Group: Teaching Quantitative Biology Online ~ Resources

Return to Overview

Below are links to our partner groups on QUBES who have resources that are ready to implement in online settings. Note that many of these resources have adaptations that are also suitable for online courses. Check back often for updates!

If you would like to contribute a resource please consider posting to a collection or submitting your material as an open educational resource.

AIMS

AIMS modules use fascinating images set in real biological research to help science students learn quantitative skills they need.

Dendroclimatology

Jeremy M Wojdak, R. S. Maxwell

Version: 2.0

Dendroclimatologists can reconstruct climate records further into the past than written records, by examining tree rings. Students "reverse-engineer" this process by considering growth rates of a tree species in response to various...

linear regression, graphing, data visualization, standardization, climate, tree rings, dendrochronology, introductory, Lab, Teaching material, High School, Undergraduate, Homework, Advanced, More than 1 hour

740

325

09.2018

3D breast cancer tissue reconstruction

Jeremy M Wojdak, Kerri-Ann Norton

Version: 2.0

This module allows students to follow a researcher as she discovers new features of breast cancer tissue architecture, using 3D reconstructions of histological specimens.

graphing, data visualization, breast cancer, DCIS, histograms, centroid, sums of squares, introductory, Lab, Teaching material, High School, Undergraduate, Advanced

493

274

09.2018

Phenotypic plasticity and predation

Jeremy M Wojdak, Justin Touchon

Version: 2.0

Students predict changes to tadpole morphology and coloration after considering characteristics of the predator species and the prey themselves then test their own hypotheses (typically with t-tests or ANOVA) by collecting novel data via image...

R, Excel, image analysis, graphing, t-tests, frequency histograms, data visualization, ANOVA, hypothesis formulation, predator-prey interactions, phenotypic plasticity, introductory, Lab, Teaching material, High School, Undergraduate, Advanced, More than 1 hour

695

367

08.2018

Featured Resource of the Week

Leaf cutter ant foraging

Jeremy M Wojdak, Justin Touchon, Myra Hughey

Version: 1.0

This module introduces students to leaf-cutter ants in the rainforests of Panama. Students derive their own research hypotheses regarding ant foraging or allometric scaling relationships.

leaf cutter ants, foraging, allometry, linear regression, graphing, data visualization, Resources @ AIMS, body size, introductory, Lab, Teaching material, High School, Undergraduate, Advanced, More than 1 hour, Extended Project

755

403

08.2018

Avida-ED

Avida-ED is an award-winning educational application developed at Michigan State University for undergraduate biology courses to help students learn about evolution and scientific method by allowing them to design and perform experiments to test hypotheses about evolutionary mechanisms using evolving digital organisms. Read more about using Avida-ED in a blog post by Jim Smith

Avida-ED Lab Book

Robert T Pennock, Louise Mead, Wendy Johnson, Amy Lark, Jim Smith, Cory Kohn

Version: 1.0

Avida-ED activities, modified for the Argentina 2019 Avida-ED Workshop, presented at the 2019 BioQUEST & QUBES Summer Workshop

Evolution, avida-ed, Presentation, Teaching material, Reference material, Undergraduate, Workshop material

585

667

05.2019

BIOMAAP

The Biology Students Math Attitudes and Anxiety Program is a resource for educators who are looking to implement non-invasive techniques to change student attitudes and reduce anxiety towards math.

Frayer model growth mindset

Heather McGray

Version: 1.0

A Frayer model worksheet for the concept of growth mindset.

growth mindset, Frayer model, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Less than 1 hour

374

130

06.2019

BLUE

Biodiversity Literacy in Undergraduate Education - Data Initiative (BLUE Data) is a community of biodiversity, data, and education specialists who are working together to identify core biodiversity data competencies for undergraduates, develop strategies for integrating these competencies into the introductory biology curriculum, and build capacity for sustained development and implementation of biodiversity and data literacy education.

