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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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    Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course
    Metagenomics is rapidly evolving due to advances in sequencing technologies and bioinformatics, but without proper training to interpret these datasets, student understanding remains limited. Aimed...

    Keywords: microbiome

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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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    DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College.
    Advances in high-throughput techniques have resulted in a rising demand for scientists with basic bioinformatics skills as well as workshops and curricula that teach students bioinformatics...

    Keywords: geneticsbioinformaticsDNAgenotypephenotypegenegene annotation

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    SIMIODE Spring 2024 Webinars - WikiModel
    WikiModel is cloud-based application and requires no installation and is run via a web-browser to facilitate rapid implementation. Equations are typed in as they appear in a textbook. ODEs are...

    Keywords: modelingSoftwaretoolapplicationWikiModelmodeling cycle

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    Climate-Induced Shifts in California Butterflies
    A module in which students generate and test hypotheses about butterfly species’ response to climate change in the Central Valley and Sierra Nevada Mountains of northern California using publicly...

    Keywords: linear regressionScatter Plotsclimate changephenologyhypothesis formulationmountainsCaliforniapublic dataCODAP

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    2016-Lofgren-EtAl-Equations of the End Teaching Mathematical Modeling Using the Zombie Apocalypse
    In this article, we explore several uses of zombie epidemics to make mathematical modeling and infectious disease epidemiology more accessible to public health professionals, students, and the...

    Keywords: simulationinfectious diseasediseaseepidemicZombieWhite Zed

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    2014-Enderling-Chaplain-Mathematical Modeling of Tumor Growth and Treatment
    Herein we describe fundamentals of mathematical modeling of tumor growth and tumor-host interactions, and summarize some of the seminal and most prominent approaches.

    Keywords: cancertumor modelingangiogenesistumor growthpatient care

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    1986-Istvan_Gyori-Connections between compartment systems pipes and integro-differential equations
    In this paper we give the mathematical description of models in which the mass transport between compartments requires a given definite time or transit times are distributed according to given...

    Keywords: physiologypipelinecompartmentbloodcirculationintegro-differential equation

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    GEA Introductory lesson on RNA-Seq
    This RNA-Seq lesson uses the CyVerse VICE Platform and Jupyter notebooks to examine the expression of the leptin gene in samples from a mouse experimental design evaluating diet (high-fat vs....

    Keywords: data sciencebioinformaticsGenome BrowserRNAseqhigh throughput sequencingmRNAAlignmentNCBI Sequence Read Archive

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    BEDE Network Data Science Skills Curriculum Map
    The Biological and Environmental Data Education (BEDE) Network has produced this data science skills curriculum map as a flexible tool to help instructors highlight data science skills that they...

    Keywords: quantitative skillsscientific literacyCurriculum developmentdata science skills trainingdata literacy skills

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    2014-XM-Huang-Ordinary Differential Equation Model and its Application in the Prediction Control of Population
    In this paper, we study two kinds of ordinary differential equation models, i.e., Malthus model and Logistic model, and discuss their applications in the prediction control of population.

    Keywords: population dynamicsLogistic modelMalthus ModelPopulation Prediction Control

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    5-010-MatrixExponential-TechniqueNarrative
    The matrix exponential is a powerful computational and conceptual tool for analyzing systems of linear, constant coefficient, ordinary differential equations (ODE's). This narrative offers a quick...

    Keywords: matrix esponentialPutzer's Algorithmdiagonalizationeigenvalueseigenvectors

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    Linear Models and Linear Mixed Effects in R: Tutorial 1
    The first of two tutorials that introduce you to linear and linear mixed models.

    Keywords: statisticsmathematicsRdata analysisconceptsstatsregressionmixed modelslinear modelsfixed effectsResources @ QUBES - Teaching & Reference

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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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    Analyzing interesting images motivates mathematics and statistics learning
    Presentation by Jeremy Wojdak made as part of the "Bringing Research Data to the Ecology Classroom: Opportunities, Barriers, and Next Steps” Session at the Ecological Society of America annual...

    Keywords: Ecological Society of America

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    Remote Sensing of Plants and Topography in R (Project EDDIE) for Advanced GIS class
    Students will explore different possible abiotic drivers of plant growth, defined as greenness and height. In the final step, students will analyze data from around the United States and consider...
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    Using Dotplots for Comparative Genomic Analysis
    In this activity, students are introduced to dotplots as a tool for analyzing phage genomic similarity.
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    2017-Alex_Honchar-Neural Networks For Solving Differential Equations
    In this post I want to show how I applied simple feed-forward NNs to different differential equations with increasing complexity: ODEs, second order ODEs, and, finally, PDEs.

    Keywords: neural networksCybenko theoremdiffusion equationfluid dynamics

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    2008-Ahmed_Mohameden-Solving initial-value second order ordinary differential equations on an Excel spreadsheet
    This paper presents a friendly method of solving initial-value second order differential equations (DEs) analytically on a MS Excel© workbook.

    Keywords: ExcelSpreadsheet

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    10-001-TilingHallway-ModelingScenario
    Students investigate difference equations through tiling hallways. They observe patterns in the tiling which lead to a difference equation. Solutions will be calculated by iteration. and the shift...

    Keywords: Geometryiterationtilingrecurrenceshift operatorpatternsclosed formanalytic solution

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