In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations. Our algorithm searches for the set of evolutionary parameters describing indel dynamics which best fits a given input MSA. In each step of the search, we use parametric bootstraps and the Mahalanobis distance to estimate how well a proposed set of parameters fits input data. Using simulations, we demonstrate that our methodology can accurately infer the indel parameters for a large variety of plausible settings. Moreover, using our methodology, we show that indel parameters substantially vary between three genomic data sets: Mammals, bacteria, and retroviruses. Finally, we demonstrate how our methodology can be used to simulate MSAs based on indel parameters inferred from real data sets.
Mathematical models of infectious diseases are a valuable tool in understanding the mechanisms and patterns of disease transmission. It is, however, a difficult subject to teach, requiring both mathematical expertise and extensive subject-matter knowledge of a variety of disease systems. In this article, we explore several uses of zombie epidemics to make mathematical modeling and infectious disease epidemiology more accessible to public health professionals, students, and the general public. We further introduce a web-based simulation, White Zed (http://cartwrig.ht/apps/whitezed/), that can be deployed in classrooms to allow students to explore models before implementing them. In our experience, zombie epidemics are familiar, approachable, flexible, and an ideal way to introduce basic concepts of infectious disease epidemiology.
Global climate models predict increases in precipitation events in the Phoenix-metropolitan area and with the proposition of more flooding new insights are needed for protecting roadways and the services they provide. Students from engineering, sustainability, and planning worked together in ASU’s Urban Infrastructure Anatomy Spring 2016 course to assess:
1. How historical floods changed roadway designs.
2. Precipitation forecasts to mid-century.
3. The vulnerability of roadways to more frequent precipitation.
4. Adaptation strategies focusing on safe-to-fail thinking.
5. Strategies for overcoming institutional barriers to enable transitions.
The students designed an EPA Storm Water Management Model for the City of Phoenix and forced it with future precipitation forecasts. Vulnerability indexes were created for infrastructure performance and social outcomes. A multi-criteria decision analysis framework was created to prioritize infrastructure adaptation strategies.