Following the Data

Anna Monfils, Debra Linton, Molly Phillips, Libby Ellwood

Version: 1.0

The video and exercise provides insight into how researchers are using digital data resources to investigate biodiversity in prairie fen wetlands.

data in the classroom, process of science, biodiversity informatics, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Advanced, Majors, Non-majors, 1 Hour

1.2K

344

05.2020

Searching for disability as biodiversity in digitized natural history collections

Kaitlin Stack Whitney

Version: 1.0

This module uses digitized natural history and biodiversity collections to explore if, how, and whether disability can be studied in nonhumans as a form of biodiversity.

348

162

03.2020

Movement: Nature's Flying Machines (Online)

Debra Linton

Version: 1.0 Adapted From: Movement: Nature's Flying Machines v1.0

Adapted for online learning: In this lab, you will explore the physics of flight, the adaptations that make powered flight possible, and the evolution of powered flight in vertebrates and invertebrates.

citizen science, quantitative skills, Digital Repository, Flight, introductory, Online course, Teaching material, Reference material, Undergraduate, Majors, Non-majors, More than 1 hour

617

124

03.2020

Data Visualization

Anna Monfils

Version: 1.0

This is an introduction to the idea of data visualization and the importance of presenting data for understanding.

data in the classroom, data visualization, introductory, Lab, Teaching material, Lecture, Undergraduate, Homework, Advanced, Majors, Non-majors, 1 Hour

397

128

03.2020

Communicating with Data: Digital Data Resources

Anna Monfils, Debra Linton

Version: 1.0

Students access, clean, configure, and standardize a dataset and create a relevant and scientifically valid data visualization to communicate science.

data in the classroom, data visualization, digital resources, biodiversity informatics, biodiversity collections, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Homework, Advanced, Majors, Less than 1 hour, Extended Project

336

109

03.2020

Communicating with Data: Infographic with Digital Data

Anna Monfils, Debra Linton

Version: 1.0

Working collaboratively in teams of 2-4 researchers, students engage in targeted projects to address critical information and research needs using digital biodiversity data.

databases, data in the classroom, undergraduate research, digital collections, course-based research experiences (CUREs), biodiversity collections, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Homework, Advanced, Majors, Less than 1 hour, Extended Project

302

100

03.2020

GBIF Tutorial - BLUE Resource

Libby Ellwood

Version: 1.0

A user guide and video instructions for GBIF

Querying databases, database, data in the classroom, biodiversity informatics, biodiversity collections, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Faculty, Homework, Graduate, Advanced, Majors, Non-majors, Less than 1 hour

310

122

03.2020

iDigBio Tutorial - BLUE Resource

Molly Phillips

Version: 1.0

A user guide and video instructions for iDigBio

databases, Querying databases, data in the classroom, biodiversity informatics, biodiversity collections, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Faculty, Homework, Graduate, Advanced, Majors, Non-majors, Less than 1 hour

309

181

03.2020

Arctos Tutorial - BLUE Resource

Erica Krimmel

Version: 1.0

A user guide and video instructions for Arctos

databases, data in the classroom, biodiversity informatics, biodiversity collections, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Faculty, Homework, Graduate, Advanced, Majors, Non-majors, Less than 1 hour

311

100

03.2020

Data Ethics

Rebecca Renirie

Version: 1.0

Data ethics and the use of digital data

data science, research ethics, data ethics, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Advanced, Majors, Non-majors, Less than 1 hour

242

03.2020

Biodiversity research using digitized, internet-based natural history collections

Kaitlin Stack Whitney

Version: 1.0

Collections based research is a critical tool for organismal biology and biodiversity research. Yet natural history collections have a complicated past. This multi-class module examines the origins, problems, and current uses of collections.

natural history, collections, digital resources, OER, Biodiversity, natural history museums, digital collections, birds, Biodiversity Collections Network (BCoN), BLUE, Website, introductory, Lab, Online course, Teaching material, Lecture, Reference material, Reference sheet, Manual, Undergraduate, Homework, Graduate, Advanced, Majors, Non-majors, More than 1 hour, Extended Project, Developing Self-awareness, Promoting Engagement and Self-Efficacy, Universal Design for Learning (UDL)

680

287

12.2019

The Effect of Climate Change on Butterfly Phenology - Intro Environmental Science

Megan Kelly

Version: 1.0 Adapted From: The Effect of Climate Change on Butterfly Phenology v1.0

In this module, students practice interpreting the relationship between variables before exploring changes in butterfly phenology through the use of natural history collections data.

