CourseSource: Resources

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Analysis of Microbiomes Using Free Web-Based Tools in Online and In-Person Undergraduate Science Courses

Our understanding of microbiomes, or the collection of microorganisms and their genes in a given environment, has been revolutionized by technological and computational advances. However, many undergraduate students do not get hands-on experiences...

Courses: Bioinformatics Ecology Ecology Microbiology

microbiomeDNA SubwayCyVerseCourse based undergraduate researchQIIME2ranacapa

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2278

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305

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Learning Quantitative Genetics: Investigation of Genetic Control for Cold Stress Response in Plants

Course-embedded undergraduate research experiences (CUREs) for students have been shown to increase students’ understanding of the process of science, affirm their scientific identity, and improve retention in STEM fields. Despite many CUREs...

Courses: Genetics

data analysisrecombinationplantsquantitative geneticsabiotic stress responsegenetic control of complex traitsinheritance of complex traits

Lesson

5032

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909

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Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy

Analyzing high-throughput DNA sequence data is a fundamental skill in modern biology. However, real and perceived barriers such as massive file sizes, substantial computational requirements, and lack of instructor background knowledge can...

Courses: Biochemistry and Molecular Biology Bioinformatics

bioinformaticsDNA sequenceRNAseqgene expression

Essay

1519

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120

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Online Adaptation to "Gotcha! Which fly trap is the best? An introduction to experimental data collection and analysis"

We present here a simple and engaging experiment capitalizing on the universal need to rid our homes of fruit flies to teach experimental design and analysis. In an earlier paper, we described an experiment in which students learn the scientific...

Courses: Science Process Skills

data analysisexperimental designolfaction

Lesson

5097

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348

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Learning to Pipet Correctly by Pipetting Incorrectly?

Beginning undergraduate students in biology need basic laboratory, data analysis, and science process skills to pursue more complex questions in course-based undergraduate research experiences (CUREs). To this end, we designed an introductory...

Courses: Introductory Biology Science Process Skills

statisticslaboratorypipetting

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3369

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916

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Assessing Urban Biodiversity With the eBird Citizen Science Project: A Course-Based Undergraduate Research Experience (CURE) Module

The eBird citizen science module takes advantage of technology tools and online resources developed by the Cornell Laboratory of Ornithology (http://ebird.org) to achieve several learning objectives embedded in a semester-long upper-level biology...

Courses: Ecology Ecology Science Process Skills

datacitizen sciencecommunityBiodiversitySpecieshypothesishabitat

Essay

923

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202

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Thinking deeply about quantitative analysis: Building a Biologist's Toolkit

Vision and Change in Undergraduate Biology Education encouraged faculty to focus on core concepts and competencies in undergraduate curriculum. We created a sophomore-level course, Biologists' Toolkit, to focus on the competencies of...

Courses: Introductory Biology

Vision and ChangeRRStudioquantitative literacystatistical analysisScientific communication

Lesson

2711

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429

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An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching

Advances in Next Generation Sequencing (NGS) technology have led to development of many research methods for analyzing genomic data. Students studying biology at the undergraduate level must hone their skills at genomic analysis to participate in...

Courses: Bioinformatics Genetics Science Process Skills

Speciationgenome evolutiongenetic variation

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914

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338

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Quantifying Uncertainty and Distinguishing Data Sets in Introductory Physics

Physics labs are moving increasingly to open-ended experiments where students develop experimental physics skills, rather than verify textbook physics concepts. This sequence of activities sets the stage for this new kind of lab early in the...

Courses: Introductory Physics: Calculus-Based

statisticsMeasurementlaboratoryuncertaintypendulumexperimental skills

Lesson

7962

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397

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Investigating Cell Signaling with Gene Expression Datasets

Modern molecular biology is a data- and computationally-intensive field with few instructional resources for introducing undergraduate students to the requisite skills and techniques for analyzing large data sets. This Lesson helps students: (i)...

Courses: Biochemistry and Molecular Biology Cell Biology

genomicstranscriptionsignaling

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1692

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518

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A Remote Introductory Biology Lab Using Backyard Birdwatching to Teach Data Analysis and Communication

Asking questions, designing experiments, collecting data and interpreting those data, and communicating the results are some of the most important concepts an undergraduate biology lab can teach students. When the SARS-CoV2 pandemic forced our...

Courses: Ecology Ecology Introductory Biology Science Process Skills

ecologydata analysisdata collection

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1808

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479

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Out of Your Seat and on Your Feet! An adaptable course-based research project in plant ecology for advanced students

University capstone projects can offer science students a rich research experience that illustrates the process of doing scientific research, and can also help students better choose future academic and career pathways. While capstone projects are...

Courses: Ecology Ecology Plant Biology Science Process Skills

statisticsactive learningecologyinterdisciplinaryplantscommunicating sciencegroup workfield workproces of science

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812

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61

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Breaking It Down: What Factors Control Microbial Decomposition Rates?

