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 https://bit.ly/QBI-virtual-lab. 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
References
Alvarez, K. S. (2021). Using Virtual Simulations in Online Laboratory Instruction and Active Learning Exercises as a Response to Instructional Challenges during COVID-19. Journal of Microbiology & Biology Education, 22(1), ev22i1.2503. https://doi.org/10.1128/jmbe.v22i1.2503
Bass, P., Washuta, N., Howison, J., Gonzalez, R., & Maier, C. (2018). Benefits and Challenges of Undergraduate Research.
Bonde, M. T., Makransky, G., Wandall, J., Larsen, M. V., Morsing, M., Jarmer, H., & Sommer, M. O. A. (2014). Improving biotech education through gamified laboratory simulations. Nature Biotechnology, 32(7), Article 7. https://doi.org/10.1038/nbt.2955
Carpi, A., Ronan, D. M., Falconer, H. M., & Lents, N. H. (2017). Cultivating minority scientists: Undergraduate research increases self-efficacy and career ambitions for underrepresented students in STEM. Journal of Research in Science Teaching, 54(2), 169–194. https://doi.org/10.1002/tea.21341
Franklin, S., & Peat, M. (2005). Virtual versus real: An argument for maintaining diversity in the learning environment. International Journal of Continuing Engineering Education and Life Long Learning, 15(1–2), 67–78. https://doi.org/10.1504/IJCEELL.2005.006793
Gilmore, J., Vieyra, M., Timmerman, B., Feldon, D., & Maher, M. (2015). The Relationship between Undergraduate Research Participation and Subsequent Research Performance of Early Career STEM Graduate Students. The Journal of Higher Education, 86(6), 834–863. https://doi.org/10.1080/00221546.2015.11777386
Hartmann, D. J. (1990). Undergraduate research experience as preparation for graduate school. The American Sociologist, 21(2), 179–188. https://doi.org/10.1007/BF02692860
Hernandez, P. R., Woodcock, A., Estrada, M., & Schultz, P. W. (2018). Undergraduate Research Experiences Broaden Diversity in the Scientific Workforce. BioScience, 68(3), 204–211. https://doi.org/10.1093/biosci/bix163
Lamb, R. (2014). Examination of allostasis and online laboratory simulations in a middle school science classroom. Computers in Human Behavior, 39, 224–234. https://doi.org/10.1016/j.chb.2014.07.017
Pyatt, K., & Sims, R. (2007). Learner performance and attitudes in traditional versus simulated laboratory experiences. Proceedings Ascilite. ascilite, Singapore.
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Hi, Team- Thank you so much for submitting your idea to the ASSETT Innovation Incubator! This is a very well-thought out draft that can be strengthened largely by demonstrating more interdisciplinarity and also by more clearly showing (in numbers) scale over time to impact undergraduate students in A&S, specifically. For example, you mention that last year the facility worked with 142 individuals and 58 research groups across the University. Can you extract from those numbers who among them were A&S UGS and also reasonably project growth due to the introduction of the Open edx platform?
A strength of your draft is direct UG student involvement as paid interns on the project. Do you have a current student that you might add to the team now? Additionally, You make a clear call for interdisciplinarity on your team by adding a team member from CS, for example. Do you have someone in mind for this role? Might you reach out to them (or to the department) in the interim between now and the final submission due date on April 11th to see if you can recruit a third member to your team?
I see potential collaboration between your proposal and the MCDB proposing team. You might consider reaching out to them to join forces over your shared drive to skill build among your students as a work force development initiative. Please give their idea submission a read: https://www.innovationincubatorsubmit.com/published/enhancing-practical-student-knowledge-through-the-skills-center/
This is a very good draft with a plan for addressing a demonstrated need. I agree with Blair Young’s suggestions above and sense of the project’s strengths. A genuine strength of the proposal is its effort to involve undergraduates in the design process. I can see such an experience being transformative for any students involved. Like Blair, I think the proposal could be strengthened by greater clarity about the numbers of undergraduate students who would use the technologies you’re developing. As I read I also thought of the MCDB Skills Lab proposal as well as the Technology and Imagination proposal (which differs in content, but shares similar general goals). I also appreciate the commitment to assessing the impact of the tools and techniques you’re developing.
