Skip to Main Content
Powered by QUBES

Network for Integrating Bioinformatics into Life Sciences Education

Resources

Want to find additional resources? Browse resources on QUBES!
QUBES hosts not only the resources shown here, but many more created by the broader QUBES community.
Text Search:
Applied Filters
    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

    2488

    views

    2266

    downloads

    1

    comments

    0

    adaptations

    Colon Cancer: A Case of Genetic Bad Luck
    Case study developed for an introductory genetics class published in the National Center for Case Study Teaching in Science

    Keywords: bioinformaticsNCBINIBLSEBLASTPublished in National Center for Case Study Teaching in Sciencecolon cancerpedigreegenetic testingAPC

    362

    views

    71

    downloads

    0

    comments

    0

    adaptations

    Making toast: Using analogies to explore concepts in bioinformatics
    Module using analogies to introduce students to genomics

    Keywords: bioinformaticsgenomicsworkflowNIBLSECourseSourceanalogiesbioinformatics workflows

    1133

    views

    257

    downloads

    0

    comments

    0

    adaptations

    BSL-4: Authorized Personnel Only
    National Center for Case Study Teaching in Science resource on the 2014 Ebola epidemic. This resource is also included in the NIBLSE Learning Resource Collection

    Keywords: infectious diseaseexperimental designbioinformaticsEbolaNIBLSECase It!PCRBLASTmultiple sequence alignmentPublished in National Center for Case Study Teaching in Sciencepolymerase chain reactionfebrile illnessvirusELISAenzyme linked immunosorbent assayfilovirusAfrica

    1011

    views

    185

    downloads

    0

    comments

    0

    adaptations

    Murder by HIV? Undergraduate edition
    Bioinformatics case study focusing on phylogenetic tree interpretation, published in the National Center for Case Study Teaching in Science

    Keywords: case studyResources @ NSF - NCCSTSbioinformaticsNIBLSEHIVnucleotide sequencingphylogenetic treeviral life cyclesmutation ratesreverse transcriptase sequences

    566

    views

    112

    downloads

    0

    comments

    0

    adaptations

    Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE): Recent Activities
    Presentation on NIBLSE at the 2019 Great Lakes Bioinformatics Conference

    Keywords: bioinformaticsNIBLSEincubators

    1292

    views

    258

    downloads

    0

    comments

    0

    adaptations

    Infectious Chocolate Joy with a Side of Poissonian Statistics: An activity connecting life science students with subtle physics concepts
    Lesson on what it means for biological processes to be Poissonian, published in CourseSource

    Keywords: quantitative biologybioinformaticsmicrobiologyphysicsNIBLSEHIVCourseSourcemultiplicity of infectionPoisson Distribution

    1264

    views

    265

    downloads

    0

    comments

    0

    adaptations

    Inquiry-based hypothesis testing using phylogenetic trees in MEGA
    A key learning objective in biology is applying bioinformatics tools to test a real-life question. These inquiry-based modules have students assemble and align data, and construct simple...

    Keywords: phylogeneticsbioinformaticsFASTANCBIBLASTmultiple sequence alignmentsequence similarityCourseSourceZika virusMEGAalcohol metabolism

    933

    views

    591

    downloads

    0

    comments

    0

    adaptations

    A Critical Guide to the UniProtKB Flat-file Format
    This Critical Guide briefly presents the need for biological databases and for a standard format for storing and organising biological data.

    Keywords: NIBLSEuniprotGOBLETInstructorResources

    829

    views

    209

    downloads

    0

    comments

    0

    adaptations

    A Critical Guide to the PDB
    This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures.

    Keywords: NIBLSEGOBLETInstructorResources

    1076

    views

    280

    downloads

    0

    comments

    0

    adaptations

    Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching
    This lesson plan was created to teach RNAseq analysis as a part of GCAT-SEEK network. It is provided here, both in finished form and with the modifiable source code, to allow flexible adaptation to...

    Keywords: statisticsR programming languagebioinformaticsNIBLSERNAseqgene expressionCourseSourcecomputer programming

    1789

    views

    472

    downloads

    0

    comments

    0

    adaptations

    Sequence Similarity: A Quick Introduction to Bioconductor
    Following the Sequence Similarity exercises by Kleinschmit, et al., this tutorial will guide students in using the Bioconductor suite of R packages to likewise compute sequence similarity.

    Keywords: bioinformaticssequencingNIBLSEmultiple sequence alignmentsequence similarityBLOSUM scoring matrixBioconductor

    902

    views

    918

    downloads

    0

    comments

    0

    adaptations

    The Ames Test
    Introduction to the Ames Test, published as GSA Learning Resource

    Keywords: geneticsNIBLSEDNAames testassay

    1362

    views

    219

    downloads

    0

    comments

    0

    adaptations

    Introduction to UNIX command line
    A laboratory module for an upper-level undergraduate biology course in which students will be able to carry out simple tasks using the Unix command-line environment.

    Keywords: NIBLSEcommand lineUNIXsequence analysis

    1386

    views

    619

    downloads

    0

    comments

    0

    adaptations

    Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans
    In this lesson, we describe an easily adaptable lab module that can be used in existing undergraduate molecular biology lab courses to conduct authentic scientific research, published in CourseSource

    Keywords: molecular biologybioinformaticsNIBLSEgene regulationmicroRNAsgene expressionCourseSourcemiRNA

    1429

    views

    345

    downloads

    0

    comments

    0

    adaptations

    Finding Selection in All the Right Places
    Lab introducing students to evolutionary genetics using bioinformatics and biocuration, published as GSA Learning Resource

    Keywords: geneticsbioinformaticssequencingNIBLSE

    1151

    views

    288

    downloads

    0

    comments

    0

    adaptations

    Developing a phylogram from computational resources.
    This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

    Keywords: phylogeneticsbioinformaticssequencingFASTANCBINIBLSEalgorithmsBLASTmultiple sequence alignmentsequence similarityneighbor-joining distance matrixCourseSourcephylogrampercent identity matrix

    956

    views

    1957

    downloads

    0

    comments

    0

    adaptations

    Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses
    This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

    Keywords: phylogeneticsbioinformaticssequencingFASTANCBINIBLSEalgorithmsincubatorsBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixneighbor-joining distance matrixCourseSourcephylogramZika virus

    4434

    views

    789

    downloads

    1

    comments

    8

    adaptations

    Bioinformatics / Neuroinformatics
    This module is a computer-based introduction to bioinformatics resources.  This easy-to-adopt module weaves together several important bioinformatic tools so students can grasp how each is used in...

    Keywords: bioinformaticsNIBLSEImageJquantitative trait locusQTL

    1179

    views

    288

    downloads

    0

    comments

    0

    adaptations

    Introductory Video and worksheets on Module 1 and 2 on "Sequence Similarity: An inquiry based and under the hood..."
    The video walks the students to complete Module 1 and 2 on Sequence Similarly and Alignment adapted from Tapprich (2019) and Hudson Alpha that teaches these modules within the context of the...

    Keywords: bioinformaticssequencingFASTANCBINIBLSEalgorithmsBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixCourseSource

    1064

    views

    1090

    downloads

    0

    comments

    0

    adaptations