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These are the materials for Math 214 offered at Rhodes College. The course description is:  "In this course students will learn how to use discrete mathematical models to analyze problems arising in the biological sciences, without using calculus. The types of models used will include discrete difference equations, matrix models, and agent-based models. Some of the biological applications explored in this course include modeling the population sizes of various species over time, describing..."

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Amy Hurford onto Teaching Resources

The Nature of Things - Invasion of the Brain Snatchers

This is a link to and episode of the The Nature of Things featuring parasites that manipulate their hosts. This is a great resource for undergraduate parasitology AND intro bio courses. I have used it for both. I show the entire episode in my Animal Parasitology course along with questions for the students to answer in groups at different time intervals throughout. Then they submit their answers as a group. In General Biology I show a 10 minute clip when I introduce parasitism as a life history strategy in the Community Ecology Chapter. 

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nice ABM labs from Erin Bodine

This is a link to Erin Bodine's contributions from her discrete math modeling course. Labs 8 and 11 are ABM's using NetLogo. 

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Jeremy M Wojdak onto Agent-Based Modeling

The Nature of Things - Invasion of the Brain Snatchers

This is a link to and episode of the The Nature of Things featuring parasites that manipulate their hosts. This is a great resource for undergraduate parasitology AND intro bio courses. I have used it for both. I show the entire episode in my Animal Parasitology course along with questions for the students to answer in groups at different time intervals throughout. Then they submit their answers as a group. In General Biology I show a 10 minute clip when I introduce parasitism as a life history strategy in the Community Ecology Chapter. 

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PARA-SITE: An interactive multimedia electronic resource dedicated to parasitology

Website hosted by The University of Queensland developed by the Australian Society of Parasitology, Inc. 

This website has useful background information on parasitology and individual parasites, their life cycles, host use, mode of transmission and clinical consequences. 

This would be a great resource for a medical parasitology course, or medical part of a general parasitology survey course. I could even see the descriptive information being useful in a general bio course for a definition of parasitism. The website also includes a nice section on fields of study within parasitology showing where it can overlap with courses in other disciplines. 

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Centers for Disease Control and Prevention Parasitology Training Materials

This website includes images associated with parasite infection events submitted to the CDC. The images represent what would be available for diagnosis, but the website is organized by date of report rather than by parasite taxonomy. 

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Sarah Orlofske onto Parasite images

Centers For Disease Control and Prevention Parasitology Resources

This homepage leads to other links for medically important parasitic infections as well as information on diagnostic  procedures. Under the case studies page you can find images and associated information with actual patient information from parasite infection reports. These have been useful in my teaching as mini-case studies on diagnosis. 

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A series of student activities using R to understand disease transmission...

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A Mutation Story

Video of sickle cell anemia, a condition with an evolutionary trade off...

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"Towards a worldwide wood economics spectrum" - Paper with the published dataset

Abstract:

Wood performs several essential functions in plants, including mechanically supporting aboveground tissue, storing water and other resources, and transporting sap. Woody tissues are likely to face physiological, structural and defensive trade-offs. How a plant optimizes among these competing functions can have major ecological implications, which have been under-appreciated by ecologists compared to the focus they have given to leaf function. To draw together our current understanding of wood function, we identify and collate data on the major wood functional traits, including the largest wood density database to date (8412 taxa), mechanical strength measures and anatomical features, as well as clade-specific features such as secondary chemistry. We then show how wood traits are related to one another, highlighting functional trade-offs, and to ecological and demographic plant features (growth form, growth rate, latitude, ecological setting). We suggest that, similar to the manifold that tree species leaf traits cluster around the ‘leaf economics spectrum’, a similar ‘wood economics spectrum’ may be defined. We then discuss the biogeography, evolution and biogeochemistry of the spectrum, and conclude by pointing out the major gaps in our current knowledge of wood functional traits.

Citation:

Chave, J., Coomes, D., Jansen, S., Lewis, S. L., Swenson, N. G., & Zanne, A. E. (2009). Towards a worldwide wood economics spectrum. Ecology letters12(4), 351-366.

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Encyclopedia of Life entry for primates

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"Comparative Data Reveal Similar Mortality Patterns Across Primates" - Paper with the published dataset

Abstract 
Human senescence patterns – late onset of mortality increase, slow mortality acceleration, and exceptional longevity – are often described as unique in the animal world. Using an individual-based dataset from longitudinal studies of wild populations of seven primate species, we show that contrary to assumptions of human uniqueness, human senescence falls within the primate continuum of aging, the tendency for males to have shorter lifespans and higher age-specific mortality than females throughout much of adulthood is a common feature in many, but not all, primates, and the aging profiles of primate species do not reflect phylogenetic position. These findings suggest that mortality patterns in primates are shaped by local selective forces rather than phylogenetic history.

