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    Hidden Markov Model
    Hidden Markov models are a set of mathematical tools that can be used to draw inferences about genomic and evolutionary processes.

    Keywords: hidden markov models

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    A Hands-on Introduction to Hidden Markov Models
    A lesson in which students will understand the basic structure of an HMM, the types of data used in ab initio gene prediction, and its consequent limitations.

    Keywords: Markov modelbioinformaticsgenomicsNIBLSEtranscriptionCourseSourceexonintronsplicing

    1457

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    Pharmacokinetics
    This Excel module explores how drugs are processed and absorbed in the human body.

    Keywords: drug metabolismpharmacokinetics

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    Frayer model growth mindset
    A Frayer model worksheet for the concept of growth mindset.

    Keywords: growth mindsetFrayer model

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    COVID-19 Model
    This Excel worksheet implements an SEAIHRD model for Covid-19 (Susceptible, Exposed, Asymptomatic infective, symptomatic Infective, Hospitalized infective, Recovered, Deceased).

    Keywords: infectious diseaseCOVID19

    219

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    Deme 2.0
    This workbook simulates the population genetics of a single gene with two alleles. It can simultaneously model up to three local populations, which may differ in their selection coefficients.

    Keywords: population geneticsGenetic DriftNatural Selection

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    Linkage Analysis
    This Excel workbook simulates a linkage analysis problem with up to four alleles. Based on the offspring produced by a multihybrid testcross, the user builds a model of the gene order,...

    Keywords: recombinationlinkage analysis

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    Mystery box puzzle for model based reasoning
    This is a computer based problem solving activity that I use to engage introductory biology students with discussions about model based reasoning.

    Keywords: Model Based ReasoningScientific reasoningpuzzle

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    An introduction to population matrix models: a swirl lesson
    Students will learn how to set up a population matrix model in R and use it for demographic analysis of a population, including projecting population growth, determining lambda and the stable age...

    Keywords: population dynamicsRpopulation growthonlinedemographypopulation projection modelquantitative biologypopulation modelmatrix modelspopulation ecologyage structurepopulation biologypopulation modelingSwirlDemographic processespopulationLeslie matrix

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    Luria-Delbruck
    These two workbooks model the evolution of phage resistance in a bacterial population under two alternative hypotheses.

    Keywords: phageLuria-Delbruckresistance

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    Tag You're It: A Lesson Investigating Study Design and Survival Analysis on an American Shad Tagging Study
    In this lesson, students will learn about the various mark-recapture and tagging methods that are used in various scientific disciplines and the information they can gather. Key elements of...

    Keywords: survival analysisAmerican ShadCox Proportional Hazards ModelStudy Design

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    SIR BuildIt
    An introduction to epidemiological models using interactive Excel worksheets

    Keywords: modelinginfectious diseaseInfectious Disease ModelingSIR modelsSIR

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    Working with plant phenology data and fitting a nonlinear model using least squares in R
    A participatory live-coding lesson on working with NEON phenology data and fitting a sine-wave model to determine when different species get and lose their leaves.

    Keywords: modelingRphenologyNEONRstatscodeparticipatory live-coding

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    Quantifying Bacterial Growth in the Guts and Hemolymph of Fruit Flies: Mathematical Modeling and Data Interpolation/Extrapolation
    In this activity, students will analyze raw data obtained from an experiment that explores the effect of overexpressing the Ssk protein in order to strengthen the intestinal barrier and prevent...

    Keywords: graphingexponential growthlinear modelsqbccinterpolationConcepts in Statistics and Precalculus Understanding exponential rates and linear slopesExtrapolation

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    Modeling Changes in Probability of Presence of Myotis lucifugus Due to White Nose Syndrome: An Introduction to Logistic Regression in R
    In this lesson, students will learn more about the wildlife disease known as white nose syndrome and how it affects certain bat species more than others. Students will learn about the important...

    Keywords: ecologyconservationRStudiobatslogistic regressionGLMWildlife DiseaseWhite nose syndromelittle brown batsmyotis lucifugus

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    Protein Analysis
    This Excel workbook allows the analysis of sample or imported protein sequences. The model can analyze protein sequences up to 500 amino acids long.

    Keywords: Protein sequencehydrophobicity/hydrophilicity

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    Leslie/Lefkovitch Matrix Models for Age or Stage-structured Populations
    This Excel workbook uses the Leslie matrix model for population projection of age-class structured populations, and also allows Lefkovitch matrix models for stage-class structured populations.

    Keywords: survivalpopulation ecologyfecundityLeslie matrixeigenvalueseigenvectorsLefkovitch matrixage-class structured populationsstage-class structured populationsreproductive value

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    Navigating Bacterial Changes in Aging Organisms: Graphs, Patterns, and Models
    Aging is an incredibly important area of research, and recent biological advances implicate the intestines in aging pathologies. Given that the gut harbors an immense amount of an organism’s...

    Keywords: statisticsgraphingmathematics for life sciencesmathexponential growthPrecalculus

    216

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    The Importance of Street Trees and Urban Avifauna: A lesson exploring the relationship between urban forest and foraging birds
    This module examines the relationship between street trees, urban avifauna, and socioeconomic gradients in the highly urbanized county of Los Angeles, California. Using edited data from a published...

    Keywords: conservationBiodiversityurbanizationGeneralized linear modelsavifaunaurban forestsocioeconomicsstreet treesnegative binomial regression

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    Human Dimensions in Amphibian Conservation: Addressing Threats
    This module introduces students to the theme of human dimensions in conservation and provides them with an opportunity to engage in practices related to social science research.

    Keywords: conservationhuman dimensionsamphibianssocial scienceconceptual modelstakeholder analysisopen standardsresearch proposalSPARCnet

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