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An Introduction to Agent-Based Modeling in Biological Systems Using NetLogo: Workshop Manual

Author(s): Susan F Bailey1, Diana White1, Faichal Ayeva1, Brandon Formoza1

Clarkson University

Summary:
An introduction to the basics of agent based models, stepping through the creation of a model of bacterial population growth in NetLogo. Aimed at undergrad and graduate students with little-to-no coding experience.

Licensed under CC Attribution-NonCommercial-ShareAlike 4.0 International according to these terms

Version 1.0 - published on 15 Sep 2022 doi:10.25334/ZJ36-XJ95 - cite this

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Description

This manual and accompanying presentation was developed for a 2021 workshop at Clarkson University, Potsdam NY, aimed at undergrads, graduate students, and faculty with little-to-no coding experience. The manual provides an introduction to agent based models (ABMs) through hands-on experiential learning. The learner is stepped through the basics of writing their own ABM to simulate a real-world biological system using the open source software Netlogo, a popular software commonly used by both beginners and experts in the ABM community. A short introductory presentation is also provided to help give learners an introduction to ABMs, how they relate to other types of modeling approaches, and a few of their applications within biological sciences. Finally the particular example of bacteria growth is outlined and example experimental data provided to give the learners an idea of what their ABM will be meant to describe. The example data are measures of bacterial population growth in different types of lab environments that vary in the concentration of agar - a gel-like substance that impacts the movement of cells. The workshop participants are asked to think about how they might use an ABM to model bacteria populations under these different conditions and then modify/ expand their model to incorporate some of these differences.

In fall 2021, hands-on workshop was run as a full-day activity, but the same manual could also be used over a shorter period of time for learners with some coding background. It could also be run over a series of short time periods (i.e. lecture or lab periods within a course), allowing the learners to work on their model more gradually. At the end of the original workshop, we wrapped up by asking the learners to briefly shared their models and any extensions/ modifications they had worked on with the group.

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