Modeling from molecules to moose

Teaching students to develop agent-based simulations in biology

Elizabeth F. Ryder1, Joseph R. Boyd1, Timothy B. Marsden1, Meagan E. Sullender1, Brian T. White2

1Worcester Polytechnic Institute, 2UMass Boston

NSF TUES Award 1140672

Motivation• Vision and Change in Undergraduate Education

(AAAS, 2010)• Biology should be taught more conceptually• Students need experience with modeling,

simulation, and systems approaches to biology.• Simulation in Biology course

• Agent-based modeling: systems approach• Similar concepts in different areas of biology:

ecology, cell biology, molecular biology• StarLogoTNG: Gentle introduction to

programming and simulation that is immediately relevant to biology

GoalsStudents in Simulation in Biology will:•Gain a deep understanding of biological content and the connections among different fields in biology. •Gain experience with use of simulation in science; hypothesis testing and predicting•Make connections between mathematics, computer science, and biology•Show increased ‘systems thinking’; understand ‘emergent properties’ of systems

Simulation in Biology class• Logistics

• Boot camp, practice simulation, project, blog• Class time mostly working in groups

Student project: Schistosomiasis

Evaluation, Dissemination & Acknowledgments

• Evaluation• Faculty development

• Implementation of Simulation in Biology at UMass Boston, Summer 2014

• Instructor is an ecologist with little programming background

• Dissemination ‘kit’• Tutorials, Boot camp problems, teacher’s guide• Practice projects with guidelines and code

• Acknowledgments• Eric Klopfer and colleagues, MIT• WPI students• NSF TUES Award