GEM3 Lab Modules

Overview

GEM3 uses a Vertically Integrated Project (VIP) strategy to increase the number, diversity and preparation of skilled scientists and engineers in GEM3 fields such as bioinformatics, computational biology, conservation genetics, and ecosystem management.

Vertically Integrated Projects (VIPs):

  • Bring together undergraduate education and faculty research in a team-based context
  • Integrate research, education and workforce development
  • Provide academic credit to undergraduate students who enroll in VIP courses
  • Learn more about VIPs

Recruitment resource:

Lab Modules: On-ramps to Undergraduate Research

To align with the VIP effort and serve as an additional on-ramp to GEM3 research, Idaho universities and 2- and 4-year colleges are invited to incorporate GEM3 lab modules into core introductory science lab courses across institutions.

GEM3 Lab Modules:

  • Teach students how to use the tools of GEM3 disciplines and find answers to scientific issues
  • Emphasize hypothesis-driven experiments, data collection and analysis, communication and collaboration
  • Are taught by faculty from 2-and 4-year colleges and/or GEM3 graduate students (in person or virtually)
  • Receive support from university faculty and GEM3 program staff to help customize modules to the needs of specific courses

If you are interested in deploying a GEM3 Lab Module in your lab course, please review the existing modules below. If you have any questions or need more information, please fill out the interest form.

Want to Develop a New Lab Module?

  • Lab modules are developed annually at participating institutions and tested on campus where it is developed.
  • Graduate students on VIP teams receive both pedagogical training and content instruction and are responsible for assisting with delivery of lab modules on their own university campuses and at the 2- and 4-year colleges.
  • Funding opportunities for faculty (and graduate students) to develop lab modules related to GEM3 are available. For more information please contact Stephanie Sevigny.

The table below contains a list of GEM3 lab modules. Use the keywords box to filter the results. Click on the name of the module for details and teaching materials.

