3D Science Visualization
Instructor: Bongsup Cho, PhD, University of Rhode Island
Location: URI
Session 1: July 10 – July 12 ( Lab: Room 292 / Lecture Room: Avedisian Rm 403)
Session 2: July 17 – July 19 ( Lab: Room 292 / Lecture Room: Avedisian Rm 403)
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, 3D bioprinting, virtual reality, protein structure prediction using machine learning algorithms, and art as research. 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 with impact. The module will be completed over 2.5 days and participants who complete the module will receive an RI-INBRE Certificate of completion.
Learning Outcomes
- Navigate molecular structure databases such as the RCSB Protein Data Bank (PDB) and PubChem
- 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 Chimera
- Print your molecular structures using a 3D printer
- Learn the basics of 3D bioprinting through a demo that includes digital light processing (DLP)-based and multi-axis robotic arm-based 3D printing
- Visualize and analyze molecular structures in virtual reality (VR)
- Predict protein structures from sequence using the AlphaFold
- Explore RISD’s Vis-a-thon program, delving into its inception, methodology, and influence in the realm of artistic visualization research
- Demo of “BioRender” Scientific Image and Illustration Visualization Software
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
- Nanome – 3D structure visualization in VR
- Chimera/ChimeraX – 3D structure visualization
- HTC Vive virtual reality headsets
- Slide Decks for lectures
- 3D Bioprinters
- BioRender Image and Illustration Software
Timeline
| Day 1 | Day 2 | Day 3 | |
|---|---|---|---|
| 9:00 AM-10:00 AM | Introduction to Molecular Visualization, and Structural Databases (Lecture)(Cho) | Protein structures prediction using AlphaFold (Lecture/Hands-on)(Hemme) | 3D Bioprinting (Lecture) (Menon) 9:00 am - 9:30 am |
| 10:00 AM-11:00 AM | Tour of Model Showcase (Cho) | Protein structures prediction using AlphaFold in ChimeraX (Hands-on)(Hemme) | Demo of 3D Bioprinting (Hands-on) (Menon) 9:30 am - 10:30 am |
| 11:00 AM-12:00 PM | Antibiotics action and resistance (Hands-on) (Cho) | Visualizing Molecular Structures in Virtual Reality with Nanome and Mol* (Hands-on)(Hemme) | Art as Research: RISD’s Vis-a-thon Program (Lecture) (Rhodes) 10:30 am - 12:00 pm |
| 12:00 - 1:00 PM | Break | Break | WDT Survey and Certificate Distribution |
| 1:00 PM-2:00 PM | 3D Projection of drug actions (demo/hands-on)(Cho & Hemme) | Demo of BioRender (Scientific image and illustration software) (Hands-on)(Izawa) | |
| 2:00 PM-3:00 PM | Pre-processing of 3D molecule printing (Hands-on)(Cho) | Post-processing of 3D molecule printing (Hands-on)(Cho) | |
| 3:00 PM-4:00 PM | Pre-processing of 3D molecule printing (Hands-on)(Cho) | Post-processing of 3D molecule printing (Hands-on)(Cho) |