CourseSource: Resources

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A Hands-on Introduction to Hidden Markov Models

In this Lesson, we describe a classroom activity that demonstrates how a Hidden Markov Model (HMM) is applied to predict a eukaryotic gene, focusing on predicting one exon-intron boundary. This HMM lesson is part of the BIOL/CS 370...

Courses: Bioinformatics Genetics Science Process Skills

transcriptionexonintronsplicing

Lesson

2289

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278

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1

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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

1517

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210

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Modeling Strep Throat Detection, Infection, and Spread Using an SIR Model and the Vensim Simulation Software

The overarching goal of this lesson is to provide students with an opportunity to gain experience making and using biological models. Biological modeling can be used to investigate complex, real-world problems so that predictions can be made about...

Courses: Cell Biology Immunology Introductory Biology Microbiology

infectious diseasebiological modelingSIR model

Lesson

3076

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453

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Moths and Frogs and E. coli, Oh My!: Agent-based Modeling of Evolutionary Systems

In evolution classrooms, introducing and reinforcing the idea of genetic drift and random selection can be challenging, as can be reinforcing appropriate mental models of evolution. Agent-based models offer students the opportunity to conduct a...

Courses: Bioinformatics Ecology Ecology Evolution Science Process Skills

modelingEvolutionecologyagent-based modelingGenetic Driftenvironmental scienceNatural Selectioncompetitive coevolutionsimulation modelingevolutionary reasoning

Lesson

1529

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306

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Promoting Climate Change Literacy for Non-majors: Implementation of an atmospheric carbon dioxide modeling activity as an inquiry-based classroom activity

Students who are directly involved in scientific activities develop a deeper understanding and appreciation of both scientific knowledge and the scientific process. This understanding is critically important in scientific areas like climate change...

Courses: Introductory Biology Science Process Skills

modelingExcelquantitativeclimate changeEnvironmental Biologyatmospheric carbon dioxide

Lesson

1289

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352

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A first lesson in mathematical modeling for biologists: Rocs

Using a fictitious population of Rocs, a mythical species of giant raptor, students accomplish two broad objectives: 1) they undertake the process of building a first mathematical model of a population, and 2) they begin to develop their...

Courses: Ecology Ecology Introductory Biology Science Process Skills

population ecologypopulation modelingdiscrete generationpopulation management

Lesson

3104

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358

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Discovering Cellular Respiration with Computational Modeling and Simulations

Cellular respiration, a common topic among introductory and cellular biology curricula, is a complex biological process that exemplifies core biological concepts, including systems, pathways and transformation of energy, and structure and function...

Courses: Introductory Biology

Cellular MechanismsCellular RespirationFermentation

Lesson

1824

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378

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Plotting Cranial and Spinal Nerve Pathways in a Human Anatomy Lab

Hands-on experiences with cadavers, animal dissections, or plastic models are effective at improving student learning and attitudes in human anatomy courses. The hands-on experience allows students to visualize and experiment with anatomical...

Courses: Anatomy-Physiology Science Process Skills

human anatomyNervous systemBrainCranial nerveNerveSpinal cordSpinal nerve

Teaching Tools and Strategies

989

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201

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Making toast: Using analogies to explore concepts in bioinformatics

Contemporary biology is moving towards heavy reliance on computational methods to manage, find patterns, and derive meaning from large-scale data, such as genomic sequences. Biology teachers are increasingly compelled to prepare students with...

Courses: Bioinformatics

bioinformaticsworkflowgenome

Lesson

4260

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410

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Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon

The trp operon exemplifies important biological concepts, including the central dogma of molecular biology, feedback inhibition, and gene regulation. For this reason, regulation of the trp operon is a common theme in introductory biology,...

Courses: Genetics Introductory Biology Microbiology

prokaryotesgene regulationattenuationfeedback inhibitionrepressible operontrp operon

Lesson

4469

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448

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1

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Teaching Advanced Concepts in Regulation of the Lac Operon With Modeling and Simulation

Success in biochemistry and other life science courses requires that students understand important biological concepts. One of these concepts is how gene regulation ensures that homeostasis is maintained in an organism. The lac operon is a...

Courses: Biochemistry and Molecular Biology

gene regulationinducible operonProkaryotic cellPhosphoenolpyruvate transferase system (PTS)

Lesson

1957

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280

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A CURE-based approach to teaching genomics using mitochondrial genomes

There is an abundance (currently over 1016 DNA bases) of publicly available genetic sequence data and a dearth of trained genomicists to process and interpret it, necessitating more trained bioinformaticians with biological expertise. For...

Courses: Bioinformatics Genetics

proteinsMitochondrial GenomesNuclear GenomesrRNAtRNA

Lesson

1503

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529

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Building a Model of Tumorigenesis: A small group activity for a cancer biology/cell biology course

The multistep nature of tumorigenesis is a foundational concept in the context of Cancer Biology. Many students do not appreciate the complex nature of cancer development nor do they understand how scientists are able to unravel the molecular...

Courses: Cell Biology Genetics Science Process Skills

pathwayscancerMolecular AlterationsRetrospective dataTumorigenesis

Lesson

7672

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1462

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0

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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

Lesson

2147

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667

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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

Lesson

999

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138

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Student-Generated Analogies for Learning about Information Flow

Using analogies is a standard practice for both teaching and communicating ideas in science. Here we upend the traditional lesson, where the instructor provides a fully constructed analogy and explains it, by having the students develop a complex...

Courses: Biochemistry and Molecular Biology Cell Biology Genetics Introductory Biology

critical thinkingcentral dogmaanalogical reasoning

Lesson

3707

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829

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Breaking Bricks: A Hands-On Model of Enzyme Kinetics and Inhibition

Enzyme kinetics and the impacts of inhibitors on the enzyme's maximal velocity and ability to bind substrates are important topics in cell biology and biochemistry. However, these topics can be difficult for students to grasp when instructed...

Courses: Biochemistry and Molecular Biology Cell Biology

kineticsEnzymecompetitive inhibition

Lesson

5040

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914

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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

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2999

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549

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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

Lesson

3779

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415

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Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four...

Courses: Biochemistry and Molecular Biology Bioinformatics Science Process Skills

bioinformaticsmolecular modelingCOVID19protein structure and functionUCSF ChimeraSARS-CoV-2 spike proteinACE2 receptor

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A Hands-on Introduction to Hidden Markov Models

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

Modeling Strep Throat Detection, Infection, and Spread Using an SIR Model and the Vensim Simulation Software

Moths and Frogs and E. coli, Oh My!: Agent-based Modeling of Evolutionary Systems

Promoting Climate Change Literacy for Non-majors: Implementation of an atmospheric carbon dioxide modeling activity as an inquiry-based classroom activity

A first lesson in mathematical modeling for biologists: Rocs

Discovering Cellular Respiration with Computational Modeling and Simulations

Plotting Cranial and Spinal Nerve Pathways in a Human Anatomy Lab

Making toast: Using analogies to explore concepts in bioinformatics

Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon

Teaching Advanced Concepts in Regulation of the Lac Operon With Modeling and Simulation

A CURE-based approach to teaching genomics using mitochondrial genomes

Building a Model of Tumorigenesis: A small group activity for a cancer biology/cell biology course

An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

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

Student-Generated Analogies for Learning about Information Flow

Breaking Bricks: A Hands-On Model of Enzyme Kinetics and Inhibition

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

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

Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

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