Workshop Introduction

Using Generative and Agentic AI
for Omics Data Analysis

Jelmer Poelstra

Lead,
CFAES Bioinformatics Core

Menuka Bhandari

Bioinformatician,
CFAES Bioinformatics Core

Hannah Toth

Postdoc,
Department of Plant Pathology

Jonathan Jacobs

Faculty,
Department of Plant Pathology

2026-07-13

Instructor introductions

What is the workshop about?

The general idea

  • Focus on general-purpose AI in the form of LLMs to help you write code —
    code then used to do the data analysis

We are not:

  • Asking the LLMs to do the analysis for us:
    • not directly, e.g. “summarize these 15 books”
    • nor indirectly, e.g. by making it run everything for us
  • Using specialized AI applications like AlphaFold, Evo2, and so on

The general idea (cont.)

  • Rather, focus on improving how you interact with LLMs:

    • From web-based chat ~ “email conversation with a smart person”
    • To in-editor, agentic chat ~ “having them sit next to you, coding while you talk”

This is very general, so:
while example data is omics data, principles and tooling apply to any data type

We are not AI experts

  • Just practitioners that are –hopefully!– a few steps ahead of you
  • (A lot of AI-for-code content is aimed at (aspiring) software developers.)

Infrastructure

  • Highly practical, many hands-on sessions: follow along with us, and try things yourself

  • Core infrastructure during hands-on work:

    • Own installation of VS Code (you should have this installed)
    • The Ohio Supercomputer (OSC)
    • In-editor AI tools (GitHub Copilot & Claude Code)

Setup/configuration

  • We will spend significant time on setup steps ☹️
  • This is one-time setup that you can continue to use after the workshop 😃

Examples and data

  • Examples will mainly:
    • Use an RNA-Seq dataset of rice infected with a fungus from Iqbal et al. (2025)
    • Involve working on shell scripts to run command-line tools
  • Your freedom:
    • Tomorrow afternoon for DIY with any dataset you like
    • Feeling on top of things? Free to try example prompts with other data or intentions in other sessions, too
    • More of an R person? We have a Positron setup page!

You don’t need to have your own dataset:
can also continue working on the example dataset

The schedule

Day 1: Monday, July 13

Section Time Instructor Topic & link
1 09:00 am – 09:45 am all Intro to the workshop
2 09:45 am – 10:45 am Menuka Intro to Generative AI and LLMs
10:45 am – 11:00 am ☕️ Break
3 11:00 am – 11:30 am Derek Ditmer, OTDI Approved genAI Tools at OSU
4 11:30 am – 12:15 pm Jonathan GenAI use cases and tools for research
12:15 pm – 01:00 pm 🍽 Lunch
5 01:00 pm – 02:00 pm Jelmer OSC and VS Code setup
02:00 pm – 02:15 pm ☕️ Break
6 02:15 pm – 03:15 pm Jelmer Code completions with GitHub Copilot
03:15 pm – 03:30 pm ☕️ Break
7 03:30 pm – 04:00 pm Evan Jaffe, OSC LLM options at OSC

Day 2: Tuesday, July 14

Section Time Instructor Topic & link
8 09:00 am – 10:00 am Jelmer Agentic chat with Claude Code
9 10:00 am – 10:30 am Hannah Prompt engineering
10:30 am – 10:45 am ☕️ Break
10 10:45 am – 11:45 am Menuka Advanced agentic options and skills
11 11:45 am – 12:15 pm Hannah Limitations and responsible use of AI
12:15 pm – 01:00 pm 🍽 Lunch
13 01:00 pm – 03:30 pm all DIY with own (or other) data
14 03:30 pm – 04:00 pm all Concluding remarks and looking forward

How to ask questions and contribute

How to ask questions and contribute

  • Don’t hesitate to interrupt if you have a question
  • Same if you want to share your experience with the group —
    you may have a different perspective, a better solution, etc.!
  • If you’re stuck, behind, or similar, always let us know —
    use your best judgement whether to interrupt or to put up hand / use a sticky note / use the Zoom chat

Sticky notes

We have sticky notes in 10 colors:

  • Use dark olive-green to say “I need a break within the next 30 seconds.”
  • Use medium sea-green to say “I am re-watching my favorite episode of Friends, but please carry on.”
  • Use cornflower blue to say “I already asked ChatGPT and it disagreed with you.”

Sticky notes (take 2)

  • Use blue to say: “Slow down / I am falling behind”

  • Use red to say “I have a (non-urgent) issue”

Final pieces of information

  • Coffee/tea, snacks, and lunch will be provided during breaks

  • Forgetting anything?


Links

Questions?

References

Iqbal, O., X. Yang, Z. Wang, et al. 2025. “Comparative Transcriptome and Genome Analysis Between Susceptible Zhefang Rice Variety Diantun 502 and Its Resistance Variety Diantun 506 Upon Magnaporthe oryzae Infection.” BMC Plant Biology 25 (1): 341. https://doi.org/10.1186/s12870-025-06357-5.