PowerShell users, replace $(cat prompt.txt) with (Get-Content prompt.txt -Raw):

Terminal window
claude (Get-Content prompt.txt -Raw)

What’s next

  • For your clinic: head to your facility group’s lesson list (see the Day 2 agenda) and pick a runtime from the decision tree above.
  • Before you paste any prompt: skim Lesson 00c (Prompt Hardening Patch Kit) for the 9 clauses you should append. They take 30 seconds to copy and they’re the difference between a tool that’s “almost right” and a tool you can hand to a colleague.