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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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    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...

    Keywords: bioinformaticsDNA sequenceRNAseqgene expression

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    Lung Capacity and Rhythms in Breathing
    This module introduces rhythmic inhaling and exhaling in the context of understanding trigonometry and sine waves. It is intended for an introductory biology audience.

    Keywords: Trigonometrysine wavesAnimal Physiology

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    Using DNA Subway to Analyze Sequence Relationships
    This is a bioinformatics exercise using the DNA Subway Blue Line, a user-friendly pipeline of bioinformatics tools, to analyze a collection of mosquito DNA bar-code sequences.

    Keywords: phylogeneticsNIBLSEDNA BarcodingDNA sequenceBLASTmultiple sequence alignmentC1. Role of bioinformaticsC2. Computational conceptsC4. Bioinformatics toolsC5. Data retrievalC8. Data typesIncubated at NIBLSE

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    1989-EY_Rodin-S_Jaques-Countercurrent Oxygen Exchange in the Swim Bladders of Deep-Sea Fish
    Oxygen diffuses from lungs into blood, nutrients diffuse from intestinal tracts into blood and from blood into various cells, and waste products diffuse from cells back into blood.

    Keywords: fishCell Membraneflowbloodbladdercountercurrent

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    Citations
    Published Avida-Ed article

    Keywords: EvolutioncurriculumSelectionDigital Organisms

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    Literature Review: Inclusive Calculus for Life Sciences
    We believe that a biology-relevant calculus experience (biocalculus) can help overcome many of these issues in calculus. While challenging to build the capacity for teaching courses, students in...

    Keywords: calculusbiocalculusidentityInclusive teachingcalculus epistemology

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    Water We Doing: A Deep Dive Into Sustainable Ocean Management & Blue Economies
    This lesson explores the concept of blue economies and includes a detailing lesson in R that involves basic statistics and building complex graphics.

    Keywords: linear regressionRStudioblue economy

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    Cardiac Output
    This module introduces Fick's principle in the context of understanding the cardiac output. It is intended for an introductory biology audience.

    Keywords: linear regressionproportionslinear equationsOpenStaxAnimal Physiology

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    Mitotic Index and Cell Division
    This module introduces the mitotic index in the context of understanding the dynamics of cell division in the root of a plant. It is intended for an introductory biology audience.

    Keywords: RatiosCell StructureCell GrowthchartCell DivisionMitotic Index

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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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    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...

    Keywords: modelingEvolutionecologyagent-based modelingGenetic Driftenvironmental scienceNatural Selectioncompetitive coevolutionsimulation modelingevolutionary reasoning

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    Science Behind the Lesson: It's a Bird! It's a Plane! It's Biomechanics!
    Active flight is a specialized mode of movement found in insects, birds, and mammals. The anatomy, morphology, physiology, and ecology of flying taxa has changed over evolutionary time. Researchers...

    Keywords: EvolutionecologybatphysiologyAnatomybiomechanicsbirdFlightinsect

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    The River Field Studies Network: Connecting rivers, people, & science through immersive field-based education (RCN-UBE Introduction)
    Connecting rivers, people, & science through immersive field-based education

    Keywords: RCN-UBE Introduction

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    2011-Cruz-Aponte-Herrera-Valdez-Mitigating effects of vaccination on influenza outbreaks given constraints in stockpile size and daily administrati
    We present a SIR-like model that explicitly takes into account vaccine supply and the number of vaccines administered per day and places data-informed limits on these parameters.

    Keywords: vaccinationinfectionSIRepidemic

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    2007-Zenker-Rubin-Clermont-From inverse problems in mathematical physiology to quantitative differential diagnoses
    The improved capacity to acquire quantitative data in a clinical setting has generally failed to improve outcomes in acutely ill patients, suggesting a need for advances in computer-supported data...

    Keywords: physiologyinverse problem

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    Using Science Education Gateways to Improve Undergraduate STEM Education: The QUBES Platform as a Case Study
    This paper describes BioQUEST's vision for the QUBES platform as an engine for science education reform. 

    Keywords: Science Education Gateway

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    For a Racially-Just, Inclusive, Open, STEM education: The RIOS Institute imagines an Open Education as the radical idea that education should be affordable, accessible, equitable, inclusive, and relevant to everyone
    As we engage in Open STEM Education, “Open for Whom?” becomes an increasingly urgent question. Why should we invest in an education that is free, if it does not attend to the inclusion of...

    Keywords: social justiceriosNABT 2022

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    6-028-SaltCompartments-ModelingScenario
    Model a phenomena in which salt mixtures from two tanks are mixed with changing volumes of water.

    Keywords: concentrationcomparmentsalttankmixing

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    Project MOSAIC
    Our goal: Provide a broader approach to quantitative studies that provides better support for work in science and technology.

    Keywords: statisticsmodelingmodulecase studycomputationalternative curriculumResources @ Project Mosaicin-class activityproblem setResources @ QUBES - Teaching & Reference

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    Application of a Bacterial Experimental Evolution System to Visualize and Teach Evolution in Action: A Course-Based Undergraduate Research Experience
    Concepts of evolution are typically taught through examples of extremely long timescales, which do not always resonate broadly. Here, we describe a course-based undergraduate research experience...

    Keywords: EvolutionmutationcompetitionNatural Selectionregulationstructure and functionreproductive fitnessgenotype to phenotypehomologs

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