Recent Submissions

  • Clustering for the neophyte: An R Shiny app for self-organizing maps

    Akman, Olcay; Betzab-Marroquin, Zury; Hay-Jahans, Christopher; Wlash, Joshua; Wesley, Trenton (Intercollegiate Biomathematics Alliance, 2022)
    This article provides an outline of clustering, key stages in creating self-organizing maps for purposes of clustering, instructions on how to use a free online R Shiny app that constructs self-organizing maps for data provided by users, and interpretations of the graphics produced.
  • Agent-based modeling for the neophyte: An application of NetLogo

    Akman, Olcay; Bhumpelli, Siddharth; Hay-Jahans, Christopher (Intercollegiate Biomathematics Alliance, 2024)
    Agent-based modeling has found applications in a wide range of fields including economics, sociology, ecology, epidemiology, transportation planning, and more. Its versatility allows researchers to investigate various “what-if” scenarios, test the effects of different policies or interventions, and gain insights into the underlying mechanisms driving complex systems. This article is intended for the curious student or researcher who is unfamiliar with agentbased modeling and is looking for a quick but reasonably informative exposure to the field.
  • Compartmental modeling for the neophyte: An application of Berkeley-Madonna

    Akman, Olcay; Bhumpelli, Siddharth; Cline, Cody; Hay-Jahans, Christopher (2024)
    Compartmental modeling serves as a necessary framework in many fields, especially biomathematics and ecology. This article introduces readers to a user-friendly approach to constructing compartmental models and solving the resulting systems of differential equations to simulate real-world applications. The platform used is Berkeley Madonna, a software package that has an intuitive graphical interface which empowers users—even those with limited mathematical and programming backgrounds—to focus on modeling concepts rather than mathematical or programming intricacies. This makes Berkeley Madonna an ideal platform for students, educators, and researchers.