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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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    REMNet Tutorial, R Part 1: Getting Started in R with Microbiome Data 5.3.19
    Video on the basics of R software from the Research Experiences in Microbiomes Network

    Keywords: VideoMicrobiology EducationR programming languagemicrobiomesresearch in the classroomREMNeturban microbiomes

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    Chapter 1: Introduction to R and RStudio
    Biostatistics Using R: A Laboratory Manual was created with the goals of providing biological content to lab sessions by using authentic research data and introducing R programming language....

    Keywords: biostatisticsR programming language

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    IPMpack: an R package for Integral Projection Models
    IPMpack is an R package (R Development Core Team 2013) that allows users to build and analyse Integral Projection Models.

    Keywords: RR-Forgeanimalbiostatisticscomparative analysisecologylongitudinal datamodel comparisonmodel estimationprojectionssurvivaltime seriestrajectoryIPMintegral projection modelsResources @ QUBES - Software

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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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    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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    REMNet Tutorial, Excel Part 6: Making Microbiome Column Charts 5.3.19
    Video on creating column charts in Excel from the Research Experiences in Microbiomes Network

    Keywords: ExcelVideoMicrobiology Educationmicrobiomesresearch in the classroomREMNeturban microbiomes

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    Home sweet home for warblers: Graphing and Analysis using R
    This resource expands on the Data Nugget "Trees and bushes, Home Sweet Home for Warblers". The analyses and graphing is done in R and there are questions that ask about the management implications.

    Keywords: graphingCommunity Ecologydata interpretationR software

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    Fitzhugh-Nagumo Model
    The FitzHugh–Nagumo model describes a prototype of an excitable system (e.g., a neuron).

    Keywords: differential equationsmathematical modeldifferential equation modelordinary differential equation modelneuroscienceexcitable

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    Web Popgen
    A Hardy-Weinberg simulation program.

    Keywords: Hardy-Weinbergpopulation geneticscomputer simulationsGenetic DriftmutationNatural Selection

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    2018-Van_Kinh Nguyen-Esteban_Hernandez-Vargas-Parameter estimation in mathematical models of viral infections using R
    Mathematical modeling has played a central role to understand mechanisms in different viral infectious diseases. In this approach, biological-based hypotheses are expressed via mathematical...

    Keywords: simulationdiseasevirusviral infection

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    Wenxiang 3.0
    Wenxiang diagrams illustrate protein helices as spirals on a plane and thus have the advantage over helical wheels of being planar graphs. Wenxiang 3.0 extends the original version by adding...
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    Wenxiang 3.0
    Wenxiang diagrams illustrate protein helices as spirals on a plane and thus have the advantage over helical wheels of being planar graphs. Wenxiang 3.0 extends the original version by adding...

    Keywords: bioinformaticsproteinsWenxiang

    556

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    148

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    Wenxiang 3.0
    Wenxiang diagrams illustrate protein helices as spirals on a plane and thus have the advantage over helical wheels of being planar graphs. Wenxiang 3.0 extends the original version by adding...

    Keywords: bioinformaticsproteinsWenxiang

    595

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    Responses to Climate Change in California Chipmunks: Move, Adapt, or Die
    A series of three modules using data from natural history museum collections to examine responses to climate change in multiple chipmunk species. Elevation and morphological data, beginner skills...

    Keywords: statisticsmodelingmodulemorphologysummary statisticsmodulesclimate datamuseumsclimate changeundergraduate educationR programming languageprogrammingelevationnatural history museumsmammalssmall mammals community dynamicsmuseum collectionsVertebrate Morphologyopen educational resourceR programming environment

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    Augmented Reality Metabolic Pathways (ARMET)
    The ARMET app is developed using Unity, 3D molecules obtained from Protein Data Bank and ChemSpider-chemical structure database, the usage data are stored into a database (MySQL) and are analyzed...

    Keywords: BiochemistryAugmented RealityMetabolic Pathways

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    Investigating Evidence for Climate Change (Project EDDIE) with CO2 and 13CO2 data: adapted for R
    This is an adaptation to work in R of Investigating Evidence for Climate Change (Project) by Hage, M. 2020. Students will investigate geologic and modern evidence for global temperature and...

    Keywords: climate changeGlobal Temperature Changeco2ice core datastable isotopesR software

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    Save the Bees, Ditch the Plow: A lesson exploring how squash bee abundance is affected by varying levels of soil disturbance.
    The purpose of this lesson is to explore the effects that three varying degrees of soil disturbance has on the squash bee abundance that is observed. We will learn about the importance of...

    Keywords: beesmutualismpollinatorscommunity-based conservationno till farmingreduced tillage

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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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    The Human Microbiome Biodiversity in Health and Disease
    The students will analyze the human gut and vaginal microbiomes in healthy and diseased states using diversity of bacteria as determined by 16SrRNA sequence.
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    Snapshot Serengeti Faculty Mentoring Network, Summer 2022
    The goal of our summer 2022 FMN was to develop a client-side interactive dashboard that allowed students to visualize and analyze data from the Snapshot Serengeti camera-trap research project.

    Keywords: Faculty Mentoring NetworkinteractiveSerengeti

    325

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