GRANT: CADD Education

This project will focus on an educational initiative that involves 3D visualization and simplified UIs for common, open-source CADD software.

Virtual Reality (a la the Oculus Rift and HTC Vive) are likely to be big. This provides new opportunities for education. This project focuses on developing a web-app that can display molecules in otherwise natural looking environments, for educational purposes.

Perhaps this grant would be a good candidate for this work.

Description for rotation students:

Virtual Reality Molecules: Visualization and Education

This project involves writing software that can visualize molecules in 3D. It will be web based and will eventually work with VR headsets. The director of the department’s outreach program has expressed real interest in the project and thinks it would be fundable through an education grant, though I think it would have useful research value as well.


  1. The basic functionality of the software is already written. So the foundation to build on is already there. I suspect that will make it easier to learn programming (since you’re not starting from scratch).
  2. I suspect a publication isn’t too far in the future. Assuming you make substantial contributions, you’d be a co-author.
  3. Through the outreach program, this project could directly benefit disadvantaged youths.


  1. Most of this project is written in Typescript, a language for web programming. Python is used mostly for my kind of computational biology. But much of what you learn about Typescript will transfer to Python later, and I’m convinced web-based comp bio will become increasingly important in the future.

Another Description I Used

I do have an interesting visualization project I’m working on. I mentioned it briefly in my talk but didn’t go into much detail. I’m creating a web-based 3D molecular visualization program that will (hopefully) work with VR headsets like the HTC Vive. It should be a useful research tool for structural biologists, but I think it could also be a powerful educational tool. In fact, the outreach program here in the department has expressed a lot of interest in the project, so aside from publishing and maintaining the software, we’ll likely work with them, too, to get disadvantaged youth excited about science.

For this web-based project, we’ll mostly use Typescript (basically Javascript) and jQuery. But we could also use the help of non-programmers for the modeling and graphics work. I’m using the open-source modeling software Blender to create the 3D scenes.

Over the long term, I’d also like to build some related tools for that VR platform. For example, scripts that can automatically generate lipid bilayers with embedded proteins that undulate like the ocean, scripts that can simulate proteins in motion, etc.

[project-management file=”Cadd-Education.xml”]

Other Comments

David Koes once emailed me about joining the TECBio REU program ( and the summer research program for high school students ( Follow up with him. Perhaps these could be incorporated into this grant.