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

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)

Authors: Pereda, M., & Zamarreno, J. M. 

About: The aim of this work is to study the feasibility of using agent-based modeling to study the activated sludge process.  A model in MetLogo has been proposed, and experiments have been developed comparing the model behavior with a classical modeling approximation for this process, the Monod model.

Published In: 2011 19th Mediterranean Conference on Control & Automation (MED) (pages 1128-1133)

Date of Conference: 20-23 June 2011

Author: Marco Martinez

This material is intended as an introductory guide to data analysis with the R system, to assist in statistical computing training for life science researchers.  It was produced as companion material for a seminar (R Tutorial for Life Sciences) given at The University of Tennessee in the spring of 2009, sponsored by the National Institute for Mathematical and Biological Synthesis (NIMBioS).

The principal aim is to provide a step-by-step guide on the use of R to carry out statistical analysis and techniques widely used in the life sciences.  In each section, there is a detailed explanation of a command in R, followed by a biological example with all the instructions (in red) needed to run the test and with the corresponding output in R (in blue).  There is assumed previous knowledge in statistics and experimental design, essentially corresponding to a basic undergraduate introductory statistic course.

How People Learn is a classic - I don’t think you can go wrong with it. 

Survey of ed psych and cognitive science research.

Full text available online. 

http://www.nap.edu/openbook.php?isbn=0309070368

I think you can order print copies of this from AAAS. 

Description here: http://www.aaas.org/news/new-aaas-resources-support-undergraduate-stem-education-reform

Download here: http://ccliconference.org/measuring-teaching-practices/

Much more focused on assessment.

This is a laboratory activity focused on identifying first and second intermediate host infections by trematodes of pond snails. 

Darkfield image of M. oregonensis stained with Lugol's solution. Specimen from a snail sampled from a VA stream.

This is an article that discusses how evolutionary constraints limit the size of arthropods.

This is a tool that is currently being developed by the working group. In this activity students will be given several interesting protists to research.  Then based on morphological characteristics students will create a hypothesis tree.  Then, students will be given a tree of their organisms based on genetic data.  They will then use Mesquite to map characters onto the tree they are given.

From the developers, "Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms." Students can use Mesquite to build trees, plot characters onto trees, and explore ancestral state reconstructions.

Mesquite can be run directly on the Hub here, or downloaded from mesquiteproject.org.

Anderson DL, Fisher KM, Norman JG. 2002. Development and validation of the conceptual inventory of natural selection. Journal of Research in Science Teaching 39: 952-978.

Interesting news article about convergent evolution of trap jaws in ants. Includes slow motion videos of the ants using these jaws to propel themselves through the air as a defense mechanism.

This module examines evidence from the fossil record, behavior, biomechanics and cladistic analysis to interpret the sequence of events that led to flight in the dinosaur lineage. The module concentrates on the process of science - how we know what we know.

The virtual lab includes four modules that investigate different concepts in evolutionary biology, including adaptation, convergent evolution, phylogenetic analysis, reproductive isolation, and speciation. Each module involves data collection, calculations, analysis and answering questions.

At what point in evolutionary development does a group of individuals become two distinct species? This case addresses that fundamental question by asking students to decide whether apple maggot flies are distinct as a species from hawthorn maggot flies. In making their decision, students examine the different models of speciation and consider the primary forces that effect evolutionary change. Developed for an advanced undergraduate course in evolutionary biology, it would be appropriate for any biology course in which students are taught about the models of speciation. It could also be used in a general ecology course in which students consider the distribution and use of resources leading to niche specialization or in a genetics course if restrictions in gene flow are taught in the context of speciation.

We encourage everyone to submit items for this collection.  Please use the table above to determine how to categorize and tag your item. 

In addition, please tag which learning outcome(s) your item addresses, and include the tag Speciation.

EXAMPLE: If you are posting a tool that addresses learning outcomes 1 & 2 you would include the following tags:   Tools, LO2.1, LO2.2, Speciation.

*Please use this format when tagging as it will make the collection easier to search.

Students will be introduced to different factors that might affect extinction risk and will work with data on artiodactyls (even-toed, hoofed mammals, such as cows, sheep, deer, antelope, and giraffes) to investigate some of these hypotheses.

We encourage everyone to submit items for this collection.  Please use the table above to determine how to categorize and tag your item. 

In addition, please tag which learning outcome(s) your item addresses, and include the tag Biodiversity.

EXAMPLE: If you are posting a tool that addresses learning outcomes 2 & 3 you would include the following tags:   Tools, LO2.2, LO2.3, Biodiversity

*Please use this format when tagging as it will make the collection easier to search.

This is a place to contribute resources, tools, and assessments that address the following learning outcomes under the broad theme of biodiversity.

Students are able to:

LO3.1 Describe the molecular and structural unity of life

LO3.2 Explain the role of endosymbiosis and horizontal gene transfer in the origins of the major lineages.

LO3.3 Justify why biodiversity is important to humans.

LO3.4 Compare the general characteristics of major lineages in evolutionary history

LO3.5 Summarize the role of extinction in shaping patterns of biodiversity

This is part of the Tree of Life working group. Click here to read about our general goals and framework.

This is a place to contribute resources, tools, and assessments that address the following learning outcomes under the broad theme of speciation.

Students are able to:

LO2.1 Illustrate how divergence in phenotype may lead to reproductive isolation

LO2.2 Recognize that species are dynamic entities, and compare the theoretical and practical uses of multiple species concepts

LO2.3 Interpret visual representations of speciation events

This is part of the Tree of Life working group.  Click here to read about our general goals and framework.

This is a natural/artificial selection model that shows the result of two competing forces on natural selection of the speed of prey. Which force dominates depends on the behavior of predators.