A general suggestion for the proposal I have–one which I will make on many of the proposals–is to specify how the incubator can help you develop your idea, your long term vision, and sustainability plan. The incubator program–like a tech incubator one might find outside of academia–provides significant support for helping teams develop and refine their ideas. How might such resources or how might the collaborative process with folks at the CTL or RIO or OIT help you develop a long term vision for the tools and pedagogic techniques you’re developing?
I love the skill training angle of this submission, but I would recommend expanding a bit on how exactly that training will be done. Specifically, I would like to see you define the virtual lab and explain how students will interact within it. “Virtual” is somewhat of a loaded term and can lead to a lot of different interpretations of this proposed lab space. For example, will this be a VR (virtual reality) experience where students are working within a 3D environment? Or will this be more of simulation, where students tweak a few settings and run a simulated experiment?
Examples of a simulated vs a virtual 3D lab:
(Simulated) PHET : https://phet.colorado.edu/
This is a research group here at CU that designs simulated experiments for students in K-12, helping them to explore and understand different phenomena.
(Virtual 3D Lab) Bacteria Identification Virtual Lab : https://www.biointeractive.org/classroom-resources/bacterial-identification-virtual-lab
This is an interactive virtual lab where students can click on different objects/equipment and work through the steps of an experiment.
Which of these examples do you feel more closely relates to your envisioned virtual lab? You list examples of virtual labs (LabXchange and StarCellBio), what aspects of these virtual labs do you want to copy? How will your approach differ?
To help the committee also understand your vision, I would recommend creating a short story board (perhaps in a Google Slide Deck that you can link/share). In your storyboard, walk us through a typical lab experience for an undergraduate student. This could include a slide providing context – what is the experiment and what will the students learn in the lab. After providing context, describe what the students will do – focus on the actions students will take within the virtual lab.
For example, consider this statement from your current proposal:
“A virtual lab will then be built to teach students the process of designing and carrying out molecular biology and genetic editing experiments to insert a fluorescent protein into a bacterial cell”
How will students “insert a fluorescent protein into a bacterial cell”? I could see this be on a low level as a “choose your own adventure”-style interaction. “Student Thomas now needs to select the next action the simulation will take. He is prompted with a multiple-choice window, where he can select to do X, Y, or Z. The simulation will perform the chosen action and either move to the next step in the experiment or provide Student Thomas feedback if his actions caused an error.” This description is something that would be fairly 2D and have the students work through a set of guiding prompts. You could also take this in a different direction and have the student be more active in the experiment. “In order to insert the fluorescent protein, Student Thomas will need to select the correct tool from his virtual lab table by clicking on it with his mouse and then dragging the tool into the work area. Based on the tool chosen, Student Thomas will be able to perform a series of actions in the virtual work area – such as using a pipet to move liquids from one container to another or a scalpel to cut materials apart”.
By understanding the style of interaction you envision and by providing more details on the virtual lab space, the reader can better understand the student experience, as well as, the required technical tools to develop it. This is very important because a fully interactive 3D environment versus a 2D simulation will require different technical skills and have different challenges for development.
To add on to this, I would also like to see more details on how you plan to use EDx’s virtual lab, especially because their use of “virtual” is not the same as yours. In the context of EDx, the “virtual” refers to “virtualized”, where students are working within a virtual machine. From their documentation, this appears to primarily target classes that do some type of programming where the virtual lab handles all of the software installation for the student and letting them focus on just writing their code for a class exercise (eg. Matlab or R Programming). But this could also include your lab, where the image for your virtual lab contains all of the software a student needs to run the experiments. However, this seems to go beyond the typical or base-case use for EDx’s virtual lab.
Consider discussing why you have chosen to use EDx’s virtual labs and compare it against other potential platforms/tools for creating a virtual lab. To help you with this comparison, there are a set of recommended resources for designing virtual labs from CU Boulder. It’s also possible that one of these resources may be a better choice for your project than Open EDx:
https://www.colorado.edu/asfacultystaff/academiccurricular-affairs/teaching-recommendations/laboratory-courses/online-remote-or-person