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

Lesson

2711

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432

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0

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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

Essay

923

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202

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0

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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

Teaching Tools and Strategies

983

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201

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0

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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

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

Teaching Tools and Strategies

976

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311

downloads

0

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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

Lesson

1281

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169

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0

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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

Lesson

1566

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300

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0

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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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2274

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351

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Learning R for Biologists: A Mini Course Grab-Bag for Instructors

As biology becomes more data driven, teaching students data literacy skills has become central to biology curriculum. Despite a wealth of online resources that teach researchers how to use R, there are few that offer practical laboratory-based...

Courses: Anatomy-Physiology Bioinformatics Ecology Ecology Genetics

Rdata analysisRStudio

Lesson

2045

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890

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0

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Exploration of the Human Genome by Investigation of Personalized SNPs

Students often shy away from tedious bioinformatics approaches to exploring their genomes. However, in our expanding digital world these skills are some of the most relevant and valuable. To increase students' interest in their own genomes, I...

Courses: Bioinformatics Genetics Science Process Skills

UCSC genome browsersingle nucleotide polymorphismGenome wide association studiesGenomic organization

Lesson

3686

views

200

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0

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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

Lesson

6121

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1235

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0

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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

Lesson

1529

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305

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0

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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

2822

views

555

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0

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Developing Data Literacy Skills and Connecting the Student Experience in the Classroom to the Community Through Biodiversity Projects

Undergraduate education and long-term science literacy are enhanced by integrating data projects with public datasets and creating analysis summaries. Underutilized public datasets are often generated by community-based or citizen science projects...

Courses: Ecology Ecology Plant Biology

species richnessBiodiversitydisturbanceHabitat rangePopulation abundance

Lesson

1955

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280

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0

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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

7669

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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

4206

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286

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0

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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

Lesson

2130

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665

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1

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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

4467

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448

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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

2141

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496

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0

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Necessary and Sufficient? Solving the Mystery of the Mitochondrial Pyruvate Transporter

While there are several available lessons for teaching introductory biology students about diffusion, facilitated diffusion, and active transport, fewer materials exist to support upper-division students' understanding of the proteins that...

Courses: Cell Biology

DiffusionActive transportfacilitated diffusionNecessary and sufficientTransport proteins

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

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

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

Making toast: Using analogies to explore concepts in bioinformatics

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

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

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

Learning R for Biologists: A Mini Course Grab-Bag for Instructors

Exploration of the Human Genome by Investigation of Personalized SNPs

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

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

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

Developing Data Literacy Skills and Connecting the Student Experience in the Classroom to the Community Through Biodiversity Projects

A CURE-based approach to teaching genomics using mitochondrial genomes

An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

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

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

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

Necessary and Sufficient? Solving the Mystery of the Mitochondrial Pyruvate Transporter

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