Responding to the need to teach remotely due to COVID-19, we used readily available computational approaches (and developed associated tutorials (https://mdh-cures-community.squarespace.com/virtual-cures-and-ures)) to teach virtual Course-Based Undergraduate Research Experience (CURE) laboratories that fulfil generally accepted main components of CUREs or Undergraduate Research Experiences (UREs): Scientific Background, Hypothesis Development, Proposal, Experiments, Teamwork, Data Analysis, Conclusions, and Presentation1. We then developed and taught remotely, in three phases, protein-centric CURE activities that are adaptable to virtually any protein, emphasizing contributions of noncovalent interactions to structure, binding and catalysis (an ASBMB learning framework2 foundational concept).
The courses had five learning goals (unchanged in the virtual format),focused on i) use of primary literature and bioinformatics, ii) the roles of non-covalent interactions, iii) keeping accurate laboratory notebooks, iv) hypothesis development and research proposal writing, and, v) presenting the project and drawing evidence based conclusions
The first phase, Developing a Research Proposal, contains three modules, and develops hallmarks of a good student-developed hypothesis using available literature (PubMed3) and preliminary observations obtained using bioinformatics, Module 1: Using Primary Literature and Data Bases (Protein Data Base4, Blast5 and Clustal Omega6), Module 2: Molecular Visualization (PyMol7 and Chimera8), culminating in a research proposal (Module 3). Provided rubrics guide student expectations. In the second phase, Preparing the Proteins, students prepared necessary proteins and mutants using Module 4: Creating and Validating Models, which leads users through creating mutants with PyMol, homology modeling with Phyre29 or Missense10, energy minimization using RefineD11 or ModRefiner12, and structure validation using MolProbity13.
In the third phase, Computational Experimental Approaches to Explore the Questions developed from the Hypothesis, students selected appropriate tools to perform their experiments, chosen from computational techniques suitable for a CURE laboratory class taught remotely. Questions, paired with computational approaches were selected from Modules 5: Exploring Titratable Groups in a Protein using H++14, 6: Exploring Small Molecule Ligand Binding (with SwissDock15), 7: Exploring Protein-Protein Interaction (with HawkDock16), 8: Detecting and Exploring Potential Binding Sites on a Protein (with POCASA17 and SwissDock), and 9: Structure-Activity Relationships of Ligand Binding & Drug Design (with SwissDock, Open Eye18 or the Molecular Operating Environment (MOE)19).
All involve freely available computational approaches on publicly accessible web-based servers around the world (with the exception of MOE). Original literature/Journal club activities on approaches helped students suggest tie-ins to wet lab experiments they could conduct in the future to complement their computational approaches.
This approach allowed us to continue using high impact CURE teaching, without changing our course learning goals. Quantitative data (including replicates) was collected and analyzed during regular class periods. Students developed evidence-based conclusions and related them to their research questions and hypotheses. Projects culminated in a presentation where faculty feedback was facilitated with the Virtual Presentation platform from QUBES20
These computational approaches are readily adaptable for topics accessible for first to senior year classes and individual research projects (UREs). We used them in both partial and full semester CUREs in various institutional settings. We believe this format can benefit faculty and students from a wide variety of teaching institutions under conditions where remote teaching is necessary.
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Virtual Reality Laboratory Experiences for Electricity and Magnetism Courses
A solid understanding of electromagnetic (E&M) theory is key to the education of electrical engineering students. However, these concepts are notoriously challenging for students to learn, due to the difficulty in grasping abstract concepts such as the electric force as an invisible force that is acting at a distance, or how electromagnetic radiation is permeating and propagating in space. Building physical intuition to manipulate these abstractions requires means to visualize them in a three-dimensional space. This project involves the development of 3D visualizations of abstract E&M concepts in Virtual Reality (VR), in an immersive, exploratory, and engaging environment.
VR provides the means of exploration, to construct visuals and manipulable objects to represent knowledge. This leads to a constructivist way of learning, in the sense that students are allowed to build their own knowledge from meaningful experiences. In addition, the VR labs replace the cost of hands-on labs, by recreating the experiments and experiences on Virtual Reality platforms.
The development of the VR labs for E&M courses involves four distinct phases: (I) Lab Design, (II) Experience Design, (III) Software Development, and (IV) User Testing. During phase I, the learning goals and possible outcomes are clearly defined, to provide context for the VR laboratory experience, and to identify possible technical constraints pertaining to the specific laboratory exercise. During stage II, the environment (the world) the player (user) will experience is designed, along with the foundational elements, such as ways of navigation, key actions, and immersion elements. During stage III, the software is generated as part of the course projects for the Virtual Reality course taught in the Computer Science Department at the same university, or as part of independent research projects involving engineering students. This reflects the strong educational impact of this project, as it allows students to contribute to the educational experiences of their peers. During phase IV, the VR experiences are played by different types of audiences that fit the player type. The team collects feedback and if needed, implements changes.
The pilot VR Lab, introduced as an additional instructional tool for the E&M course during the Fall 2019, engaged over 100 students in the program, where in addition to the regular lectures, students attended one hour per week in the E&M VR lab. Student competencies around conceptual understanding of electromagnetism topics are measured via formative and summative assessments. To evaluate the effectiveness of VR learning, each lab is followed by a 10-minute multiple-choice test, designed to measure conceptual understanding of the various topics, rather than the ability to simply manipulate equations.
This paper discusses the implementation and the pedagogy of the Virtual Reality laboratory experiences to visualize concepts in E&M, with examples for specific labs, as well as challenges, and student feedback with the new approach. We will also discuss the integration of the 3D visualizations into lab exercises, and the design of the student assessment tools used to assess the knowledge gain when the VR technology is employed.
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- Award ID(s):
- 1945573
- NSF-PAR ID:
- 10318170
- Date Published:
- Journal Name:
- 2021 ASEE Virtual Annual Conference Content Access
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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This paper presents and discusses the use of simulation-based customizable online learning activities, virtual laboratories, and comprehensive e-Learning environments for teaching subjects such as materials science, chemistry, and biomanufacturing. The virtual equipment and lab assignments have been used for: (i) authentic online experimentation, (ii) homework and control assignments with traditional and blended courses, (iii) preparing students for hands-on work in real labs, (iv) lecture demonstrations, and (v) performance-based assessment of students’ ability to apply gained theoretical knowledge for operating actual equipment and solving practical problems. Using the associated learning and content management system (LCMS) and authoring tools, instructors kept track of student performance and designed new virtual experiments and more personalized learning assignments for students. Virtual X-Ray Laboratory and Web-based Environment for Single-Use Upstream Bioprocessing have been used to illustrate the implementation of the concept of Interactive and Adjustable Cloud-based e-Learning Tools. The virtual labs and e-learning environments have been used at two-year and four-year colleges and universities in the USA, UK, Tanzania and some other countries. The virtual X-Ray lab has also been integrated with the MITx course delivered via the MOOC (massive open online course) edX platform for Massachusetts Institute of Technology undergraduate students.
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