Research & Publications

SimBio receives competitive grants from the NSF and the NIH

Our grants, and the resulting collaborations, allow us to perform research on student misconceptions in biology and how simulated labs can help overcome those misconceptions. We’re excited about the educational research aspects of our projects and welcome collaborations with other biology education researchers. We work with academic and non-profit groups on educational projects and provide biological models for researchers using our core modeling framework.

Publications

SimBio’s research team publishes on biology teaching, and collaborates on basic and applied biology studies involving simulations. The following papers are co-authored by SimBio employees and collaborators and are directly related to our work at SimBio.

• Meir, E., Pope D., Abraham J.K., Kim, K.J., Maruca, S., Palacio, J. 2024. Designing Activities to Teach Higher-Order Skills: How Feedback and Constraint Affect Learning of Experimental Design. CBE Life Sciences Ed. 23(1).
  Shows that SimBio’s Understanding Experimental Design tutorial is very effective at helping students learn how to do better experiments, and explores through controlled testing which elements of the tutorial contribute to these learning gains.
• Meir, E., Gardner, S.M., Maruca, S., Suazo-Flores, E., Abraham, J.K. (2023). Building a Performance-Based Assessment of Graph Construction Using Evidence-Centered Design Spector, M.J., Lockee, B.B., Childress, M.D. (eds) Learning, Design, and Technology. Springer, Cham.
  Provides an example and lessons learned from applications of design-based research to a new performance-based graph construction assessment.
• Meir, E. 2022. Designing a Simulation Lab: The Process that Led to Action Potentials Explored and Extended, Two Simulation-Based Neurobiology Labs. J. Undergrad. Neurosci. Ed. (JUNE). 20(2): A232-A239
  Describes the process we followed in developing our two action potentials tutorials, Action Potentials Explored and Action Potentials Extended, and by extension how we go about developing and revising many of our teaching tools.
• Meir, E. 2022. Strategies for targeting the learning of complex skills like experimentation to different student levels: The intermediate constraint hypothesis. In Trends in Teaching Experimentation in Life Sciences. Eds. N. J. Pelaez, S. M. Gardner, & T. R. Anderson. Springer Nature Switzerland AG, Cham, Switzerland.
  An essay about what features of technology-based educational tools one might manipulate to maximize learning in your target population, drawing on years of data and thinking at SimBio.
• Gardner, S.M., Suazo-Flores, E., Maruca, S., Abraham J.K., Karippadath, A., Meir, E. 2021. Biology Undergraduate Students’ Graphing Practice in Digital Versus Pen and Paper Graphing Environments. J Sci Educ Technol
  The first publication from a large multi-institution effort to develop performance-based assessments of graphing ability among biology students, this paper compares the results from the SimBio-written digital graphing assessment to a pen and paper assessment.
• Uhl, J.D., Sripathi, K.N., Meir, E., Merrill, J, Urban-Lurain, M., Haudek, K.C. 2021 Automated Writing Assessments Measure Undergraduate Learning after Completion of a Computer-Based Cellular Respiration Tutorial CBE Life Sciences Ed. 20 (3).
  Reports on a partnership between SimBio and the AACR research team working on automated grading of essay questions where AACR researchers gathered pre/post data with their essay questions around SimBio’s Cellular Respiration Explored tutorial. The tutorial led to apparent large gains in students moving towards a more expert-like view of respiration.
• Cerchiara J. A., Kim K. J., Meir E., Wenderoth M.P., Doherty J.H. 2019. A new assessment to monitor student performance in introductory neurophysiology: Electrochemical Gradients Assessment Device. Adv Physiol Educ4 3: 211–220.
  Introduces a new assessment for student understanding of electrochemical gradients (membrane and action potentials) for an intro bio class, as well as showing that SimBio’s Action Potentials Extended lab is effective in helping students learn these key concepts.
• LaCommare, K.S., Van Zandt P.A. 2019. Evolution by Natural Selection in Oldfield Mice. Nat. Center for Case Study Teach in Sci.
  An interrupted case study on evolution of coat color in oldfield mice that makes use of SimBio’s Evolution for Ecology interactive chapter (part of the SimUText Ecology series) along with other peer-to-peer and instructor led activities.
• Meir E., Wendel D., Pope D.S., Hsiao L., Chen D., Kim, K.J. 2019. Are intermediate constraint question formats useful for evaluating student thinking and promoting learning in formative assessments?. Computers & Education 141.
  Shows that question formats that are less constrained than multiple choice but more constrained than short answer are very useful for providing information about student understanding, giving students good feedback, and even promote better learning than other question types. SimBio has built on this research to incorporate intermediate constraint questions in many of our learning tools.
• Clarke-Midura J., Pope D.S., Maruca, S., Abraham, J.K., Meir, E. 2018. Iterative design of a simulation-based module for teaching evolution by natural selection. Evolution: Education and Outreach Volume 11 Number 4, 1-17.
  Describes SimBio’s efforts to use previous research results (Abraham et al, 2009 in this case) to improve our teaching tools, in this case revising the Darwinian Snails tutorial to successfully help students overcome a natural selection misconception which previously was persistent.
• Kim, K.J., Pope D.S., Wendel D., Meir E. 2017. WordBytes: Exploring an Intermediate Constraint Format for Rapid Classification of Student Answers on Constructed Response Assessments. Journal of Educational Data Mining, Volume 9 Number 2, 45 – 71.
  A technical discussion of how certain question formats that are less constrained than multiple choice but more constrained than short answer essays may facilitate automated grading while still capturing many benefits of essays.
• Pope D.S., Rounds C. M., Clarke-Midura J. 2017. Testing the effectiveness of two natural selection simulations in the context of a large-enrollment undergraduate laboratory class. Evolution: Education and Outreach Volume 10 Number 3, 1-16.
  Compares two different active learning approaches to teaching natural selection, showing that the simulations in Darwinian Snails are as effective at helping students learn as an activity not involving computers.
• Whiteley, A. R., E. Steinberg, and E. Meir. 2016. Flipping virtual labs into team–based learning tools. Article 22 in Tested Studies for Laboratory Teaching, Volume 3.
  We demonstrate how interactive simulations in virtual labs can be incorporated into the Team-Based Learning (TBL) flipped classroom framework. We adapted three SimBio Virtual Labs for use in a 300-level TBL course. Students complete structured portions of the labs on their own and an open-ended inquiry in class as part of a team activity.
  
