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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

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    Neochromosomes: Creating transcriptional units with yeast Golden Gate assembly
    This resource is a series of protocols using the yeast Golden Gate (yGG) method as developed by Neta Agmon and Leslie Mitchell in Jef Boeke’s lab to assemble a functional yeast gene with...
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    Intro videos and terminology for GMOs, Transcription, Translation
    Compiled resources around GMOs and protein production including vocabulary, animations, videos, and games

    Keywords: geneticsagricultureplantstranscriptiongenomesGMOtranslation

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    The p53 Gene and Cancer
    This tutorial describes the structure and function of the p53 protein, how its activity is regulated in cells, and how mutant versions of p53 can lead to cancer.

    Keywords: Resources @ HHMI - BioInteractiveBiochemistrymolecular biologymacromoleculesGenetic disease

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    Teaching Advanced Concepts in Regulation of the Lac Operon With Modeling and Simulation
    Success in biochemistry and other life science courses requires that students understand important biological concepts. One of these concepts is how gene regulation ensures that homeostasis is...

    Keywords: gene regulationinducible operonProkaryotic cellPhosphoenolpyruvate transferase system (PTS)

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    Using Synthetic Biology and pClone Red for Authentic Research on Promoter Function: Introductory Biology (identifying new promoters)
    Students often memorize the definition of a transcriptional promoter but fail to fully understand the critical role promoters play in gene expression. This laboratory lesson allows students to...

    Keywords: bacteriasynthetic biologygene regulationtranscriptionstudent researchcentral dogmacloningpromoterreporter gene/protein

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    2009-Peter-Howard-Modeling With ODE
    This is a set of class notes rich in examples and ideas for modeling. There is some MatLab code in support of some of the activities.

    Keywords: ratescompetitionpopulationepidemicpendulumcarbon datingreaction chemistrymechanicsplanetary motiondrag racingHamilton’s methodvariational method

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    2013-Alicia_Caldwell-Students Rise to the Challenge of Modeling Yeast Growth Despite Sour Hiccups from Imperfect Data
    This paper describes a lab in which students in an Applied Mathematics in Biology course observe the growth of Saccharomyces cerevisiae, a yeast strain, in differing sugar concentrations for use in...

    Keywords: Saccharomyces cerevisiaelogisticyeastdeathgrowthsugaralcohol

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    2019-Ekici_Plyley. Inquiry-Based_Modeling_of_Population_Dynamics_With_Logistic_Differential_and_Difference_Equations
    Inquiry-based learning activities on modeling and controlling the growth of locally relevant species, such as lionfish or sea turtles, are developed by the authors.

    Keywords: population dynamicslogisticInquiry-based modelingIBL

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    Investigating the Function of a Transport Protein: Where is ABCB6 Located in Human Cells?
    One of the challenges of teaching Cell Biology is helping students understand important research methods used to study cells.  The goal of understanding cell biology methods is especially...

    Keywords: ABC transporter familyDifferential centrifugationImmunoblottingImmunofluorescence assayProtein localizationPurifying organellesSDS-PAGE

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    2013-Clarke-Skirba-Rationale and resources for teaching the mathematical modeling of athletic training and performance
    It is advisable that the professionals involved learn the various tools available for designing effective training programs.

    Keywords: fitnessexercise physiologycritical power modelBanister impulse-response modelcoaching educationphysical fitnessperformance modeling

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    2015-H_Sayama-Intro to Modeling and Analysis of Complex Systems
    Introduces students to mathematical/computational modeling and analysis developed in the emerging interdisciplinary field of Complex Systems Science.

    Keywords: textbooktext

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    1988-EY_Rodin-N_Taber-Yeast Growth Modelling in a Laboratory
    Modeling simple growth with some missing data and doing linear regression for parameter estimation in closed form solution of differential equation model and data.

    Keywords: regressionyeastgrowth

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    Trout modeling example
    This is an open-ended modeling example using difference equations and Algebra II skills.

    Keywords: population biology

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    Modeling: A Primer - The crafty art of making, exploring, extending, transforming, tweaking, bending, disassembling, questioning, and breaking models
    Explore how to use, analyze, and criticize some important and historically influential models in biology in this text only module.

    Keywords: modelingsimulationmoduleResources @ BioQUESTtextbookmodulesmathematical modeling

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    A CURE-based approach to teaching genomics using mitochondrial genomes
    There is an abundance (currently over 1016 DNA bases) of publicly available genetic sequence data and a dearth of trained genomicists to process and interpret it, necessitating more trained...

    Keywords: proteinsMitochondrial GenomesNuclear GenomesrRNAtRNA

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    2011-Nguyen-Shi-Modeling the absorption circulation and metabolism of tirapazamine
    This apparently is a student project and it develops the kinetic model, uses Matlab for numerical solution, analytic solution and numerical solution.

    Keywords: absorptionMichaelis-MentenMetabolismdrug metabolismcirculation

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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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    Data from: Agent-based and Individual-based Modeling: A Practical Introduction, Chapter 5, Exercise 10 [Elevation]
    Supplemental data for ABM

    Keywords: elevationChapter 5exercise

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    Data from: Agent-based and Individual-based Modeling: A Practical Introduction, Chapter 5, Section 5.5 [Elevation]
    Elevation data input file for Section 5.5 (tab-separated plain text).

    Keywords: dataelevationChapter 5Section 5.5

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