April 9, 2024

3D Science Visualization

Instructor: Bongsup Cho, PhD, University of Rhode Island

Location: URI   
Session 1: July 7-9 ( Location TBD)
Session 2: July 21-23 (Location TBD)

Course Overview

This WDT Module aims to train students in modern methods of 3D science visualization. The module will include lectures and hands-on experience in molecular modeling, 3D molecule printing, protein and DNA structure prediction using machine learning AlphaFold algorithms, BioRender Science Illustration app, and the use of AI-based art as a research tool. The module will provide sufficient background for students to understand and appreciate how scientists could benefit from the available state-of-the-art 3D visualization software and tools to enhance their scientific data and disseminate it with impact. The module will be completed over 2.5 days, and participants who complete it will receive an RI-INBRE Certificate of Completion.

Learning Outcomes

    • Navigate molecular structure databases such as the RCSB Protein Data Bank (PDB): Opioid Receptor as an example (4dkl)
    • Visualize the molecular mechanism of antibiotics and cancer drugs in molecular modeling and 3D models
    • Get hands-on with processing molecular structures in visualization software such as ChimeraX
    • Print your molecular structures using a 3D printer
    • Explore DNA structures and hands-on modeling of the origin of double helical structures
    • Tour of Human Cell
    • Closer inspection of phospholipid transmembrane structures and functions
    • Hands-on practice on predicting protein structures from sequence using the Nobel prize-winning machine learning algorithm AlphaFold (Chris Hemme)
    • Explores how AI tools are challenging visual artists today. Hands-on Experiments: Making Images with AI. How do AI Image Models Work? Discussion of our Images (Griffin Smith, Critic and Lecturer, Rhode Island School of Design (RISD))
    • Demo of “BioRender” Scientific Image and Illustration Visualization Software (Chris Hemme)
    • Reflection on scientists/artists’ interdisciplinary collaboration

Lab Report

Students will be expected to maintain detailed laboratory notes to include:

  • Structures analyzed and their relevance
  • 3D molecule printing procedures
  • Data analysis protocols (e.g., workflows, software used, etc.)
  • Results of AlphaFold analysis
  • Reflection on scientists/artists’ interdisciplinary collaboration

Resources Used in this Module:

  • Standard Operating Procedure – 3D Printing of Protein Structures
  • ChimeraX – 3D structure visualization of PDB files
  • Slide Decks for lectures
  • BioRender Image and Illustration Software
  • “3D Molecular Designs” Kits (DNA, Phospholipid membrane models)
  • Illustration of a Human Cell

Proposed Timeline (subject to change)

Day 1Day 2Day 3
9:00 AM-10:00 AMIntroduction to Molecular Visualization and Structural Databases (Lecture)(Cho)Protein structures prediction using AlphaFold (Lecture/Hands-on)(Hemme)Let’s play. Modeling of DNA structures and the origin of double helical structures (Hands-on)
10:00 AM-11:00 AMTour of Model Showcase (Cho)
Tour of a Human Cell		Protein structures prediction using AlphaFold (Hands-on)(Hemme)DNA structure…continues. Modeling of phospholipid transmembrane (Hands-on)
11:00 AM-12:00 PMAntibiotics action and resistance (Hands-on) (Cho)Demo of BioRender (Scientific image and illustration software) (Hemme)Reflections
12:00 - 1:00 PMBreakBreakCertificate Distribution
1:00 PM-2:00 PM3D Projection of drug actions (demo/hands-on)(Cho & Hemme)Introduction: Griffin’s work at Brown, RISD, and Harvard (Griffin Smith)
Lecture: How Visual Artists Are Using AI
2:00 PM-3:00 PMChimeraX Prep of 3D molecule printing (Hands-on)(Cho)Making Images with AI (Hands-on Experiments)
Discussion of our Images
3:00 PM-4:00 PMChimeraX Prep of 3D molecule printing (Hands-on)(Cho)Lecture: How do AI Models Work?
Wrap-up