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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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    REMNet: A Student’s Introduction to Urban Microbiomes 5.3.19
    Video on urban microbiomes from the Research Experiences in Microbiomes Network

    Keywords: VideoMicrobiology Educationresearch in the classroomREMNeturban microbiomesmicrobiology research

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    Downloading and Visualizing Project Data from the iNaturalist Database
    In this activity you will learn how to create a query, export, and download data from iNaturalist; load data into R; explore pollinator-plant interactions with R, and create heat map, bipartite,...

    Keywords: data visualizationplantsPlant EcologyPlant-insect interactionsnetwork#iNaturalistBLUEpollinators

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    Importing Data into R
    This short swirl lesson on importing data is designed to 1) get a basic understanding in how tables are read into R and some common issues and 2) develop an individual set of instructions for...

    Keywords: teaching with technologySwirl

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    A Multi-Institutional Alternative Assessment Faculty Learning Community: Supporting Teaching in Higher Education
    Faculty learning communities (FLCs) provide opportunities for professional development for faculty, teaching staff, and educational developers in a collaborative and open environment. In this...

    Keywords: professional developmentAlternative AssessmentFaculty Learning Community

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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...

    Keywords: computationpythonJupyter notebookFunctionscentral dogmaDictionaries

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    Cookbook for R
    The goal of the cookbook is to provide solutions to common tasks and problems in analyzing data.

    Keywords: Rdata analysisdata manipulationdata

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    NetLogo refresher course
    This is a supplemental resource from ABM

    Keywords: moduletextbookNetLogoagent-based modelingIndividual & Agent Based Modelingin-class activityproblem set

    1006

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    Evolutionary Ecophysiology swirl lesson
    Uses swirl to walk students through how to use R and analyze their own data.
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    Histograms and Boxplots
    This lesson, created for an introductory ecology course, focuses on helping novice R users to import a data file, apply base R plotting functions, and use R Markdown to generate a reproducible report.

    Keywords: RStudiodata visualizationSwirl

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    Plants in the Human-Altered Environment (PHAE): EREN-NEON Flexible Learning Project
    A project to compare effects of a continuum of landscape alteration intensities on plant diversity, biomass, and ecosystem services, and to explore human socioeconomic connections to plants in the...

    Keywords: erenNEONdiversitybiomass4DEE Frameworkecosystemsocioeconomic effects

    1616

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    Bio 18: Statistics for Scientific Data Analysis
    Poster on the a data science course presented at the 2019 BioQUEST & QUBES Summer Workshop
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    Rstudio cheatsheets
    Cheatsheets are quickstart guides to using some of the most popular packages and features of Rstudio.

    Keywords: R

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    The Three Sisters of Agriculture: An Active Learning Activity on Symbiotic Nitrogen Fixation
    This active learning exercise introduces students to the plant microbiome and the contributions that bacteria make to plant growth and food production. The Three Sisters are an ancient indigenous...

    Keywords: SymbiosisPlant microbiomeNitrogen fixationNutritional content of foodElectron flowSociety impact of microorganisms

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    Painting turtles: an introduction to species distribution modeling in R
    This module uses R software to introduce students to the process of accessing databases and building species distribution models based on occurrence records.

    Keywords: RResources @ ESA - TIEEfmnDIGspecies distributionshabitat suitabilitycooperative learningjigsaw

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    Undergraduates Learn Evolution Through Teaching Kindergartners About Blind Mexican Cavefish
    The development and implementation of a scientific outreach activity comes with a number of challenges. A successful outreach event must match the sophistication of content to the audience, be...

    Keywords: Evolutionecologymorphologysensory biologycave biologycomparative biologyenvironmental differencesregressive lossstructure and function

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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...

    Keywords: epidemiologyresearchbioinformaticsgenomicspublic healthAntibiotic Resistant BacteriaSalmonellaDNA sequencingpathogenic bacteria

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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...

    Keywords: Speciationgenome evolutiongenetic variation

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    Working with Datasets in R swirl
    The goal of this lesson is to learn how to import datasets into R, understand variable types, make adjustments to variables, perform basic calculations, and begin data visualization. The exercise...

    Keywords: graphingRStudioclimate change datatidyverseWorking with datasets

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    2008-Ratneesh_Suri-Optimal harvesting strategies for fisheries-differential equations approach
    We develop and investigate the harvesting model in both deterministic and stochastic settings. We first employ the Expected Net Present Value approach and determine optimal harvesting policy using...

    Keywords: optimal controlsustainable yieldmaximum sustainable yieldharvestExpected Net Present Valuecalculus of variationsdynamic programmingmaximum economic yield

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    Digital Herbarium Lab with RStudio: Are shifting abundances of native species detectable over time?
    This 2- to 3-hour lab activity introduces sophomore-level students to digitized herbarium collections, R-coding, and potential reasons for shifting abundances in native and non-native plant species...

    Keywords: data analysistool:rstudionatural historyplant biologyinvasive plantsherbariumnative plantsdigitized natural history collectionsR code

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