Excel, Resources @ ESA - TIEE, graphing, climate change, fmn, phenology, natural history collections, DIG, butterfly, interspecific interactions, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Non-majors, More than 1 hour

418

227

06.2019

Data is the New Science

Anna Monfils, Debra Linton, Libby Ellwood, Molly Phillips

Version: 1.0

In this module, students will be introduced to some emerging biodiversity data resources. They will be asked to think critically about the strengths and utility of these data resources and apply what they have learned to research question.

data in the classroom, biodiversity informatics, natural history collection, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Homework, Advanced, Majors, Non-majors, More than 1 hour

1.3K

549

04.2019

Exploring Data with BISON

Erica Krimmel

Version: 1.0

A module to explore aggregated observation and collection information, through BISON, or Biodiversity Information Serving Our Nation (https://bison.usgs.gov), a tool for visualizing GBIF data.

Querying databases, data in the classroom, biodiversity informatics, natural history collections, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Homework, Less than 1 hour

569

183

03.2019

Botanical Society of America

BSA is a nonprofit membership society. Their mission is to: promote botany, the field of basic science dealing with the study and inquiry into the form, function, development, diversity, reproduction, evolution, and uses of plants and their interactions within the biosphere.

Transpiration

J. Phil Gibson

Version: 1.0

In this lab, students will examine differences between C3 and C4 plants in their transpiration rates.

plant physiology, botany, laboratory, Teaching material

611

150

03.2018

Transpiration has been featured in a Teacher Talk

Data Nuggets

Data Nuggets are free classroom activities, co-designed by scientists and teachers. They are an innovative approach to bring contemporary research and authentic data into the classroom. Data Nuggets include a connection to the scientist behind the data and the true story of their research process. Data Nuggets give students practice working with “messy data” and interpreting quantitative information. Students are guided through the entire process of science, including identifying hypotheses and predictions, visualizing and interpreting data, making evidence based claims, and asking their own questions for future research. Because of their simplicity and flexibility, Data Nuggets can be used throughout the school year, and across grades K-16, as students grow in their quantitative abilities and gain confidence. Data Nuggets have the potential to improve the understanding of science in society and help engage and motivate the next generation of scientists and engineers.

What do trees know about Rain? Adapted for an online, non-majors botany course

Liz Martin

Version: 1.0

Minor modifications were made to this Data Nugget in order to use it in a fully online version of the introductory, non-majors botany course, Plants and People.

introductory, Online course, Teaching material, Undergraduate, Non-majors, 1 Hour

1.1K

306

03.2018

Featured Resource of the Week

Winter is Coming! Can you handle the freeze?

Liz Martin

Version: 1.0

This publication contains the adaptations I made to the Data Nuggets module in order to use it with an online, introductory, non-majors botany class. I used this with a unit on natural and artificial selection in plants.

introductory, Online course, Teaching material, Undergraduate, Non-majors

1.6K

1.1K

03.2018

DIG

The Data Incubator Group focuses on promoting quantitative education through expanding the adoption of data-centric resources and facilitating large-scale collaboration on approaches to classroom implementation

Investigating Determinants of Richness in Ephemeral and Permanent Wetlands Using Linear Models in Shiny

Kristofor Voss

Version: 1.0 Adapted From: Environment-Richness Relationships in Ephemeral and Permanent Wetlands: Guided Inquiry with Graph Interpretation (Abstract) | TIEE v1.0

This resource seeks to provide a quantitative platform by which students can be taught about interactive effects using the TIEE module created by Little (2018). Key to the adaptation is the use of a Shiny app to create figures and R output.

aquatic macroinvertebrates, linear regression, hypothesis testing, shiny, wetlands, Lab, Online course, Teaching material, Lecture, Undergraduate, More than 1 hour

428

01.2019

The nose knows: How tri-trophic interactions and natural history shape bird foraging behavior

Kaitlin Bonner, Gregory Cunningham

Version: 1.0

Students investigate the role of olfaction and infochemicals on bird foraging behavior through three different quantitative modules. In this module students create graphs, generate statistics, draw conclusions, and apply their knowledge.

