CourseSource: Resources

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Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

Next-generation sequencing is radically changing the study of biology, but there are currently few resources aimed at teaching the required laboratory and data-analysis skills to undergraduate students. This gap is especially true at primarily...

Courses: Bioinformatics Introductory Biology

statisticsbioinformaticsRNAseqgene expressioncomputer programming

Teaching Tools and Strategies

907

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132

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0

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Biology from Molecules to Embryos, Interactive Animated Lessons

Visualizing kinetic processes can be an impediment to student mastery of basic science coursework. To remedy this obstacle, I created an educational program called Biology from Molecules to Embryos© (BioME), which provides 28 animated lessons...

Courses: Developmental Biology Genetics Introductory Biology

geneticsBIOMEEmbryologycomputer assisted instructioneducational programeducational videosonline lessonsanimated lessonseducational website

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2992

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549

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2

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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

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1220

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84

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Responsible and Ethical Conduct of Research: Instruction on Plagiarism

Helping students understand where they should provide citations in research manuscripts is an essential aspect of training them in the responsible and ethical conduct of research. This Lesson comprises about 35 minutes of in-class work to help...

Courses: Science Process Skills

citationwritingethicsplagiarismparaphrasequote

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6121

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1235

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A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics

Rapid advances in genomics and bioinformatics, the vast amount of data generated by next-generation sequencing, and the penetration of the ‘-omics’ into many areas of biology have created a need for students with hands-on experience with...

Courses: Biochemistry and Molecular Biology Bioinformatics Ecology Ecology Microbiology

epidemiologyresearchbioinformaticsgenomicspublic healthAntibiotic Resistant BacteriaSalmonellaDNA sequencingpathogenic bacteria

Teaching Tools and Strategies

976

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311

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A Customizable Inquiry-Based Statistics Teaching Application for Introductory Biology Students

Building strong quantitative skills prepares undergraduate biology students for successful careers in science and medicine. While math and statistics anxiety can negatively impact student learning within biology classrooms, instructors may reduce...

Courses: Introductory Biology

introductory biologyQuantitative reasoningInclusive teachingauthentic inquiryInferential statisticsInstructional scaffolding

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2285

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278

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Discovering Prokaryotic Gene Regulation by Building and Investigating a Computational Model of the lac Operon

The ability to construct and reason through a biological system is an important skill to develop in science education. This level of understanding forces students to recognize the interrelatedness of components within a biological process and...

Courses: Introductory Biology

prokaryotesgene regulationLac Operoninducible operon

Lesson

7669

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1462

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An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture environment, but students often fail to master and...

Courses: Biochemistry and Molecular Biology Bioinformatics Genetics

bioinformaticsGenome BrowsergenomicsRNAseqsplicingComputer ModelGene Structure

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1757

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286

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Using Gamification to Teach Undergraduate Students about Scientific Writing

Despite its importance, scientific writing is often deprioritized in undergraduate biology classes. Reasons include assumed prior knowledge, lack of class time, tedious grading, and the complexity and challenges associated with quality writing. To...

Courses: Science Process Skills

gamificationscientific writingE-LearningInstant FeedbackInteractive LearningReading Scientific PapersVIdeo/computer game

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1281

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169

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Central Dogma, Dictionaries, and Functions: Using Programming Concepts to Simulate Biological Processes

Technologies like next-generation sequencing, proteomics, and high-throughput phenotyping have transformed the way we do biology. There is a continued need for scientists with computational skills to analyze biological data while understanding the...

Courses: Bioinformatics

computationpythonJupyter notebookFunctionscentral dogmaDictionaries

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1566

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300

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Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

Metagenomics is rapidly evolving due to advances in sequencing technologies and bioinformatics, but without proper training to interpret these datasets, student understanding remains limited. Aimed at undergraduate juniors and seniors and graduate...

Courses: Biochemistry and Molecular Biology Bioinformatics Ecology Ecology Microbiology Science Process Skills

microbiome

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183

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Teaching the Photoelectric Effect Using an Open-Source Interactive Simulation

The photoelectric effect is one of the fundamental experiments that established the basis of quantum mechanics. Students studying this experiment in modern physics courses struggle to understand what it actually measured and why it is significant....

