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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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    BLAST-HGT PROJECT
    Genome Solver modules were combined to make one project for students using tools within NCBI BLAST to explore phylogenetics and horizontal gene transfer from phage to Chlamydia.
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    Lesson V - Phylogenetics
    Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson V is an introduction to Phylogenetics.

    Keywords: Bioinformatics EducationBioinformatics and Genomics

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    Teaching introductory bioinformatics with Jupyter notebook-based active learning
    Presentation on teaching introductory bioinformatics with Jupyter notebook-based active learning at the 2019 Great Lakes Bioinformatics Conference

    Keywords: biostatisticsstatistical analysisavian malariaSummer Workshop 2018

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    Expanding the pipeline: Engaging urban secondary school and college students in science and the environment
    This speed talk will describe three education projects that engage urban minority students in science and the environment.
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    Estimating Tree Heights: Right Triangle Trigonometry
    This module introduces basic trigonometry calculations in the context of understanding tree height calculations. It is intended for an introductory biology audience.

    Keywords: ecologyTrigonometryTrigonometric Functions

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    Avian Censys Analysis
    This Swirl course uses ecological data of bird counts and habitat variables to estimate inter-observer variability and the relationship of birds with habitat variables.

    Keywords: ecologyregressionaverageserror estimates

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    Seed Dispersal in Tropical Forests: Learning How Plants Move Around
    This module focuses on the dispersal of seeds from trees in fragmented tropical forests. Students use data from published studies to understand patterns of seed dispersal and apply these ideas to...

    Keywords: ecologyResources @ HHMI - BioInteractivecommunityplantsdiversityScientific Process

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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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    Dendroclimatology
    Dendroclimatologists can reconstruct climate records further into the past than written records, by examining tree rings. Students "reverse-engineer" this process by considering growth rates of a...

    Keywords: linear regressiongraphingdata visualizationstandardizationclimatetree ringsdendrochronology

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    3D FractaL-Tree
    3D FractaL-Tree allows scientists to collect data from actual specimens in the field or laboratory, insert these measurements into a spatially explicit L-system package, and then visually compare...

    Keywords: Resources @ ESTEEMfractalsL-systems

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    Outstanding Oaks: Quercus Phenology at NEON Sites
    This resource uses an app hosted on QUBES to visualize similarities and differences in Quercus phenology at three NEON sites in California, Florida, and Massachusetts.

    Keywords: ecologyphenology

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    Using DNA Subway to Analyze Sequence Relationships
    This is a bioinformatics exercise using the DNA Subway Blue Line, a user-friendly pipeline of bioinformatics tools, to analyze a collection of mosquito DNA bar-code sequences.

    Keywords: phylogeneticsNIBLSEDNA BarcodingDNA sequenceBLASTmultiple sequence alignmentC1. Role of bioinformaticsC2. Computational conceptsC4. Bioinformatics toolsC5. Data retrievalC8. Data typesIncubated at NIBLSE

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    What do trees know about Rain? Adapted for an online, non-majors botany course
    Minor modifications were made to this Data Nugget in order to use it in a fully online version of the introductory, non-majors botany course, Plants and People.
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    What Do Trees Know About Rain?
    The data nugget was introduced to a freshman General Biology lecture class as a culminating activity for the chapter entitled "Photosynthesis". Students worked independently and collaboratively...

    Keywords: General Biology

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    Biometeorology of Asthma in South Florida: From Statistical Analysis to Mathematical Modeling
    Part of the 2015 SMB Minisymposium: Topics in Biomathematics Education

    Keywords: data analysisdynamical systemsmathematical modelingsynchronizationasthmaimmune systemcomplex systemsfeedback loopsself-organized criticalitychaos

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    A BioGraphy of Life: How Graph Theory Makes Mathematics Recognizable, Relevant, and Research-Rich in Biology Education
    Presentation given at the 2106 SIAM Conference on Applied Mathematics Education on graph theory.

    Keywords: graph theory

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    Counting the Forest and the Trees: Quantitative Undergraduate Biology Education and Synthesis (QUBES) is a tool for Vision and Change
    Presentation focusing on how QUBES plans to improve learning opportunities for all students enrolled in undergraduate biology courses, presented at Botany 2015.

    Keywords: QUBEScommunityconferencedigital tools

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    Modification to What do Trees Know about the Rain
    Use of the tree ring data vs. precipitation to discuss how trees respond to drought

    Keywords: discussionslecture slidesgraphsgroup-ldcfmn

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    DNA Subway Learning Resources
    DNA Subway is a NIBLSE Recommended resource. This is a collection of learning resources associated with DNA Subway.

    Keywords: phylogeneticsIntroductoryLabbioinformaticsUndergraduateNIBLSEDNA BarcodingDNA sequenceBLASTmultiple sequence alignmentDNA SubwayInstructional SettingAudience LevelAdvancedActivity LengthExtended ProjectC1. Role of bioinformaticsC2. Computational conceptsC4. Bioinformatics toolsC5. Data retrievalC8. Data types

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