Resources @ ESA - TIEE, foraging, fmn, behavioral ecology, DIG, trophic cascades, Antarctic foodd webs, introductory, Lab, Online course, Teaching material, Undergraduate, Advanced, Majors, More than 1 hour

595

171

06.2018

Investigating Sexually Transmitted Disease (STD) Ecologies Using Geographic Information Systems (GIS) (Abstract) | TIEE

Maruthi Bhaskar

Version: 1.0

Identifying, mapping and understanding the magnitude and the spatial prevalence of the Sexually Transmitted Diseases (STDs) such as chlamydia and gonorrhea diseases. Analyzing the spatial trends of the disease patterns at National, State and...

Resources @ ESA - TIEE, Disease ecology, fmn, DIG, human ecology and behavior, bacterial infections, spatial and temporal spread of disease, Geographic Information System (GIS), introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Advanced, More than 1 hour

670

167

06.2018

Diseasebots

Arietta Fleming-Davies, Skylar Hopkins

Version: 1.0

This module explores the effects of host density on contact rates and transmission of pathogens or mutualist symbionts using a hands-on simulation, a computer agent-based model in NetLogo, and an authentic ecological dataset.

NetLogo, Disease ecology, density dependence, Spreadsheet, host-parasite, mutualism, Open-inquiry group projects, manipulative models (‘beanbag biology’), plotting, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Dataset, Cleaned, Advanced, Majors, More than 1 hour

669

358

06.2018

Do urban yards serve as a refuge for native land snail species?

Kathryn Elizabeth Perez

Version: 1.0

This module contains a series of take-home activities to prepare students to analyze their own dataset collected in lab.

urban ecosystems, refugia from habitat loss, group homework, introductory, Lab, Online course, Teaching material, Undergraduate, Dataset, Homework, Cleaned, Advanced, Majors, More than 1 hour, Extended Project

636

418

05.2018

Earth Lab

Earth Lab capitalizes on the data deluge from space and other platforms to accelerate science, reduce environmental risk, and train a new generation of earth data scientists. The Earth Lab Earth Analytics Education Initiative provides undergraduate, graduate, and professional students as well as online learners around the globe with core in-demand technical skills at the intersection of earth and environmental science and data science. All work is guided by a commitment to open and reproducible science, open education and expanding the reach of earth data science education to students across varying academic, professional, socio-economic and geographic dimensions.

Featured Resource of the Week

Earth Analytics in Python Course

Leah Wasser, Jenny Palomino, Chris Holdgraf

Version: 1.0

Earth analytics is an intermediate, multidisciplinary course that addresses major questions in Earth science and teaches students to use the analytical tools necessary to undertake exploration of heterogeneous ‘big scientific data’.

data analysis, data, data types, data science, earth science, open education resources, python, permafrost, remote sensing, floods, Geographic Information System (GIS), data science education, computer programming, wildfire, earth analytics, Online course, Teaching material, Undergraduate, Faculty, Graduate, Extended Project

588

11.2019

Get Started With GIS in Open Source Python Workshop

Leah Wasser, Jenny Palomino, Joe McGlinchy

Version: 1.0

There are a suite of powerful open source python libraries that can be used to work with spatial data. Learn how to use geopandas, rasterio and matplotlib to plot and manipulate spatial data in Python.

data analysis, data, data types, data visualization, data science, earth science, open education resources, python, remote sensing, Geographic Information System (GIS), data science education, computer programming, wildfire, earth anlaytics, Online course, Teaching material, Undergraduate, Faculty, Graduate, More than 1 hour