• Price, R.M, Pope, D.S., Abraham, J.K., Maruca, S. Meir, E. 2016. Observing populations and testing predictions about genetic drift in a computer simulation improves college students’ conceptual understanding. Evolution: Education and Outreach Volume 9 Number 8, 1-14.
  Uses a concept inventory on genetic drift to test student learning from SimBio’s Genetic Drift and Bottlenecked Ferrets tutorial, finding a strong learning effect, while students in control classes not using the SimBio tutorial actually got worse in some respects after instruction.
• Abraham, J.K., Perez, K., Downey, N., Herron, J.C., Meir, E. 2012. Short Lesson Plan Associated with Increased Acceptance of Evolutionary Theory and Potential Change in Three Alternate Conceptions of Macroevolution in Undergraduate Students. CBE Life Sciences Education Volume 11 Number 2, 152-164.
  Reports on testing of SimBio’s Evolutionary Evidence lab, including concepts and misconceptions where students improve after doing the lab, and those where they don’t.
• Allan, W.C., Erickson, J. L. Brookhouse, P. and Johnson, J. L.. 2010. Teacher Professional Development Through a Collaborative Curriculum Project—an Example of TPACK in Maine. TechTrends 54: 36-43.
  Describes middle school environmental science teaching tools that SimBio helped build along with a research team and a number of science teachers in Maine. The resulting tools were used in almost 1/2 the middle school science classes in Maine for the better part of a decade.
• Abraham, J.K., Meir, E., Perry, J., Herron, J.C., Maruca, S., Stal, D. 2009. Addressing Undergraduate Student Misconceptions about Natural Selection with an Interactive Simulated Laboratory. Evolution: Education and Outreach 2: 393-404.
  SimBio’s first research results on our popular Darwinian Snails lab, showing it is very effective at helping students learn many, but not all, targeted evolution concepts and overcome common misconceptions.
• Perry, J., Meir, E.,Herron, J., Stal, D., Maruca, S. 2008. Evaluating Two Approaches to Helping College Students Understand Evolutionary Trees Through Diagramming Tasks. CBE Life Sciences Education.
  An evaluation of SimBio’s Flowers and Trees lab, including a comparison to a control activity, showing this lab helps students improve on several concepts associated with reading and constructing evolutionary trees, as well as reducing three of four targeted misconceptions.
• Mundt, A. 2008. Report on EvoBeaker Labs for Use in the Evolution Class at the University of Denver [PDF 323K].
  A grad student’s independent report on using some of the earlier SimBio evolution labs in a class at University of Denver.
• Meir, E., Perry, J., Herron, J., Kingsolver, J. 2007. College Students’ Misconceptions About Evolutionary Trees. ABT Online, Volume 69 Number 7, September 2007.
  Introduces an influential assessment SimBio developed for capturing student ability to read and construct evolutionary trees.
• Meir, E., J. Perry, D. Stal, S. Maruca, and E. Klopfer. 2005. How Effective Are Simulated Molecular-Level Experiments for Teaching Diffusion and Osmosis? Cell Biology Education (4) Fall 2005.
  Publishes an assessment of student conceptual knowledge of diffusion and osmosis, and uses this assessment to test SimBio’s Diffusion and Osmosis labs, both of which led to large learning gains.
• Reed TE, Schindler DE, Hague MJ, Patterson DA, Meir E, et al. (2011) Time to Evolve? Potential Evolutionary Responses of Fraser River Sockeye Salmon to Climate Change and Effects on Persistence. PLoS ONE 6(6): e20380. doi:10.1371/journal.pone.0020380.
  While SimBio’s simulations are designed for education, this study used a custom-built simulation within SimBio’s modeling engine to predict the response of a population of salmon to climate change.