Project Overview

Undergraduate research experiences increase the participation and retention of students in academic and professional STEM careers by providing students with an opportunity to gain hands-on experience designing and conducting experiments (Hartmann, 1990; Gilmore et al., 2015). These experiences are important in increasing both student confidence and career ambitions, particularly among underrepresented students (Carpi et al., 2017; Hernandez et al., 2018). Despite the benefits, challenges exist which prevent students from participating in research (Bass et al., 2018). New researchers require time to learn skills before they can contribute meaningfully. This is often compounded by the fact that students must maintain their academic standing, reducing their availability during the semester. Finding sufficient faculty mentors can also be challenging due to cost, resulting in many students initially participating in unpaid internships. However, this practice greatly disadvantages under-resourced students who may need to financially support themselves.

To address these issues, we propose the development of virtual laboratories which simulate scientific experiments. Virtual laboratories are interactive computer applications which will allow students to perform activities and actions which mimic working in a physical laboratory. We hypothesize that these virtual laboratories will improve student learning by supplementing or even replacing training that currently occur within physical labs (Franklin & Peat, 2005; Alvarez, 2021). Simulated laboratories can provide more open-ended experiences, allowing students more freedom to explore and learn through experience, compared to expository, recipe-based laboratories (Pyatt & Sims, 2007; Lamb, 2014). Additionally, virtual laboratories can be “gamified” (e.g., by providing virtual awards), which can help motivate students compared with traditional learning methods (Bonde et al., 2014).

For this project, we propose the development of a virtual laboratory to simulate an experiment utilizing quantitative imaging techniques. Quantitative imaging is an interdisciplinary technique which combines molecular biology techniques, microscopy, and computational analysis to obtain quantitative information about individual cells. The initial experiment would task students with genetically-engineering bacteria to insert a fluorescent gene, observe the cells using a microscope, then measure the length of each cell in the image. Written protocols and videos will also be developed to teach biological concepts and lab skills related to each simulation. This experiment would generally take an undergraduate student with no prior research experience a full semester to conduct.

We will start by researching existing platforms to build these virtual labs, such as PhET, MATLAB and Simulink, or developing our own code libraries using HTML5/JavaScript. Of these options, PhET appears to best meet our requirements and has the added benefit of being developed by CU researchers. We aim to develop two “modules” during the funding period: a molecular biology lab and a microscopy lab. 2D graphical interfaces representing lab equipment found in these settings will be designed. Clicking on the graphics will allow equipment to be interacted with in a realistic manner (e.g., changing volume of a pipette or focusing a microscope). A storyboard with additional conceptual material can be found at We chose these modules as they can be configured to simulate many common biological experiments in the future.

We propose that this intervention will enable students to acquire research skills beyond those taught in traditional courses, reducing training time and allowing students to better compete for limited paid research positions. To assess the efficacy of our intervention, we will develop in-person skill tests to determine if students were able to learn how to use lab equipment. Students will also be given the opportunity to perform the same experiment in a real laboratory setting and their outcomes will be recorded and compared against students who did not use the virtual lab.

Project Purpose

This project aims to provide a new resource for students to gain research skills to supplement or as an alternative to in-person training in a lab. While virtual laboratories exist (e.g, LabXchange and StarCellBio), previous implementation focused on skill acquisition, such as pipetting and gel electrophoresis, and do not simulate complete experiments. Our project will enable students to learn lab skills and “soft” skills such as experimental design (e.g., deciding on the number and type of control samples that need to be collected), that are otherwise difficult to acquire outside of mentored research.

Additionally, common experimental errors will also be included within the simulations. For example, the molecular biology module would allow plating the bacteria on the wrong antibiotics, which would result in contaminated samples. If issues arise in the simulation, a dialog box will appear informing the student of the problem and how to avoid it in the future. By allowing students to rapidly repeat the experiments, these labs will enable learning through experience.

Stakeholders + Needs

The key stakeholders for the initial project will be undergraduates who intend to use molecular biology or microscopy in their research. We plan to expand our audience by including the resource as part of the training pipeline at the BioFrontiers Advanced Light Microscopy core and other imaging cores. We will also engage with research labs at CU to incorporate the simulations as part of training or to develop new simulations to incorporate techniques needed for their research.