366

10.2019

Introduction to Version Control and Git Workshop

Leah Wasser, Max Joseph

Version: 1.0

Learn how to use version control with Git to work collaboratively and back up your work.

data analysis, data, data types, data science, earth science, open education resources, python, remote sensing, github, version control, data science education, computer programming, wildfire, earth analytics, v, geographic information systems, Online course, Teaching material, Undergraduate, Faculty, Graduate, More than 1 hour

364

10.2019

Writing Clean Code in R Workshop

Max Joseph, Leah Wasser

Version: 1.0

When working with data, you often spend the most amount of time cleaning your data. Learn how to write more efficient code using the tidyverse in R.

data analysis, data types, data visualization, data science, earth science, open education resources, R programming language, remote sensing, Geographic Information System (GIS), data science education, computer programming, wildfire, earth analytics, Online course, Teaching material, Undergraduate, Faculty, Graduate, More than 1 hour

376

10.2019

Introduction to Earth Data Science Textbook

Jenny Palomino, Leah Wasser

Version: 1.0

Introduction to Earth Data Science is an online textbook for anyone new to open reproducible science and the Python programming language. There are no prerequisites for this material, and no prior programming knowledge is assumed.

data analysis, data, data types, data visualization, data science, earth science, open education resources, python, remote sensing, Geographic Information System (GIS), data science education, computer programming, wildfire, earth analytics, Online course, Teaching material, Undergraduate, Graduate, Extended Project

323

10.2019

Earth Analytics in R Course

Leah Wasser

Version: 1.0

Earth analytics is an advanced, multidisciplinary course that addresses major questions in Earth science and teaches students to use the analytical tools necessary to undertake exploration of heterogeneous ‘big scientific data.’

data analysis, data, data types, data visualization, data science, earth science, open education resources, R programming language, remote sensing, Geographic Information System (GIS), data science education, computer programming, wildfire, earth analytics, Online course, Teaching material, Undergraduate, Faculty, Graduate, Extended Project

284

10.2019

Earth Analytics Bootcamp Course

Jenny Palomino, Leah Wasser

Version: 1.0

The Earth Analytics Bootcamp is a three-week introductory-level course taught by instructors in Earth Lab and is a part of the Professional Certificate in Earth Data Analytics - Foundations at CU Boulder.

data analysis, data, data types, data visualization, data science, earth science, open education resources, python, remote sensing, Geographic Information System (GIS), data science education, d, computer programming, wildfire, earth analytics, Online course, Teaching material, Undergraduate, Faculty, Graduate, Extended Project

286

10.2019

EDSIN

Growth in large ecological datasets and large environmental synthesis projects has resulted in the need for a diverse workforce with technical data science skills. A variety of organizations support underrepresented groups entering the data science field through training, mentoring, and networking opportunities. However, many of these initiatives have been developed in isolation, limiting opportunities for an exchange of ideas and lessons learned. The Environmental Data Science Inclusion Network (EDSIN) is intended to strengthen initiatives across existing alliances and organizations to recruit and retain individuals from underrepresented groups in data science careers.

Calling Bull in an Age of Big Data with R

Carrie Diaz Eaton

Version: 2.0

Use the calling bull course to introduce students to data, ethics, visualization, and R.

data science, information literacy, data literacy, ethics, callin bull, calling bull, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors

1.1K

579

05.2019

ESA

The Ecological Society of America (ESA) is a nonpartisan, nonprofit organization of scientists founded in 1915 to promote ecological science and improve the quality of ecology education at all levels.

Modification of "Exploring the population dynamics of wintering bald eagles through long-term data" module

Kaitlin Stack Whitney

Version: 1.1 Adapted From: Exploring the population dynamics of wintering bald eagles through long-term data v1.0

This module is a modification of the Beckstead et al. module in TIEE Volume 7. It includes a meta-cognition based model and self reflection, no statistics, and is organized to be done in 1-2 lab/in-class periods (no advance reading, no homework).

