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    Modeling Strep Throat Detection, Infection, and Spread Using an SIR Model and the Vensim Simulation Software
    The overarching goal of this lesson is to provide students with an opportunity to gain experience making and using biological models. Biological modeling can be used to investigate complex,...

    Keywords: infectious diseasebiological modelingSIR model

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    2017-Bonin-EtAl-Mathematical modeling based on ordinary differential equations - promising approach to vaccinology
    As a proof of concept, we developed a model of the immune response to vaccination against the yellow fever. Our simulations have shown consistent results when compared with experimental data...

    Keywords: immune systemyellow fevercomputational immunologycomputational vaccinology

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    Discovering Cellular Respiration with Computational Modeling and Simulations
    Cellular respiration, a common topic among introductory and cellular biology curricula, is a complex biological process that exemplifies core biological concepts, including systems, pathways and...

    Keywords: Cellular MechanismsCellular RespirationFermentation

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    RNAseq data analysis using Galaxy
    This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.

    Keywords: LabbioinformaticsNCBImappingUndergraduateworkflowNIBLSEGalaxyRNAseqgene expressionAdvancedExtended ProjectArabidopsisC1. Role of bioinformaticsC2. Computational conceptsC3. Statistical conceptsC5. Data retrievalIncubated at NIBLSEdifferentially expressed genes

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    How do we do Bioinformatics?
    A description of the computational setup for “Foundations of Bioinformatics” (BGGN-213) See: http://thegrantlab.org/bggn213/

    Keywords: bioinformaticsgenomicsyoutubescreen cast

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    Data is the New Science - Modified and combined with Following the Data Module
    In this module, students will be introduced to some emerging biodiversity data resources. They will be asked to think critically about the strengths and utility of these data resources and apply...

    Keywords: data in the classroombiodiversity informaticsnatural history collection

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    Data is the New Science
    In this module, students will be introduced to some emerging biodiversity data resources. They will be asked to think critically about the strengths and utility of these data resources and apply...

    Keywords: data in the classroombiodiversity informaticsnatural history collection

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    Diseasebots
    This module explores the effects of host density on contact rates and transmission of pathogens or mutualist symbionts using a hands-on simulation, a computer agent-based model in NetLogo, and an...

    Keywords: NetLogoDisease ecologydensity dependenceSpreadsheethost-parasitemutualismOpen-inquiry group projectsmanipulative models (‘beanbag biology’)plotting

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    2003-Knorrenschild-Gross-Text Books on Mathematical Modeling in Biology
    Text Books on Mathematical Modeling in Biology Compiled from the Internet by Michael Knorrenschild,

    Keywords: biologyMathematical Biologytextbooktext

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    2016-Bonin-EtAl-Mathematical modeling based on ordinary differential equations-vaccinology
    We developed a model of the immune response to vaccination against the yellow fever. Our simulations have shown consistent results when compared with experimental data available in the literature.

    Keywords: Immunologyimmune systemAntigenvaccinologyyellow fever

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    What is a species? Using DNA barcodes to identify species and determine insect responses to global warming
    Combining ecology, molecular tools and physiology, students investigate insect adaptation to temperatures along tropical mountains. Students integrate species concepts, DNA barcoding and thermal...

    Keywords: global warmingbeetleBiological species conceptCephaloleiacrticial thermal maximumcryptic specieselevational gradientsthermal limitstropical insectsZingiberales

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    Implementing an online module about acoustic biodiversity monitoring in the tropics for use in an undergraduate course
    This implementation plan for an online module organizes activities for understanding physical concepts and biological considerations regarding acoustic monitoring, and provides a Spanish version of...

    Keywords: Biodiversityconservation biologyTropical ecologyacoustic monitoring

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    A 360˚ View of COVID-19
    In March 2020, institutions underwent a massive transition to distance learning as a result of the COVID-19 pandemic. With so little time to devise new materials to maximize learning in the new...

    Keywords: geneticsImmunologyBiochemistrybioinformaticsmolecular evolutionpublic healthvirusCOVID19

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    Moths and Frogs and E. coli, Oh My!: Agent-based Modeling of Evolutionary Systems
    In evolution classrooms, introducing and reinforcing the idea of genetic drift and random selection can be challenging, as can be reinforcing appropriate mental models of evolution. Agent-based...

    Keywords: modelingEvolutionecologyagent-based modelingGenetic Driftenvironmental scienceNatural Selectioncompetitive coevolutionsimulation modelingevolutionary reasoning

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    Investigating Cell Signaling with Gene Expression Datasets
    Modern molecular biology is a data- and computationally-intensive field with few instructional resources for introducing undergraduate students to the requisite skills and techniques for analyzing...

    Keywords: genomicstranscriptionsignaling

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    The ml4bio Workshop: Machine Learning Literacy for Biologists
    Presentation on machine learning literacy for biologists at the 2019 Great Lakes Bioinformatics Conference

    Keywords: bioinformaticsmachine learning

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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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    Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway
    Students are frequently overwhelmed by the complexity of metabolic pathways and they think they have "learned" the pathway when they have memorized the individual reactions.  This...

    Keywords: SelectionyeastMetabolismcysteinemediamethioninemutantPathwaysulfur

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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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    Tools: New tools for new science
    A collection of computational, modeling and data analysis tools developed at Microsoft Research Labs.

    Keywords: modelingdata analysisdatacomputational toolsdata visualization

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