Molecular Biology Simulations for Case Based Learning

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Title of Abstract: Molecular Biology Simulations for Case Based Learning

Name of Author: Karen Klyczek
Author Company or Institution: University of Wisconsin-River Falls
Author Title: Professor
PULSE Fellow: No
Applicable Courses: Agricultural Sciences, Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Cell Biology, Evolutionary Biology, General Biology, Genetics, Immunology, Integrative Biology, Microbiology, Virology
Course Levels: Introductory Course(s), Upper Division Course(s)
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: computer simulations case studies bioinformatics molecular biology

Name, Title, and Institution of Author(s): Mark Bergland, University of Wisconsin-River Falls

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Our goal is to facilitate case studies and other active learning strategies via development of computer simulations of molecular biology lab techniques. This project addresses Vision and Change recommendation to relate biology concepts to real-world examples and make biology content relevant for students. The NSF-funded Case It project has produced case studies mainly in genetic and infectious diseases, in which students use simulation software to analyze authentic DNA and proteins sequences associated with the cases. By analyzing these cases, students address several core competencies, including applying the process of science, using quantitative reasoning, using modeling and simulation, and understanding the relationship between science and society. Based in part on the recommendations in the Vision and Change report, we have developed materials designed to prepare students for research projects involving bioinformatics analysis, to extend the existing case studies and for use with student-generated experiments. The software and materials are made available free of charge on the Case It web site ( and have been used by secondary and undergraduate schools worldwide. Case It was awarded a 2011 Science Prize for Inquiry-based Instruction (Bergland et al. 2012, Science 337, 426 (2012).

Describe the methods and strategies that you are using: Case It is an open-ended simulation that reads any nucleotide or amino acid sequence file, and includes methods for analyzing DNA and proteins. These methods include restriction digestion and mapping, polymerase chain reaction (PCR), DNA electrophoresis, Southern blotting and dot blotting, microarray analysis, protein electrophoresis, Western blotting, and ELISA. Bioinformatics capabilities (sequence alignment, tree building) have been added via integration with MEGA software. The download includes the simulation as well as all of the sequences necessary to run the cases described on the web site. The case descriptions can be viewed from the Case It home page or downloaded as a pdf file. Students read case scenarios and explore background information for the case. They then use the simulation to open sequence files associated with the case and run the appropriate procedure to analyze the sequences, generating results in the form of images that can then be incorporated into presentations or reports. At the introductory-biology level, students can assume roles of persons in the cases, such as health-care professionals, lab technicians, researchers, or hypothetical family members. They then discuss results either in person or online. The open-ended nature of the simulation encourages inquiry by enabling users to analyze any DNA sequence, including entire viral or bacterial genomes, with any probe, primer, or restriction enzyme. For example, freshmen at UWRF participating in the HHMI Science Education Alliance PHAGES project use the Case It simulation to generate virtual digests of known phage genomes for comparison with actual gels of their newly discovered phages.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Assessment of the use of the Case It materials has demonstrated that it provides an active and collaborative learning environment that engages and motivates students. Pre- and post testing as well as individual and focus group interviews were used to assess its impact on student learning and perceptions in courses at several institutions in the United States and Puerto Rico. In all courses, students demonstrated significant learning gains as a result of using the simulation to analyze case studies involving bioinformatics analysis. In addition, students reported that the activities allowed them to explore science concepts from multiple perspectives in a real world context. The instructor-independent efficacy demonstrated in these studies indicates that the use of Case It materials has the potential to be scalable in a variety of institution types.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Since 2012, the Case It software has been used by more than 10,000 students at 60 schools around the world. It was downloaded by many more faculty, from 105 different countries, so there is likely to be additional use that we have not been able to document. When we have assessed the impact on students in classes as described above, students using Case It showed improved post-test scores, and students' confidence in their knowledge also increased (Wolter et al., 2012, J Sci Educ Technol DOI 10.1007/s10956-012-9387-7). Faculty involved in software development, case writing, and assessment have been able to cite this work as scholarly activity for retention, promotion and tenure purposes.

Describe any unexpected challenges you encountered and your methods for dealing with them: Barriers to implementation of the Case It software include the need for faculty training in the use of the simulation. To address this issue, we have given many workshops at professional meetings and at the invitation of biology departments. We also have developed screencast tutorials that are posted on the web site. The web site also includes discussion forums where questions about the use of the simulation can be addressed. Finally, we are exploring the development of mobile applications of the software for use on tablets and other devices.

Describe your completed dissemination activities and your plans for continuing dissemination: We have given over 50 presentations, including workshops, oral presentations, and posters, at science education meetings in a variety of venues. In 2013 so far, we have presented at the NSF/AAAS TUES conference, American Society for Microbiology Conference for Undergraduate Educators, Science Case Network conference, and HHMI Quantitative Biology/BioQUEST workshop. We no longer have grant funding, but still plan to present at conferences as funding allows. Limited travel funds are available through the University of Wisconsin-River Falls, and from conference organizers when we are invited to present. We have published several papers describing strategies for implementing Case It and assessing its effectiveness, in Science, the Journal of Science Education Technology, American Biology Teacher, and others. In 2011 we joined the Science Case Network RCN-UBE project, and are collaborating with other case study and problem based learning projects to dissemination information and resources for faculty interesting in incorporating these active learning strategies ( In 2012, the Case It web site,, has been updated to include more interactive features and facilitate more effective dissemination of materials, and will continue to be updated.

Acknowledgements: The National Science Foundation has provided funding to support development, dissemination, and assessment of Case It materials (DUE grants 9455425, 9752268, 0229156, 0717577). Mary Lundeberg, formerly at Michigan State University and the University of Wisconsin-River Falls, has coordinated assessment of the project, with assistance from undergraduate and graduate students; in particular, Bjorn Wolter, former MSU graduate student. Chi-Cheng Lin assisted with critical aspects of the software that allowed incorporation of bioinformatics features. Rafael Tosado, Interamerican University of Puerto Rico-Metro Campus, Arlin Toro, Interamerican University of Puerto Rico-San German, and C. Dinitra White, North Carolina A & T State Unviversity, assisted in case development and assessment in their courses. Kim Mogen, Brad Mogen, University of Wisconsin-River Falls, and Eric Ribbens, Western Illinois University, have written case scenarios. Numerous faculty and student users have provided feedback on software features and ideas for new cases. The University of Wisconsin-River Falls College of Arts & Sciences and Provost’s office have provided support for faculty time and travel to conferences.