Resources @ ESA - TIEE, case study, population ecology, endangered species, conservation biology, migration ecology, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Advanced, Majors, Non-majors

460

274

05.2019

Modification of "The Effect of Climate Change on Butterfly Phenology" module by Linton et al.

Kaitlin Stack Whitney

Version: 1.1 Adapted From: The Effect of Climate Change on Butterfly Phenology v1.0

This is a modification of the Linton et al. module in TIEE Volume 13. Students use data from digitized museum records of butterfly specimens in a modification with no homework (lab/workshop format) or statistics knowledge required.

Excel, Resources @ ESA - TIEE, climate change, fmn, phenology, natural history collections, DIG, butterfly, interspecific interactions, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Majors, Non-majors, More than 1 hour

502

348

05.2019

Investigating the footprint of climate change on phenology and ecological interactions in north-central North America

Todd Levine, Kellen Calinger

Version: 1.0.0 Adapted From: Investigating the footprint of climate change on phenology and ecological interactions in north-central North America v1.0

Practice module included in Teaching Issues and Experiments in Ecology (TIEE) Volume 10

data analysis, Resources @ ESA - TIEE, climate change, phenology, species diversity, problem set, Worksheet, Online course, Teaching material, Lecture, Undergraduate, Homework

546

167

05.2018

Changes in Lake Ice: Ecosystem Response to Global Change

Todd Levine, Robert Bohanan, Marianne Krasny, Adam Welman

Version: 1.0.0 Adapted From: Changes in Lake Ice: Ecosystem Response to Global Change v1.0

Data Set included in included in Teaching Issues and Experiments in Ecology (TIEE) Volume 3

data analysis, Resources @ ESA - TIEE, assessment, Worksheet, limnology, aquatic, lake, Lab, Online course, Teaching material, Lecture, Undergraduate, Homework

429

143

05.2018

Project EDDIE

Project EDDIE (Environmental Data-Driven Inquiry and Exploration) is a suite of education projects composed of STEM disciplinary and educational researchers. We develop flexible classroom teaching modules using large, publicly available datasets to engage students in STEM and improve their quantitative reasoning. Teaching modules span topics such as ecology, limnology, geology, hydrology, and environmental sciences. EDDIE also helps build the associated professional development needed to ensure effective use of the teaching modules.

Spectral Seismology Module (Project EDDIE)

D. S. Soule, M. Weirathmuller, G. Kroeger, R. D. Gougis

Version: 1.0

Based on a conceptual presentation of waveforms and filters

Project EDDIE, Lab, Teaching material, Lecture, More than 1 hour

355

11.2019

Water Quality Module (Project EDDIE)

C. A. Gibson, D. N. Castendyk

Version: 1.0

Students utilize real-time nitrate data from the US Geological Survey to statistically evaluate water quality impacts and to identify their causes

data, concentration, Project EDDIE, n, nitrogen cycle, Teaching material, More than 1 hour

346

11.2019

Climate Change Module (Project EDDIE)

Catherine O'Reilly, D. C. Richardson, R. D. Gougis

Version: 1.0

Students explore how climate is changing from the recent record. Produced by Project EDDIE.

Lab, Teaching material, Lecture, More than 1 hour

317

11.2019

Lake Mixing Module (Project EDDIE)

Cayelan Carey, Jen Klug, R. L. Fuller

Version: 1.0

Students explore spatial and temporal patterns of lake mixing using high-frequency temperature data from lakes around the world.

stratification, Project EDDIE, Lab, Teaching material, Lecture, More than 1 hour

251

11.2019

Soil Respiration Module (Project EDDIE)

L. E. Nave, N Bader, Jen Klug

Version: 1.0

Soils hold more carbon (C) than any other component of the terrestrial biosphere!

