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Workshops

From ChatGPT to AI Agents: Practical RNA-seq Workflows with Codex CLI  
3:00 - 5:00 pm, April 13, 2026
Click here to register for this workshop


The objective of this workshop is to demonstrate how an AI Agent can support and streamline bioinformatics workflows through a practical example: RNA-seq data analysis using an AI agent, ChatGPT’s Codex CLI. It focuses on using AI as an orchestration and assistance layer on top of existing bioinformatics tools—not on AI-based bioinformatics algorithms, e.g. ‘AI-powered RNA-seq method’.

We will introduce an AI-assisted workflow using a structured, layered framework:

  1. Research & Planning Layer (ChatGPT / human decision-making)
  2. Guardrail Layer (AGENTS.md for rules and constraints)
  3. Agent Layer (Codex CLI / AI agents for execution)
  4. Pipeline / Software Layer (STAR, DESeq2 and pipeline tools like nextflow)
  5. Hardware Infrastructure Layer (local computing vs. SLURM, parallelization)
  6. Exploration & Interpretation Layer (Jupyter, Rstudio, VS Code, and data visualization)


This workshop presents a practical framework based on current tools and some limited experience, as best practices in this area are still evolving. Participants will work through a hands-on RNA-seq analysis project and experience how these six layers interact in practice—from planning and execution to visualization and interpretation. The main goal is to help you use AI tools effectively, and also understand their limitations. 

The workshop is through Zoom and will be recorded. Stream videos will be available on the BioHPC web site after the workshop.

 

Machine allocation.

Workshop Outline  
Session 1 Apr 13 2026 3:00PM - 5:00PM Zoom
Lecture and hands-on
Session 2 Apr 14 2026 3:00PM - 4:00PM 624 Rhodes Hall
Office hour
 
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