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Resources created by our members and partners.

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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    The ml4bio Workshop: Machine Learning Literacy for Biologists
    Presentation on machine learning literacy for biologists at the 2019 Great Lakes Bioinformatics Conference

    Keywords: bioinformaticsmachine learning

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    Machine Learning Meets Medicine with Jenessa Peterson
    Jenessa Peterson is a former teacher turned data scientist/engineer and Director of Learning Engineering at The Learning Agency. Her more recent work in data science has included building a...

    Keywords: data sciencemachine learningmedicine

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    An Introduction to Statistical Learning: with Applications in R
    This book provides an introduction to statistical learning methods and is aimed for upper level undergraduate students, masters students and Ph.D. students in the non-mathematical sciences.

    Keywords: linear regressiontextbookclassificationcourseclustering coefficientR programming languagestatistical learningmachine learninglogistic regressionresamplingmodel selectionGeneralized additive modelsdecision treesprincipal components analysisMOOCResources @ QUBES - Teaching & Reference

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    DataCamp
    DataCamp: The Easiest Way to Learn Data Science Online

    Keywords: statisticsRcurriculumdata visualizationdata scienceonline learningcoursemachine learningpythonlab protocol

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    Using genomic data and machine learning to predict antibiotic resistance: a tutorial paper
    Antibiotic resistance is a global public health concern. Bacteria have evolved resistance to most antibiotics, which means that for any given bacterial infection, the bacteria may be resistant to...

    Keywords: Tutorialmachine learningantibiotic-resistanceArtificial Intelligence

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    CyVerse: Scalable Image Informatics
    Poster on cyberinfrastructure for the machine learning ere presented at the 2020 BIOME Institute: Cultivating Scientific Curiosity

    Keywords: image analysisundergraduate researchmachine learningCyVerse

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    50 Years of Data Science
    This paper reviews some ingredients of the current “Data Science moment”, including recent commentary about data science in the popular media, and about how/whether Data Science is really...

    Keywords: statisticsbig datadata sciencemachine learning

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    Artificial Intelligence
    This video explores what artificial intelligence is and features people who work on different aspects of intelligence. How do we make machines that think like humans? How can we tell when we’ve...

    Keywords: videosbig datamachine learningArtificial IntelligenceScience Forward

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    7-008-MachineReplacement-ModelingScenario
    Students build an integro-differential equation model using a convolution for machine replacement strategies for two different machine failure models.

    Keywords: Probabilityreplacement numberLaplace transformindustrial engineeringmachineconvolutiondistributiojstep functionderivative definition

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    Science of Sorting
    Children possess an innate curiosity about the natural world. This Discovery Trunk explores the topic of sorting, or classification, in the study of life science.

    Keywords: species interactionsphylogenyscience educationPropertytaxonomyindividual traitsLife ScienceSortOrganizationReproductionclassifycharacteriesticlivingnonlivingobjectsadvantagedichotomous keyliving systemsoffspringphysical traitbehavioral traitcladecladogramtaxonomistnatural worldkingdomsbinomial nominclatureone class periodgradesK-8K-8

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    5-005-Dialysis-ModelingScenario
    We design a compartment model of a kidney dialysis machine and compare 3 and 9 compartments for the machine as well as determine the effect of change in one of the parameters in the model on the...

    Keywords: countercurrent multiplierkidneydialysisconcurrentcompartment

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    NIBLSE Learning Resource Collection
    NIBLSE Learning Resource Collection

    Keywords: database

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    2016-Manheim-EtAl-Improving Decision Support for Infectious Disease Prevention and Control
    This report describes decision-support tools, including models and nonmodeling approaches, that are relevant to infectious disease prevention, detection, and response and aligns these tools with...

    Keywords: infectious diseaseecosystemepidemicmodel policy

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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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    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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    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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    Learning Journal Assignment on Learning Spaces
    Learning Spaces are the zones where interaction between students & students and students & professor occurs. The learning spaces are of two types major learning space and minor...

    Keywords: mathematicsactive learningstembiologyeducatorsfaculty developmentenvironmental sciencephysicschemistrysciencecritical thinkingFacultyTeachers traininglearning spaceteacher professional development

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    SCIENCE/Fiction: Modular Template for Class Design
    We present a modular scaffold for designing an introductory seminar using speculative fiction and science papers to welcome university undergraduates to the biology major. A list of twelve possible...

    Keywords: geneticscell biologyneurosciencesystems biologyScience Fiction

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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...

    Keywords: bioinformaticsgenomicscodingJupyter notebookcommand lineCyVersescriptingnext generation sequencing analysis

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    Design Your Own Flow Cytometry Experiment: A Four-Week Inquiry Laboratory
    Due to its importance to the field, flow cytometry should be one of the hallmark methods a student learns in the lab portion of an undergraduate immunology course. Flow cytometry is a classic lab...

    Keywords: Immunologyexperimental designFlow cytometryMice

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