UW-Madison Core Facility Training

AI-Powered Bioinformatics Tools

Two-day workshop for core facility staff

April 9-10, 2026 UW-Madison Campus

Before You Arrive

Day 1 uses browser tools you already have through your UW NetID. No installation required.

Zero setup

Your AI Tools

Claude

Build interactive tools & visualizations with Artifacts

claude.ai

ChatGPT

Reasoning, analysis, and document synthesis

chatgpt.com

Gemini

AI chat, coding, and image generation

gemini.google.com

NotebookLM

Upload-based research with inline citations

notebooklm.google.com

Interested in command-line AI tools? Day 2 includes an optional advanced track using Claude Code via AWS Bedrock. Workbench Setup (optional) →

Following the 11:00 AM AI policy and data governance session led by Charles Konsitzke...

Day 1

Thursday, April 9

12:30 - 4:30 PM · Browser-based, large group

Time	Session
12:30	Welcome + Browser Setup Orientation, WiFi, and everyone opens Claude or ChatGPT. Goal: a working AI chat session in your browser.
12:45	Your First AI Prompt Guided exercise: the difference between a vague prompt and a detailed one. The workflow pattern: Think → Plan → Build → Verify → Refine.
1:05	Guided Build: Sequence Analysis Dashboard Full-room guided build using browser chat. FASTA parsing, GC content, ORF finder — paste the prompt, save the output as HTML, open in your browser. L1: Sequence Analysis Dashboard →
1:55	Break
2:05	Product Showcase: What CLI Tools Build Instructor demonstrates 8 pre-built bioinformatics tools, each built from scratch using Claude Code. Several were built in parallel. 20 min Sequence Analysis Dashboard HTML + Chart.js 25 min Usage Billing Dashboard HTML + Chart.js 25 min Instrument Schedule Visualizer HTML + Chart.js 25 min CRISPR Guide RNA Tool React + Vite 25 min Single-Cell Expression Explorer Canvas 35 min RNA-Seq DE Dashboard Streamlit 25 min Chain-of-Custody Tracker HTML + PDF 45 min RNA-Seq Workflow Orchestrator Snakemake
2:45	Facility Prompt Workshop Each table picks a real workflow from their facility and builds a tool using Claude, ChatGPT, or NotebookLM. Sequencing QC, CRISPR pre-screening, spectra viewing, sample intake, billing, or admin reporting.
3:35	Break
3:45	Share-Outs + Day 2 Track Selection Each table shares their adapted tool. Choose your Day 2 track: continue with browser tools, or try the command-line advanced track.
4:15	Wrap Recap, next steps, and optional homework: think about what you'd build with 45 minutes of uninterrupted AI time.

Day 2

Friday, April 10

8:30 AM - 1:00 PM · Large group opener, staggered facility clinics, optional advanced capstone

Large Group (8:30 - 9:30 AM)

Time	Session
8:30	Recap + Day 1 Highlights Review the workflow pattern and common issues from Day 1. Introduce the runtime tracks for today's mixed-tooling clinics — browser, Copilot CLI, Gemini CLI, or Claude Code — same prompts, your choice. L0b: Pick Your Runtime →
8:45	Live Troubleshooting + Prompt Hardening Real issues from Day 1 — we fix them together and extract the 9-clause Patch Kit you'll append to every clinic prompt today. The fix for "almost right" tools. L0c: Prompt Hardening Patch Kit →
9:10	Showcase: Best Day 1 Adaptations Highlight 2-3 strong facility-specific tools from Day 1. Extract reusable prompt patterns.

Staggered Workflow Clinics (9:45 AM - 12:00 PM)

~45 minutes per facility group, flexible schedule. Each clinic follows: orient → demo → hands-on → share. Staff return to work between their group’s session.

Slot	Facility Group	Tools	Lessons
9:45	Sequencing & Genomics NGS + GEC + BRC	Claude, ChatGPT	L1 L17 L18
10:30	CRISPR & Animal Models GEAM	Claude, ChatGPT	L2 L9 L10 L19
11:15	Proteomics & Isotope Mass Spec + IRMS	Claude, ChatGPT	L4 L11 L12 L20
11:15	Research Administration Grants, HR, Accounting, Admin Support	Claude, ChatGPT, NotebookLM	L7 L8 L22
TBD	Forensics & Field Science MIA + eDNA · Scheduled later in the day	Claude, ChatGPT	L13 L14 L15 L16 L21

Advanced Capstone (12:00 - 1:00 PM)

CLI / Advanced Session

Optional · Self-selected

For participants who want to go further: build tools from the terminal using Claude Code, connected to UW’s AWS Bedrock. Self-directed with peer support.

Prerequisites