Project EDDIE, Lab, Teaching material, Lecture, More than 1 hour

243

11.2019

Stream Discharge Module (Project EDDIE)

N E Bader, T. Meixner, C. A. Gibson, Catherine O'Reilly, D. N. Castendyk

Version: 1.0

Stream discharge is a fundamental measure of water supply in stream systems. Low discharge may cause problems with water supply and fish passage, while high discharge may mean flooding. In this module, students explore real-time stream discharge...

floods, Project EDDIE, urbanization, streams, Lab, Teaching material, More than 1 hour

231

11.2019

Cross-Scale Interactions (Project EDDIE)

Cayelan Carey, Kaitlin Farrell

Version: 1.0

Students explore new modeling and computing tools while learning fundamental concepts about how lake phytoplankton blooms occur through cross-scale interactions.

modeling, Project EDDIE, Lab, Teaching material, Lecture, More than 1 hour

224

11.2019

Climate Change Effects on Lake Temperatures (Project EDDIE)

Cayelan Carey, S Aditya, K. Subratie, R. Figueiredo, Kaitlin Farrell

Version: 1.0

Students explore new modeling and computing tools while learning fundamental concepts about how climate change will affect lakes

climate change, Project EDDIE, lakes, Lab, Teaching material, Lecture, More than 1 hour

241

11.2019

Genome Solver

Genome Solver began in 2012 with the goal to create a community of undergraduate educators interested in the Human Microbiome Project (HMP) as a means to teach the fundamentals of bioinformatics. Since then, Genome Solver instructors have provided training to more than 250 faculty members from approximately 125 institutions in a 1- or 2-day workshop. All Genome Solver curriculum materials are available on QUBES.

Mini-Workshop August 14, 2020

Vinayak Mathur, Anne Rosenwald, Gaurav Arora

Version: 1.0

We reviewed the materials available on Genome Solver (other lessons here) and described our new python pipeline for examining horizontal gene transfer and a new synteny lesson in detail.

Bioinformatics Education, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Majors, Non-majors, More than 1 hour, Fostering a Sense of Belonging, Promoting Engagement and Self-Efficacy

08.2020

Pre-lesson: Introduction to BLAST

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.

Bioinformatics Education, Bioinformatics and Genomics, introductory, Teaching material, High School, Undergraduate, Majors, Non-majors

08.2020

Lesson VII - Synteny

Gaurav Arora, Anne Rosenwald, Vinayak Mathur

Version: 3.0

The lesson teaches about synteny or the order of genes along a chromosome, which is useful for looking at orthologous genes between two species or strains.

Bioinformatics Education, introductory, Lab, Online course, Teaching material, High School, Undergraduate, Faculty, Homework, Majors, Non-majors, 1 Hour

08.2020

Lesson III - Annotation

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 3.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson III introduces Annotation, or assigning meaning to all the A's, C's, T's, and G's.

Bioinformatics Education, Bioinformatics and Genomics, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, 1 Hour

08.2020

Lesson VI - The Community Science Project

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 1.1

Genome Solver's Community Science Project was developed as a way to use the skills taught in the previous lessons. We're asking members of the community to provide instances of potential phage genes embedded in bacterial genomes.

Bioinformatics Education, Bioinformatics and Genomics, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, Extended Project

419

211

11.2019

Featured Resource of the Week

Genome Solver: Complete Set of Lessons

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

The Genome Solver Project began as a way to teach faculty some basic skills in bioinformatics - no coding or scripting. These Lessons also work well in the undergraduate classroom, culminating with an authentic community research project.

bioinformatics, NIBLSE, Bioinformatics Education, Bioinformatics and Genomics, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, C8. Data types, C9. Implications, Recommended by NIBLSE, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, Extended Project

523

10.2019

Lesson III - Annotation

Gaurav Arora

Version: 1.0 Adapted From: Lesson III - Annotation v1.0

227

10.2019

Lesson III - Annotation

Gaurav Arora

Version: 1.0 Adapted From: Lesson III - Annotation v1.0

224

10.2019

Lesson V - Phylogenetics

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson V is an introduction to Phylogenetics.

Bioinformatics Education, Bioinformatics and Genomics, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, 1 Hour

382

937

10.2019

Lesson IV - Comparative Genomics

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson IV, Comparative Genomics, discusses some of the tools available for looking at genes across different genomes.

