Week 10: Using generative AI

Author

Affiliation

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Published

October 28, 2025

Modified

October 31, 2025

1 Overview

This week, you will learn about using generative AI (genAI) tools to help you with tasks in omics data analysis, especially coding talks.

2 Learning goals

This week you will learn:

Lecture A: Using generative AI when coding and beyond

Basic background of generative AI (genAI) and large language models (LLMs)
What GenAI applications exist in bioinformatics and omics data analysis
About Ohio State’s genAI adoption and approved tools
What options you have for using genAI tools, including for coding
Example prompts and outputs relevant to this course
Tips and pitfalls when using genAI tools, especially for coding

Lecture B: GenAI with GitHub Copilot

Using your local VS Code installation at OSC
Enabling and configuring GitHub Copilot within VS Code
Using GitHub Copilot within VS Code to help you with coding tasks

3 Readings

Lubiana et al. (2023): Ten quick tips for harnessing the power of ChatGPT in computational biology
Pearson (2025): Universities are embracing AI: will students get smarter or stop thinking?

4 Exercises & assignments

Graded assignment 5: Using GenAI when coding (Due 11/03)

5 Further resources

Rahman and Wong (2023): How Much Can ChatGPT Really Help Computational Biologists in Programming?
Helmy et al. (2025): Ten simple rules for optimal and careful use of generative AI in science (Added 10/31)
Guest et al. (2025): Against the Uncritical Adoption of ‘AI’ Technologies in Academia

References

Guest, Olivia, Marcela Suarez, Barbara Müller, Edwin van Meerkerk, Arnoud Oude Groote Beverborg, Ronald de Haan, Andrea Reyes Elizondo, et al. 2025. “Against the Uncritical Adoption of ’AI’ Technologies in Academia,” September. https://doi.org/10.5281/zenodo.17065099.

Helmy, Mohamed, Lingling Jin, Amr Alhossary, Tamer Mansour, Diogo Pellagrina, and Kumar Selvarajoo. 2025. “Ten Simple Rules for Optimal and Careful Use of Generative AI in Science.” PLOS Computational Biology 21 (10): e1013588. https://doi.org/10.1371/journal.pcbi.1013588.

Lubiana, Tiago, Rafael Lopes, Pedro Medeiros, Juan Carlo Silva, Andre Nicolau Aquime Goncalves, Vinicius Maracaja-Coutinho, and Helder I. Nakaya. 2023. “Ten Quick Tips for Harnessing the Power of ChatGPT in Computational Biology.” PLOS Computational Biology 19 (8): e1011319. https://doi.org/10.1371/journal.pcbi.1011319.

Pearson, Helen. 2025. “Universities Are Embracing AI: Will Students Get Smarter or Stop Thinking?” Nature 646 (8086): 788–91. https://doi.org/10.1038/d41586-025-03340-w.

Rahman, Chowdhury Rafeed, and Limsoon Wong. 2023. “How Much Can ChatGPT Really Help Computational Biologists in Programming?” December. https://doi.org/10.48550/arXiv.2309.09126.