ASSETT Virtual Labs completes its first year

May 01, 2024

By Jian Wei Tay

Image showing pictures hanging along a wall.
Software Development Team demonstrating the new simulated lab at the Engineering Projects Expo 2024.

The ASSETT Virtual Labs team, led by Dr. Jian Wei Tay (Biological Image Analysis Group Leader, ALMC) and Dr. Kristin Moore (Teaching Professor, MCDB), has completed its first year. The project aims to build a simulated laboratory environment to teach new researchers how to run cell biology experiments, including training students to use a microscope. By doing so, these simulations will enable students to acquire research skills in a faster time.

The simulations will encompass interdisciplinary topics and integrate molecular biology and quantitative microscopy as core techniques. Compared to other simulations, the virtual lab will allow users to make mistakes, such as putting oil on air objectives, simulating the resulting consequences. The team believes that this will mimic natural learning experiences, allowing students to learn techniques faster, and hopefully leading to less mistakes when operating actual equipment.

The project is primarily student-driven (listed below). There are two main groups carrying out the project: The Software Development group comprises 6 students from the Computer Science Department who worked on the project as part of their Capstone project. The students proposed and developed a simulation framework in the Godot game engine. More recently, a Digital Artist from the ATLAS Institute was recruited to join the group to develop graphical assets. The Curriculum Design team consists of a Biochemistry graduate student and two recent grads from the MCDB department. The team was responsible for developing a detailed outline of the simulated experiments, including identifying common mistakes and their consequences. The team has also developed a preliminary plan for testing and evaluation.

To demonstrate the capabilities of the program, the team has put together a prototype simulation of a gel electrophoresis experiment. The prototype allows a user to carry out a simple gel electrophoresis experiment, including making a gel, loading DNA, and running current through a rig. The speed of the bands through the gel is simulated and affected based on the concentration of agarose, current, and running time. If the user connects the rig backwards or runs the program for too long, the bands will run off the gel. The Software Development team exhibited the project during the recent Engineering Projects Expo organized by the College of Engineering and Applied Science.

Image showing pictures hanging along a wall.
A mockup showing new graphics by Digital Artist Sahba Satareh. The new graphics will be incorporated into the simulation this summer.

The team plans to improve the existing simulation through the summer to update the graphics, as well as resolve existing bugs in the program. The project was also selected for a poster at the upcoming HHMI Microscope Technology Dissemination to Underserved Communities meeting in May 2024. During the next academic year, the team also plans to build a new simulation of a microscope based on those available in the facility.

The ASSETT Virtual labs team gratefully acknowledges funding from the ASSETT (Arts & Sciences Support of Education Through Technology) Innovation Incubator at the University of Colorado’s Center for Teaching & Learning.


Software Development

  • Tyler Hand (Computer Science)
  • Jeffrey Collins (Computer Science)
  • Justin Astalos (Computer Science)
  • Michael Jordan (Computer Science)
  • Conor Harris (Computer Science)
  • Jonas Courtney (Computer Science)
  • Sahba Satareh (ATLAS)

Curriculum Design

  • Erin Richards (Biochemistry)
  • Kerrie Macmillan (MCDB)
  • Nishanth (Ike) Narayan (MCDB)