You are here: Home / Resources / Browse Resources

Open. Adaptable. Free.

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.

Text Search:
Applied Filters
    2015-Boggess-EtAl-Mathematical Modeling in Ecology - Simulating the Reintroduction of the Extinct Passenger Pigeon
    To determine under which conditions a Passenger Pigeon could survive a reintroduction into a natural habitat, we used two types of models.

    Keywords: simulationagent-based modelingallee_effectPassenger Pigeonsforest envirnomentHolling Type III functional responseBio-energeticstree distributions

    163

    views

    83

    downloads

    0

    comments

    0

    adaptations

    2007-Ramsay-Hooker-Campbell-Cao-Parameter estimation for differential equations-a generalized smoothing approach
    We propose a new method for estimating parameters in models that are defined by a system of non-linear differential equations.

    Keywords: estimating equationfunctional data analysisGauss–Newton methodparameter cascadeprofiled estimationdynamic system

    118

    views

    41

    downloads

    0

    comments

    0

    adaptations

    The Science Behind the ACTN3 Polymorphism
    A common polymorphism in the alpha-actinin-3 (ACTN3) gene results in the lack of ACTN3 protein expression in fast twitch muscle fibers in ~16% of the human population (1). This genetic change has...

    Keywords: protein structure and functionhuman genetic variationskeletal muscle physiology

    1372

    views

    191

    downloads

    0

    comments

    0

    adaptations

    Learning Journal Assignment on Biofilms
    This is a learning journal assignment with constructive response questions on Biofilms which undergraduate students can complete with aid of reading a research article and listening to a podcast.

    Keywords: educationPodcastmicrobiologygenomicsUndergraduateAnalysisBioflimsLearning Journal Assignmet

    327

    views

    56

    downloads

    0

    comments

    0

    adaptations

    Pre-lesson: Introduction to BLAST
    Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.

    Keywords: Bioinformatics EducationBioinformatics and Genomics

    969

    views

    494

    downloads

    0

    comments

    0

    adaptations

    Pre-lesson: Introduction to BLAST
    Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.

    Keywords: Bioinformatics EducationBioinformatics and Genomics

    770

    views

    309

    downloads

    0

    comments

    1

    adaptations

    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...
    1616

    views

    838

    downloads

    0

    comments

    0

    adaptations

    Ethics in Synthetic Biology
    This collection of five activities provide students with an introduction to thinking about ethical concerns in human genome synthesis, gene editing, metabolic engineering, and synthetic genomes.

    Keywords: biostatisticsstatistical analysisavian malariaSummer Workshop 2018

    1078

    views

    232

    downloads

    0

    comments

    0

    adaptations

    Pre-lesson: Introduction to BLAST
    Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.

    Keywords: Bioinformatics EducationBioinformatics and Genomics

    1281

    views

    1531

    downloads

    0

    comments

    1

    adaptations

    Module 1: Introduction to the Genome Browser: What is a Gene?
    This lesson introduces the University of California Santa Cruz genome browser to students, walking them through some of the key features so that it can be used for analysis of gene structure.

    Keywords: geneticsbioinformaticsGenome BrowserSimilarity searchesExonsIntronsEvidence TrackStart CodonStop Codon

    1279

    views

    2100

    downloads

    0

    comments

    0

    adaptations

    BLAST Exercises for Analyzing Cloning Results
    Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. These activities have modified Lesson 1: Introduction to Genome...

    Keywords: Bioinformatics EducationBioinformatics and Genomics

    1239

    views

    384

    downloads

    0

    comments

    0

    adaptations

    Databases: A Study of Influenza
    This lesson introduces the student to the Influenza Research Database. Students will select Influenza genome sequences to see how they are related. Students tests hypotheses about evolutionary...

    Keywords: Bioinformatics EducationBioinformatics and Genomicsmolecular evolutionInfluenza

    1722

    views

    575

    downloads

    0

    comments

    0

    adaptations

    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

    1678

    views

    2252

    downloads

    0

    comments

    2

    adaptations

    Should we synthesize a human genome?
    Two articles introducing the Human Genome Project-Write and asking questions about the ethics of the project.

    Keywords: biostatisticsstatistical analysisavian malariaSummer Workshop 2018

    1272

    views

    717

    downloads

    0

    comments

    0

    adaptations

    Hands-On, Hands-Off: The Community College Genomics (ComGen) Course-Based Undergraduate Research Experience
    Science is a process of discovery where failure is inherent and iteration is necessary, yet instructors often teach the scientific process as if it is a controlled, highly supervised, confirmatory...

    Keywords: geneticssequencingDNAbacterium

    1437

    views

    178

    downloads

    0

    comments

    0

    adaptations

    A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!
    This resource is a fun computer-based intro to command line programming. The activity takes FASTQ NGS data files and runs a fun program called FASTQE.

    Keywords: data sciencebioinformaticsnext generation sequencingquality controlFASTQgenomicsprogrammingNIBLSElinuxmicrobiomeIllumina sequencingcommand lineFASTQEFASTPNGS analysisterminalMacemojiPhred scoreTrimmingshort read

    2705

    views

    2378

    downloads

    1

    comments

    0

    adaptations

    A Hands-on Introduction to Hidden Markov Models
    A lesson in which students will understand the basic structure of an HMM, the types of data used in ab initio gene prediction, and its consequent limitations.

    Keywords: Markov modelbioinformaticsgenomicsNIBLSEtranscriptionCourseSourceexonintronsplicing

    1414

    views

    361

    downloads

    0

    comments

    0

    adaptations

    2016-Wilkie-EtAl-Using ODEs to Explore Cancer-Immune Dynamics and Tumor Dormancy
    Here we present a general method using ordinary differential equations (ODEs) to model and analyze cancer-immune interactions, and in particular, immune-induced tumor dormancy.

    Keywords: cancertumor-inhibiting cytotoxic actiontumor-promoting inflammationimmune-induced tumor dormancytumor growth dynamics

    156

    views

    50

    downloads

    0

    comments

    0

    adaptations

    1-054-GrowthInFarmland-ModelingScenario
    An enriching project developing a model from data with missing temporal information is described. Students fit functions to the data that leads to the creation of a differential equations model,...

    Keywords: fittingfarmfarmland

    243

    views

    215

    downloads

    0

    comments

    0

    adaptations

    You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”
    With limited time available for laboratory activities, introductory science courses for non-science majors typically use the laboratory period to reinforce material that was previously presented...

    Keywords: bacteriamicrobiomeBLASTmicrobesDNA replicationPolymerase chain reaction (PCR)

    2269

    views

    281

    downloads

    0

    comments

    0

    adaptations

    Close

    Home

    Search