EML Project Snapshot: 3D Metabolism


Visualizing Metabolism in 3D


Team this summer: Dr. Lindsay Rogers (PI), Dr. Patrick Pennefather (Consultant), Michael Sider (Consultant), Dante Cerron (Developer, EML staff), Kim Nipp (EML staff – UBC Studios), Rayyan Saiyed (Work Learn student), Joshua Yoon (Work Learn student), Nikko Dumrique (Work Learn student)  


Learning about metabolic pathways can be one of the most challenging parts of studying biochemistry and molecular biology at the undergraduate level. This challenge, however, also presents an opportunity to transform the way the metabolic network is taught and studied.  

Initiated by UBC biochemistry professors Dr. Lindsay Rogers and Dr. Scott Covey, 3D Metabolism is a project done in collaboration with the UBC Emerging Media Lab to create an immersive and interactive visualization of the metabolic network by leveraging 3D modeling. The project team started off in a proof-of-concept phase in summer 2020 during which they prototyped how this network would look in a 3D space. By using the iterative process of user testing, the team sought to understand what biochemistry students were having trouble with and respond to their needs by creating user-friendly features in the model.  

This term, the team is working to scale up their application for use in a 200-level biochemistry course setting so students and staff can use it to visualize the metabolic network. They are also leveraging Wikibase as a resource connected to 3D Metabolism in Unity. Wikibase is being used as a database and an additional source of information to supplement the visual aid provided by the 3D model. It contains more detailed material from 200-level biochemistry courses that can help students understand the 3D model in conjunction with descriptive text. In practice, a user would be able to click on links in the 3D model which would then display more detailed information from the Wikibase metabolism database. 

The software development process involves Blender for designing the network before putting it into Unity and Docker for prototyping the Wikibase database. The team hopes to have the final application available through the internet.  

When asked about the challenges in developing this project, the team noted that a tricky aspect is figuring out how much detail to include in the model and database and not having them be overly congested as they currently exist in 2D depictions and textbooks. For more upper-level courses, however, the team thinks that this model can be developed further to include more details on pathways. UX/UI design plays a key role in this process, as the more interactive and accessible it looks, the less overwhelmed students would feel by the material. 

In the future, it might also be possible to leverage VR technology to further develop interactive visualizations of the metabolic network.  

Beyond metabolism too, there is tremendous potential for 3D models in physiology and biochemistry in general. Another EML project currently in the works is Fossa Finder, which depicts a very hard-to-see component of the human skull in a 3D model for anatomy and medicine students.  

It is important to note that the more diverse learning tools get developed, the better the student experience becomes. While visual learners might primarily benefit from emerging media and 3D technologies, even verbal and auditory learners can use them as additional resources which complement textbooks, slides, and other lecture materials.  

Metabolism is typically known as a hard and cumbersome subject to learn. The team hopes that the work that they are doing through the 3D Metabolism project helps remove this stigma and makes it more interesting and fun for learners. Students tend to memorize metabolic pathways, and this application could make the pathways easier to remember.  

Stay tuned for the end-of-term EML showcase to hear more about the project’s developments from the developers this semester! 

For more information about 3D Metabolism, visit the 3D Metabolism project page.