Lab Module Summary Institution PI(s)
A Beginner's Guide to R and RStudio In this lab, students will be introduced to R and RStudio, and create a map in RStudio using the leaflet package. This introductory module is meant for students who are familiar with basic computer system use but have little to no experience with R. University of Idaho Travis Seaborn
Anna Chase (creator)
Assessing the Influence of Environment on Morphology in Rainbow Trout The labs in this module compare internal organ sizes between wild and hatchery rainbow trout to see if dietary differences during early development influence relative organ size and digestive system morphology. Specifically, we are going to remove and measure the mass of the fish's heart and liver and count the number of pyloric caeca. Idaho State University Janet Loxterman
Jessica Fultz
Bear Foraging Behavior The aim of this module is to catalog and observe behavioral foraging patterns in bears using a key-logging program (BORIS). This project and ethogram are based on a 2009 article found in The Journal of Mammalogy. Boise State University
Amy Ulappa
Chukar Diet In this module, students will: (1) understand the relevancy of diet quality and the physiology of animals, (2) use scientific practices to compare diet diversity and digestibility, (3) understand how the environment and animal morphology influence the physiological process of digestion, (4) archive digital data on diet diversity and digestion by your animal for future iteration, collaboration and discovery. Boise State University Jennifer Forbey
Chukar Dissection In this module, students will: (1) process animal carcasses, (2) dissect tissues and link these to physiological function, (3) isolate the intestines to test diet selection, (4) understand the relevancy of game birds, (5) use scientific practices to dissect and measure the intestinal tissues, (6) use scientific practices to measure features of intestinal contents and prepare contents for future analysis, (7) archive digital data on morphometrics of your animal to compare to past data and for future iteration, collaboration and discovery. Boise State University Jennifer Forbey
Intake and absorption (proteins, tannins, coumarins and phenolics) In this module, students will: (1) understand the relevancy of toxin and nutrient absorbance to understand the physiology of animals, (2) use scientific practices to quantify and compare toxin absorbance by animals, (3) understand how the environment and animal morphology influences the physiological process of absorption, (4) archive digital data on toxin absorbance by your animal for future iteration, collaboration and discovery. Boise State University Jennifer Forbey
Introduction to R This module introduces students to R. Boise State University
Amy Ulappa
Mammal Microbiomes The aim of this module is to: (1) Understand the relevancy of linking genomes to phenomes to understand physiology leveraging knowledge of collaborative research projects in the gut microbiome of herbivores; (2) Demonstrate basic analyses of microbiota data; (3) Determine if and how communities differ by variables of interest; and (4) Perform various measurements characterizing microbial community diversity, composition, and structure. Boise State University
Amy Ulappa
Manual Annotation of Functional Genes in Non-Model Species This module aims to provide a template for individuals to manually annotate genes of interest from non-model species using publicly available genomic data. To do this, we aim to walk readers through the process with a specific example: the manual annotation of toll-like receptors (TLRs) in Falco peregrinus and Falco rusticolus. College of Western Idaho Miranda Striluk
Milkweed Genecology and Adaptive Traits Curriculum about phenotypic plasticity, genecology and adaptation. This module has been designed to be delivered over two lab periods. College of Western Idaho Stephanie Sevigny
(contact)
Milkweed Leaf Character Evaluation Using ImageJ This lab orients and trains about how to use some functions of a common and powerful tool for evaluating phenotypic traits in plants, while contributing to original undergraduate research. This module fits into a larger course-based undergraduate research (CURE) about plant ecophysiology and restoring degraded habitats (focuses on concepts evaluated by the sagebrush components of mapping and modeling). This module has been designed to be delivered over one lab period and can be used for remote instruction as needed. College of Western Idaho Stephanie Sevigny
(contact)
Native Plant Restoration In this lab, we will cover topics related to restoration ecology, examine real datasets pertaining to restoration, follow the scientific method, run appropriate analyses, and draw conclusions about an ongoing ecological restoration project at Boise State University. Boise State University
Sarah Dalrymple
Pharmokinetics In this lab, students will: (1) be able to conduct searches on publicly available databases and interpret results; (2) be able to compare and contrast chemical ADME properties in small groups to determine which chemical is more likely to have a biological effect in the consumer; (3) formulate hypotheses to determine outcomes of chemical interactions within the body; and (4) conduct literature searches to support their formulated hypothesis. Boise State University
Celin Younan
Plant Identification In this lab, students will identify four angiosperms and develop understanding of their role in the environment. Boise State University
Amy Ulappa
Rainbow Trout Respiration This module aims to teach students how to analyze rainbow trout respirometry data using R Programming software. Designed specifically for use with data collected by students on an experiment measuring rainbow trout ventilation rate in response to differences in temperature and dissolved oxygen, the script herein provides methods which will allow students to both visualize and interpret these data. University of Idaho Jonathan Masingale, Travis Seaborn
Sagebrush This module uses argumentation as a method to get students to not only analyze or interpret data and develop claims to support their analysis and interpretations, but to do this with their peers. To incorporate both a biological focus and an argumentation focus, Day 1 of the module is designed to have students explore seed weight variation in Big Sagebrush subspecies at various sampling locations when provided with environmental data such as precipitation, elevation and temperature. This provides students opportunities to work with their peers in developing claims to answer a guiding question and describe and justify that claim using the data. Day 2 of the module is designed for students to share their Claim, Evidence, and Reasoning to the guiding question from Day 1 with their peers and then shift their thinking to a slightly different question and work individually to do the same thing they did during Day 1, but individually through a written homework assignment. Idaho State University Kathryn Turner
Squirrel Energy Budgets In this module, students will catalogue and observe behavioral foraging patterns in squirrels using an event logging program (BORIS). This module has been used in BSU’s Animal Physiology & Nutrition (ZOOL 409) course. Boise State University Jennifer Forbey
Thermoregulation In this module, students will: (1) understand the relevancy of temperature in the physiology of animals, (2) use scientific practices to quantify and compare how morphology influences thermal exchange with the environment, (3) understand how the environment and animal morphology influences the physiological process of thermal balance and exchange, (4) develop protocols for future iteration, collaboration and discovery of thermal balance in animals. Boise State University Jennifer Forbey