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Workshops

From ChatGPT to AI Agents: Practical RNA-seq Workflows with Codex CLI  
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This is a virtual workshop, you can participate by reading workshop materials, watching video presentations and carrying out exercises on an assigned BioHPC Cloud server (server assignments are listed here). If you need help, please sign up for our Office Hours. The server assigned to you for hands-on exercises will be available for a limited time, see server assignment page or bottom of this page for details. Please note, the server is assigned to you for hands-on exercises, NOT heavy computing, using the server for workshop unrelated computing is not allowed and will result in assignment termination.

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.

Video

 

Server assignment length 5 days  
 
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