Demonstrating and modeling changes in ecosystem processes in the laboratory classroom can be logistically difficult and expensive. This complexity often leaves little time for students to generate and test hypotheses. Yet, we must foster student...

Courses: Ecology Ecology Microbiology Science Process Skills

data analysishypothesis testingdata visualizationdata managementMicrobial RespirationDecompostionAbiotic ConditionsResults Communication

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1646

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Single Cell Insights Into Cancer Transcriptomes: A Five-Part Single-Cell RNAseq Case Study Lesson

There is a growing need for integration of “Big Data” into undergraduate biology curricula. Transcriptomics is one venue to examine biology from an informatics perspective. RNA sequencing has largely replaced the use of microarrays for whole...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Genetics Introductory Biology

bioinformaticscancertranscriptomicshigh-throughputData wranglingSingle cell RNA sequencingq

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Three Research-Based Quantitative Reasoning Modules for Introductory Organismal Biology Laboratories

We have designed three laboratory modules for an introductory organismal biology course with an emphasis on quantitative reasoning and data analysis skills. Module 1 tests for dimorphism in crayfish chelae using a paired statistical design. Module...

Courses: Introductory Biology Science Process Skills

allometryplantsAnatomytranspirationdimorphisminvertebrate biologyarthropodsplatyhelminths

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242

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Integrating Community Ecology Into the Study of Parasites: Exploring the Effect of Host Behavior on Parasite Transmission Rates

Organismal life cycles are often presented as a set of facts to memorize in undergraduate biology courses. This approach is cognitively demanding for students and fails to convey how central life cycle diversity is in shaping ecological and...

Courses: Ecology Ecology Science Process Skills

statisticsspecies interactionsQuantitative reasoninggraphsCommunity EcologyParasitologyfood webs

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A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

Radical innovations in DNA sequencing technology over the past decade have created an increased need for computational bioinformatics analyses in the 21st century STEM workforce. Recent evidence however demonstrates that there are significant...

Courses: Bioinformatics

bioinformaticsgenomicscodingJupyter notebookcommand lineCyVersescriptingnext generation sequencing analysis

Teaching Tools and Strategies

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A Remote-Learning Framework for Student Research Projects: Using Datasets to Teach Experimental Design, Data Analysis and Science Communication

Remote learning often requires an alternative to hands-on, student-designed research projects. To this end, we created a package of scaffolded assignments to support introductory students through the research process using datasets from past...

Courses: Introductory Biology Science Process Skills

population growthphysiologyecotoxicologyphotosynthesis

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2893

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A Case Study for Teaching Toxicology: Using Whales as an Indicator for Environmental Health

One of the challenges of teaching scientific courses is helping students understand research methods, biological models, and data analysis, which can be especially difficult in classes without a laboratory component. Within the field of...

Courses: Science Process Skills Toxicology

absorptionone environmental health hypothesismetals

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1763

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226

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Using a Sequential Interpretation of Data in Envelopes (SIDE) approach to identify a mystery TRP channel

This lesson sought to engage students in data interpretation and to encourage critical thinking about neurophysiology in the context of temperature sensation. A family of receptors called Transient Receptor Potential (TRP) channels are activated...

Courses: Anatomy-Physiology Cell Biology Neurobiology

Cell communicationChannel specificity and activationLimitations of tools of Cell BiologyNeuronal Signaling

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Analysis of Microbiomes Using Free Web-Based Tools in Online and In-Person Undergraduate Science Courses

Learning Quantitative Genetics: Investigation of Genetic Control for Cold Stress Response in Plants

Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy

Online Adaptation to "Gotcha! Which fly trap is the best? An introduction to experimental data collection and analysis"

Learning to Pipet Correctly by Pipetting Incorrectly?

Assessing Urban Biodiversity With the eBird Citizen Science Project: A Course-Based Undergraduate Research Experience (CURE) Module

Thinking deeply about quantitative analysis: Building a Biologist's Toolkit

An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching

Quantifying Uncertainty and Distinguishing Data Sets in Introductory Physics

Investigating Cell Signaling with Gene Expression Datasets

A Remote Introductory Biology Lab Using Backyard Birdwatching to Teach Data Analysis and Communication

Out of Your Seat and on Your Feet! An adaptable course-based research project in plant ecology for advanced students

Breaking It Down: What Factors Control Microbial Decomposition Rates?

Single Cell Insights Into Cancer Transcriptomes: A Five-Part Single-Cell RNAseq Case Study Lesson

Three Research-Based Quantitative Reasoning Modules for Introductory Organismal Biology Laboratories

Integrating Community Ecology Into the Study of Parasites: Exploring the Effect of Host Behavior on Parasite Transmission Rates

A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

A Remote-Learning Framework for Student Research Projects: Using Datasets to Teach Experimental Design, Data Analysis and Science Communication

A Case Study for Teaching Toxicology: Using Whales as an Indicator for Environmental Health

Using a Sequential Interpretation of Data in Envelopes (SIDE) approach to identify a mystery TRP channel

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