Courses: Introductory Physics: Calculus-Based

photoelectric effectquantum mechanicsquantalight-matter interactions

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3469

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724

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Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics approaches

Constructing a robust understanding of homologous chromosomes, sex chromosomes, and the particulate nature of genes is a notoriously difficult task for undergraduate biology students. In this lesson, students expand their knowledge of human...

Courses: Bioinformatics Genetics Introductory Biology Science Process Skills

bioinformaticsautosomehomologous chromosomeshomologous recombinationsex chromosomesex determinationsex reversal mutations

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1480

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435

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Using Images of Foraging Leaf-Cutter Ants to Teach Linear Regression

This lesson offers students a realistic, open-inquiry research experience, even when lab or field research is not possible. We first introduce students to leaf-cutter ants and how they forage. Then we provide images and videos of foraging...

Courses: Ecology Ecology Introductory Biology Science Process Skills

linear regressionexperimental designPlant-insect interactionsSymbiosisForaging behavior

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7962

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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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The Great Petunia Carnage of 2017: A Clicker Case Study Using Petunias to Describe the Effect of Genetic Modification on the Biochemistry of Flower Color and Phenotype in Plants

In this single class period case study, students examine the difference between genotype and phenotype by studying the mechanisms by which commercially available petunias have been bred to have different phenotypes (flower colors). Students review...

Courses: Genetics Introductory Biology Plant Biology

case studyGenetic ModificationsBiochemistry of Flower ColorGMO regulationsGenotype-Phenotype Connections

Teaching Tools and Strategies

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A Pandemic Pivot: Podcast as an Active Engagement Tool in the Classroom and Beyond

Higher education in STEM undoubtedly integrates the use of technology as a primary mode for content delivery to undergraduate students. This became especially salient throughout the shift to online education during the COVID-19 pandemic. Despite...

Courses: Science Process Skills

VaccinesReplication of virusesCOVID-19 transmission

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Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

Introductory bioinformatics exercises often walk students through the use of computational tools, but often provide little understanding of what a computational tool does "under the hood." A solid understanding of how a bioinformatics...

Courses: Biochemistry and Molecular Biology Bioinformatics Introductory Biology

BLASTmultiple sequence alignmentsequence similarityphylogramZika virusAlgorithmScoring Matrix

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3344

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Predicting and classifying effects of insertion and deletion mutations on protein coding regions

Mutations in genes can affect the encoded proteins in multiple ways, and some of these effects are counterintuitive. As for any other knowledge, students must create their own deep understanding of the Central Dogma. Students may not develop this...

Courses: Bioinformatics Genetics Science Process Skills

mutationcentral dogmatranslationframeshift

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4109

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Splicing it Together: Using Primary Data to Explore RNA Splicing and Gene Expression in Large-Lecture Introductory Biology

At the heart of scientific ways of knowing is the systematic collection and analysis of data, which is then used to propose an explanation of how the world works. In this two-day module, students in a large-lecture course are immersed in a...

Courses: Biochemistry and Molecular Biology Cell Biology Genetics Introductory Biology

gene regulationtranscriptiongene expressioncentral dogmarepressoralternative splicingmRNA processingActivatorTranscription factors

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Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

Biology from Molecules to Embryos, Interactive Animated Lessons

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

Responsible and Ethical Conduct of Research: Instruction on Plagiarism

A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics

A Customizable Inquiry-Based Statistics Teaching Application for Introductory Biology Students

Discovering Prokaryotic Gene Regulation by Building and Investigating a Computational Model of the lac Operon

An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Using Gamification to Teach Undergraduate Students about Scientific Writing

Central Dogma, Dictionaries, and Functions: Using Programming Concepts to Simulate Biological Processes

Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

Teaching the Photoelectric Effect Using an Open-Source Interactive Simulation

Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics approaches

Using Images of Foraging Leaf-Cutter Ants to Teach Linear Regression

Investigating Cell Signaling with Gene Expression Datasets

The Great Petunia Carnage of 2017: A Clicker Case Study Using Petunias to Describe the Effect of Genetic Modification on the Biochemistry of Flower Color and Phenotype in Plants

A Pandemic Pivot: Podcast as an Active Engagement Tool in the Classroom and Beyond

Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

Predicting and classifying effects of insertion and deletion mutations on protein coding regions

Splicing it Together: Using Primary Data to Explore RNA Splicing and Gene Expression in Large-Lecture Introductory Biology

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