Bioinformatics Education, Bioinformatics and Genomics, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, 1 Hour

361

186

10.2019

Lesson II - Databases

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 1.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson II introduces the principal databases for microbial genomics.

Bioinformatics Education, Bioinformatics and Genomics, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, 1 Hour

631

456

10.2018

Lesson I - Introduction to Genome Solver

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 1.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Part I is the Introduction to the Genome Solver Project.

Bioinformatics Education, Bioinformatics and Genomics, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, 1 Hour

764

547

10.2018

HHMI BioInteractive

At BioInteractive, you can find award-winning multimedia resources, including apps, animations, videos, interactives, and virtual labs, to bring the excitement of scientific discovery into your classroom. Our rich video resources range from a series of short films on evolution, hosted by an award-winning author-scientist, to lectures on the brain given by a Nobel-prize winner—all supplemented by teacher guides and classroom activities.

Sickle Cell Disease Case Study

Elizabeth Co

Version: 1.0 Adapted From: Sickle Cell Disease and Natural Selection in Humans v2.0

A short film explores the evolutionary connection between an infectious disease, malaria, and a genetic condition, sickle cell anemia. The animation explores the genetic causes and biological effects of sickle cell disease.

HHMI BioInteractive, introductory, Teaching material, High School, Reference material, Undergraduate, Dataset, Advanced, Majors, Non-majors, 1 Hour, Less than 1 hour

162

05.2020

Data Analysis and Cancer

Lynn Marie Diener

Version: 1.0 Adapted From: The p53 Gene and Cancer v1.0

This is a flipped classroom approach, students will learn the basic content about cell-signaling, p53, and transcription factors before class. During class students will focus on data analysis applying what they learned to their interpretation of the data

Resources @ HHMI - BioInteractive, Biochemistry, molecular biology, data interpretation, Biological Data Analysis, cell cycle, macromolecules, Genetic disease, Cell signaling, introductory, Online course, Teaching material, Lecture, Undergraduate, Homework, Majors, 1 Hour, Promoting Engagement and Self-Efficacy

394

155

12.2019

Electrical and chemical communication in the nervous system

Patrick Cafferty

Version: 1.0 Adapted From: Electrical Activity of Neurons v1.0

This activity guides students through an online tutorial to examine the electrical and chemical communication of neurons.

introductory biology, neurobiology, anatomy and physiology, Cell communication, introductory, Online course, Teaching material, Lecture, Undergraduate, Homework, Majors, Non-majors, Less than 1 hour

470

227

08.2019

Examining human impacts on tusk evolution in elephants using authentic research data using Serenity

Kaitlin Bonner

Version: 1.0 Adapted From: Examining human impacts on tusk evolution in elephants using authentic research data v1.0

In this activity students explore and analyze real, authentic research data paired with HHMI’s “Selection for Tuskless Elephants” video in a hands-on investigation of human impacts on elephant evolution using the R-Shiny App, Serenity.

introductory, Lab, Presentation, Online course, Teaching material, Lecture, Reference material, Undergraduate, Homework, Advanced, Majors, Non-majors, 1 Hour, Conference material

426

157

07.2019

Amylase Copy Number and Diet

Rebecca Orr, Ruth Buskirk, Kristin Harvey

Version: 2.0.0

An adapted module from HHMI Spreadsheet Tutorials using amylase data for students to gain data analysis and excel skills

Scientific Process, Statistics and Math, Scientific Methodology, Teaching material, 1 Hour

292

204

03.2019

Regulation of Sex Determination

Jessica Ashley Allen, Christie Landry, Laura Pickell, Deborah Taylor

Version: 1.0

This activity accompanies the HHMI BioInteractive module Sex Verification of Athletes (https://www.hhmi.org/biointeractive/testing-athletes). It provides students with exercises to explore the aspects of human anatomy and physiology.

introductory, Teaching material, Undergraduate, Majors, Non-majors, Less than 1 hour