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    Aging and Circular RNAs
    A science FIT seminar presented to incoming freshmen at UNR

    Keywords: videosbioinformaticsRNAaginggenomicsyoutubecircular rna

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    2013-Antonin_Slavik-Mixing Problems with Many Tanks
    Discusses many tank configurations, circular, cascading, in a row, etc. and the attendant matrix representation of the linear mixing model of differential equations.

    Keywords: lineartankmixingcircularcascading

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    1-029-ConeToCubeFlow-ModelingScenario
    An inverted right circular cone with a hole at the bottom is suspended above an open-topped cube which also has a hole in the center of the bottom. The cone is filled with water and we model...

    Keywords: waterflowTorricelli's Lawconecube

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    Dynamic Programming
    In bioinformatics, dynamic programming is mainly used to align nucleotide and amino acid sequences, and to predict RNA and protein folding from primary sequence data.

    Keywords: RNAamino acid sequenceSequence alignmentdynamic programmingprotein folding

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    Module 4: Removal of Introns from pre-mRNA by Splicing
    In this module, students will learn to identify splice donor and acceptor sites that are best supported by RNA-Seq data, and use the canonical splice donor and splice acceptor sequences to identify...

    Keywords: geneticsdata visualizationmolecular biologygenomicsexonintronsplicingSimilarity searchesRNA Maturation

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    RNA-seq Analysis
    In this computer lab module, students learn how to process an RNA-seq data set to identify differentially expressed genes (DEGs). The samples for this data set were collected from yeast cells...

    Keywords: LabRNAsequencingUndergraduateNIBLSEincubatorsRNAseqInstructional SettingAudience LevelActivity LengthMore than 1 hourC4. Bioinformatics toolsC5. Data retrievalReviewed at NIBLSEdifferentially expressed genes

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    1-055-WaterFallingInCone-ModelingScenario
    We offer an opportunity to model the height of a falling body of water in a right circular cone (funnel) and to estimate an appropriate parameter based on data collected from a video of the...

    Keywords: Torricelli's Lawdischarge coefficientconecontraction coefficient

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    5-010-DNADegradation-ModelingScenario
    We ask students to use the system of first order linear differential equations given in a source paper and estimates of the data from laboratory procedures from a plot to estimate the parameters...

    Keywords: DNA\kinetisplasmaratpharmacokinetis

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    Genomics Lessons with GEA - RNA-Seq CURES
    Our BIOME Group worked towards developing a set of learning goals for faculty who plan to launch a CURE based on RNA-Seq data. We also developed a workflow for analysis of either prokaryotic or...
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    Building creatures with the central dogma of biology
    Activity that demonstrates how nucleotide changes can affect phenotypes

    Keywords: amino acidsnucleotidesRNADNAgenotypephenotypecentral dogma

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    Circle Train Problem TCM 2018_Hernandez.pdf - Google Drive
    In this math modeling lesson, students build mathematical models for the horizontal and vertical position of a train moving along a circular track. The math topics includes transformations of...

    Keywords: mathematical modelTrigonometryPrecalculusdata collectionLoggerProtransformation of functionsparametric equations

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    Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy
    Analyzing high-throughput DNA sequence data is a fundamental skill in modern biology. However, real and perceived barriers such as massive file sizes, substantial computational requirements, and...

    Keywords: bioinformaticsDNA sequenceRNAseqgene expression

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    Long-read Sequencing Technology
    This 50 minute lecture on long-read sequencing technology covers the following items: 1) Review of RNA-Seq Short-read Sequencing, 2) Overview and benefits of Long-read Sequencing, 3) Oxford...

    Keywords: sequencingDNA sequenceRNA sequencingNanoporepacbiopacific biosciences

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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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    Module 3: Transcription, Part II: What Happens to the Initial Transcript Made by RNA pol II?
    This module teaches about the three key steps that are involved in converting the pre-mRNA into a mature mRNA: 1) The addition of a 5’ cap, 2) The addition of a 3’ poly(A) tail, 3) The removal of...

    Keywords: geneticsmolecular biologyGenome BrowsergenomicssplicingmRNAcDNA5' Cap3' Poly(A) TailRNA Maturation

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    Making bioinformatics tools classroom-friendly
    Poster on using Cyverse resources to make classroom that make using bioinformatics in the classroom a more manageable experience presented at the 2020 BIOME Institute: Cultivating Scientific Curiosity

    Keywords: bioinformaticsJupyterJupyter notebookBLASTCyVerseRNA sequencing

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    2014-Brun-EtAl-An introduction to the mechanics of the lasso
    Here, we study the mechanics of the simplest rope trick, the Flat Loop, in which the rope is driven by the steady circular motion of the roper’s hand in a horizontal plane.

    Keywords: bifurcationmotionlassorod modelrodeo

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    1-014-DrainingContainers
    Given two rectangular circular cylinders of water with the same volume, but different radii, with a small bore hole of same radius on the center of the bottom through which water exits the...

    Keywords: containerstankflowTorricelli's Lawdrainingfixed volume

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    1-120-CircularRollerCoaster-ModelingScenario
    Students study the dynamics of a circular roller coaster and work out the equations of motion in the ideal case as well as considering the interesting complication of including kinetic friction....

    Keywords: population dynamicsenergyFluid Mechanicsmfrictionroller coasterintegration by8 parts

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    3-080-PendulumModeling-ModelingScenario
    We lead students through building model for several pendulum configurations in motion and ask students to compare results.

    Keywords: pendulumperiodlinearization

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