Intended Impact

This project will impact the undergraduate experience by allowing students to gain research experience which might otherwise be too expensive or time-consuming to attain. Critically, our approach will enable under-resourced students, who might not be able to participate in unpaid research, to gain important skills and confidence to advance their careers. The virtual labs will also allow disabled students who might otherwise be unable to access physical laboratories the opportunity to gain similar experience. While we aim to make the virtual labs available to any student, effort will be made to ensure the material is as inclusive as possible. For instance, virtual avatars will have a range of skin tones and appearances to visually represent different ethnic or cultural groups. Other proposed design choices include providing options to increase font size, providing colorblind palettes for the microscopy module, and full transcripts for all videos.

Team Description/Gaps

We have assembled an interdisciplinary team of faculty and graduate and undergraduate students. Dr. Tay is the Image Analysis Specialist at the BioFrontiers Institute and has the computer skills and microscopy background to design the simulations. Dr. Moore is a Teaching Assistant Professor in the MCDB department and has the skills to design the curriculum and formative assessments to evaluate the efficacy of the intervention. Erin Richards is a Biochemistry graduate student, who is also working towards the CTL Teaching Certificate. Erin will work with Dr. Tay to design and record lectures for microscopy curriculum to gain the teaching experience required for this qualification. Kerrie Macmillan is a TA and recent MCDB graduate and will work with Dr. Moore to generate content for the molecular biology simulations. Nishanth Narayan (MCDB), Kolya Dols (Biochemistry) and Ayden Smith (Computer Science) are undergraduate students who will form a testing panel to provide feedback and guidance on the developed content. Additional undergraduates from other disciplines, including computer science and the arts, will be hired to assist with programming simulations and content creation.

Intended Scale

Initially, students in Dr. Tay’s Quantitative Optical Imaging course, which typically has ~10 undergraduates and ~20 graduate students, will be invited to participate and test the developed simulations. The final simulations will be integrated with web-based learning management systems (e.g., Canvas), allowing us to scale to include any students interested in biology research. We also intend to make the developed content open access for students outside of CU. Additionally, the simulations can be expanded to any other discipline on campus which might benefit from virtual training environments. For instance, a virtual cleanroom could be simulated for aerospace engineering students could learn to build spacecraft components, or a simulated archeological site could be developed to teach anthropology students the basics of finding and preserving artifacts. Thus, the project has potential to impact undergraduate students in any discipline.

Anticipated Long-term Needs

The proposed project will establish the framework to develop virtual research experiences at CU. Our long-term plan is to partner with local employers to develop training pipelines for CU graduates entering the biotechnology workforce, as well as partnering with faculty beyond STEM. Continued development beyond the funding period will be funded by external grants. The outcomes of this project will be critical to demonstrate feasibility by providing a working example and preliminary data of student outcome.

Funding Request + Intended Use of Funds

  • Course development: Kerrie Macmillan and Erin Richards will be responsible for course development. Salary support is requested for Kerrie Macmillan ($21/hour, ~4 months). Erin has requested no support due to conflict with existing funding. Total: $13,410.
  • Developers: Funds are requested for wages for 2 undergraduate developers (TBD) for 2 years ($19/hour, 20 hours/week for 15 weeks for 2 semesters, 40 hours/week for 12 weeks during summer). Total: $41,040.
  • Testing panel: A panel of up to 5 students (Kolya Dols, Ayden Smith, Nishanth Narayan, 2 TBD) will test developed material and provide feedback and guidance to the development team ($19/hour, ~10 hours/year, 2 years). Total: $1,900.
  • Computers: Two computers, estimated using Dell’s website, are requested for the student developers. Total: $2,550.
  • Lab supplies: $1,500/year is requested for laboratory supplies for in-person assessments. The supplies include consumables and service fees (e.g., for oligo synthesis). Total: $4,500.
  • Microscope fees: $800/year is requested for microscopy fees at the ALMC for in-person assessments ($20/hour, 4 hours for 10 assessments). Total: $1,600.

Total requested: $65,000



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