Citation:

Bronikowski AM, Altmann J, Brockman DK, Cords M, Fedigan LM, Pusey A, Stoinski T, Morris WF, Strier KB, Alberts SC (2011) Aging in the natural world: comparative data reveal similar mortality patterns across primates. Science 331(6022): 1325-1328.

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Natural history and additional images of artiodactyls

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"Hunting to extinction: biology and regional economy influence extinction risk and the impact of hunting in artiodactyls" - Paper with published dataset

Abstract 
Half of all artiodactyls (even-toed hoofed mammals) are threatened with extinction, around double the mammalian average. Here, using a complete species-level phylogeny, we construct a multivariate model to assess for the first time which intrinsic (biological) and extrinsic (anthropogenic and environmental) factors influence variation in extinction risk in artiodactyls. Globally artiodactyls at greatest risk live in economically less developed areas, have older weaning ages and smaller geographical ranges. Our findings suggest that identifying predictors of threat is complicated by interactions between both biological and anthropogenic factors, resulting in differential responses to threatening processes. Artiodactyl species that experience unregulated hunting live in significantly less economically developed areas than those that are not hunted; however, hunted species are more susceptible to extinction if they have slower reproductive rates (older weaning ages). In contrast, risk in non-hunted artiodactyls is unrelated to reproductive rate and more closely associated with the economic development of the region in which they live.

Citation:

Price SA, Gittleman JL (2007) Hunting to extinction: biology and regional economy influence extinction risk and the impact of hunting in artiodactyls. Proceedings of the Royal Society B 274: 1845-1851.

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The true cost of an egg

Local vs commercial eggs and the many costs.

From SISL:  In this lab activity, students compare nutrient data and the cost of locally produced eggs and commercially produced eggs. They will use Excel for data entry, rudimentary formula writing, and the creation of tables.

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Carrie Diaz Eaton onto Math and agricultural systems

Consumption of food in the US over time

In this activity, students research the historical food consumption data from the U.S. Department of Agriculture to observe trends, develop regressions, predict future behavior, and discuss broader impacts.

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Carrie Diaz Eaton onto Math and agricultural systems

Breakfast footprint

From SISL site:

"How does an individual calculate a carbon footprint? Can personal decisions alter the magnitude of a carbon footprint? How much does one person's carbon footprint really matter?

In this module students will explore the size, value and significance of personal carbon emissions. In particular, students will estimate the carbon footprint of a breakfast meal consisting of cereal, fresh berries, milk, and fruit juice. After comparing breakfast carbon emissions values with group members and the class, students will contextualize these results through analysis of the mathematical model, comparison with known carbon "sinks" and reflection on the meaning of the output."

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Carrie Diaz Eaton onto Math and agricultural systems

Dryad Lab modules

 

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Sam S Donovan onto sam test

Agent-Based Modeling of the Immune System: NetLogo, a Promising Framework

Author: F.  Chiacchio, M. Pennisi, G. Russo, S. Motta, F. Pappalardo

About: Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents. This behavior is unpredictable, as it does not follow linear rules. There are a lot of works that investigates the immune system with agent-based modeling and cellular automata. They have shown the ability to see clearly and intuitively into the nature of immunological processes. NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena. It is designed for both research and education and is used across a wide range of disciplines and education levels. In this paper, we summarize NetLogo applications to immunology and, particularly, how this framework can help in the development and formulation of hypotheses that might drive further experimental investigations of disease mechanisms.

Published In: BioMed research international, 2014

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Is the Whole the Sumof Its Parts? Agent-Based Modelling of Wastewater Treatment Systems

Authors: A. J. Schuler, N. Majed, V. Bucci, F. L. Hellweger, Y. Tu and A. Z. Gu

About: Agent-based models (ABMs) simulate individual units within a system, such as the bacteria in a biological wastewater treatment system. This paper outlines past, current and potential future applications of ABMs to wastewater treatment. ABMs track heterogeneities within microbial populations, and this has been demonstrated to yield different predictions of bulk behaviors than the conventional, “lumped” approaches for enhanced biological phosphorus removal (EBPR) completely mixed reactors systems. Current work included the application of the ABM approach to bacterial adaptation/evolution, using the model system of individual EBPR bacteria that are allowed to evolve a kinetic parameter (maximum glycogen storage) in a competitive environment. 

Published In: Water Science and Technology Volume 63 Issue 8 (pages 1590-1598)

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