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The QUBES platform hosts hundreds of teaching materials, reference materials, and cloud-based software free to use and adapt using open Creative Commons licenses.

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    Using Phyre2
    How to use Phrye2 and 3DLigandSite to computationally predict protein and active site structure and binding partners (substrates/cofactors/coenzymes).

    Keywords: videosbioinformaticsproteinsgenomicsyoutubephyre23DLigandSite

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    Investigating Enzyme Structure and Function Through Model-Building and Peer Teaching in an Introductory Biology Course
    A foundational knowledge of the relationship between structure and function is critical to understanding how enzymes work. The seemingly invisible nature of these molecular interactions makes it...

    Keywords: structure-functionEnzymeallosteric regulationcompetitive inhibitionfeedback inhibitionnoncompetitive inhibitionproductsubstrate

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    Redox Chemistry and Coral Bleaching
    Mapping coral bleaching using NOAA data to set the stage for reviewing redox chemistry concepts

    Keywords: ecologyResources @ HHMI - BioInteractiveclimateScientific ProcessStatistics and Mathearth and environmenthuman impacts

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    It's a Substrate... It's a Protein...No - It's an Enzyme! Teaching Using 3D Serine Protease Physical Modeling Activities to Confront Misconceptions.
    Reported misconceptions of enzyme-substrate interactions highlight the necessity for better, targeted instructional tools and assessments. A series of active learning activities with corresponding...

    Keywords: Protein StructureEnzymes-Substrate InteractionsNoncovalent InteractionsGeometric ComplementaryElectronicsStereochemistrySerine Proteases

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    Analysis of Amylase Activity
    This lab is an exploration of enzyme function and the effects of environmental conditions on the activity of the enzyme amylase. The lab utilizes analytical and graphing skills to assess enzyme...

    Keywords: data analysisintroductory biologyconcentrationgraphinglinear equationsBiochemistryscientific methodstandard curveenzyme functionMicrosoft ExcelInterpreting GraphsenzymesqbccCreate graphsInterpret graphsSolving Equations and Inequalitiesinterpret tablesAmylaseAlpha-amylaseEnzyme activityMaltoseDNS assayAbsorbancelab reportspectrophotometryregression linemanipulating equationsline of best fitgraphing by hand

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    Serotonin in the Pocket: Non-covalent interactions and neurotransmitter binding
    This lesson introduces beginning biochemistry students to the concept of a biomolecule binding site, such as a neurotransmitter receptor site or an enzyme active site. A simple organic molecule,...

    Keywords: active sitebindingbinding sitehydrogen bondinghydrophobic effectionic interactionsnon-covalent forces

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    BioMolViz - Development of an Inclusive Community for the Instruction of Visualizing Biomolecules (RCN-Introduction)
    BioMolViz is a community dedicated to advancing biomolecular visualization education. We provide training, teaching tools and validated visual literacy assessments. The BioMolViz Library—our online...

    Keywords: RCN-UBE Introduction

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    Preparing Student Study Guides through Peer Collaboration in the Technological Era
    Incorporating active learning exercises into large lecture courses is particularly challenging, especially when it comes to examination preparation materials. Traditionally, study guides are used...

    Keywords: active learningDiscussionStudy Skills

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    Using Collaborative Projects to Promote Active Learning of Microbial Skin Diseases and Their Impact on Everyday Lives
    One of the most daunting aspects of introductory clinical microbiology is learning details about a vast number of different microbial diseases that can infect humans. Each of these diseases has...

    Keywords: infectious diseasecollaborationpathogenesisTreatment of diseasesReal-life Microbiology

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    Functional trait-based restoration. Can hybrid restoration enhance invasion resistance and ecosystem services?
    A hybrid restoration experiment in Hilo, Hawaiʻi, in an area of high biocultural conservation value, that address the ecological and philosophical issues involved in conducting restoration with a...

    Keywords: Invasive SpeciesagroforestryHawaii CountyRestoration Ecologyplant functional traitstropical forest

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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...

    Keywords: transcriptionexonintronsplicing

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    Exploring the March to Mars Using 3D Print Models
    With the increased availability of 3D printers and open databases containing 3D print files, academic institutions are giving more thought into how such technology can be used in the classroom to...

    Keywords: waterMarsmicroorganismsproperties of life

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    Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging
    Organelle structure has been studied and visualized for decades; however, publicly available databases that use improved high-throughput microscopy of gene-edited cell lines have recently...

    Keywords: modelingcase studymicroscopystructureOrganellesHigh-throughput (HT)Endoplasmic Reticulum (ER)Fluorescent microscopyHuman Cell Biology

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    Designing an Asynchronous, Self-Led Aquatic Ecology Field Trip
    Due to the COVID-19 pandemic and increasing need to teach students online, aquatic scientists are looking for ways to give students field experiences virtually. Asynchronous, self-led field trips...

    Keywords: observationecosystem structureexploration

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    Walkabout: An Easy to Use, Experiential Learning Activity for Applying Abstract Concepts to the Real-World
    Students can have difficulty recognizing examples of course concepts in the real-world. They particularly struggle with phenomena that are ambiguously defined, have mimics, or are hard to...

    Keywords: data gatheringgreen technologyobservations

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    Simulating Cortical Rotation, Axis Induction, and Experimental Embryology in Amphibian Embryos Using Clay Models
    The study of development requires learners to understand spatially complex concepts like embryo anatomy. Embryo anatomy is dynamic over time, and it is often manipulated by researchers in...

    Keywords: developmentXenopusfertilizationEmbryologyinductionSymmetry breakingOrganizerCortical rotationPatterning

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    Data, Distributions, and Hypotheses: Exploring Diversity and Disturbance in the Tallgrass Prairie
    Proper hypothesis generation, data handling, graphing, and communication are essential skills that undergraduate majors in biology are expected to master. However, students rarely get hands-on...

    Keywords: Quantitative reasoningRestoration EcologyScience process skillstall grass prairie ecosystem

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    Introduction to Probability, Statistics, and Random Processes
    This site is the homepage of the textbook Introduction to Probability, Statistics, and Random Processes by Hossein Pishro-Nik.

    Keywords: textbookcurriculumcourseproblem setsolutions

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    Active Learning: Developing Self-Directed Learners Through Strong Intellectual Engagement
    When they were students, many current science instructors learned through traditional lectures. This mode of passive knowledge transmission has been shown to be less effective for student learning...

    Keywords: active learningmetacognitionconstructivism

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    Avida-ED User Manual
    Basic User manual to use Avida-ED

    Keywords: EvolutionArtificial LifeAvidaavida-ed

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