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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.

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    Working with spreadsheet-style data in Python with pandas and seaborn
    This 4-hour participatory live-coding workshop takes learners through the basics of programming in Python via the Jupyter Lab interface and culminates with exploration and visualization of...

    Keywords: datapythonopenSpreadsheetbicylepandasseabornmatplotlib

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    QUBES: Building a community to promote undergraduate quantitative biology education
    This was a poster session at the 2015 Ecological Society of America meeting in Baltimore, MD.

    Keywords: Ecological Society of America

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    Perspectives and practices in sharing data-centric adaptations in the biology classroom: How, why, when, and where are instructors sharing these high-impact pedagogies?
    Poster presented at the 2019 meeting of the National Association of Biology Teachers on barriers to fully utilizing the complete Open Education Resources lifecycle

    Keywords: data-centric teachingoer life cycle

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    Bates College DCS 105 Calling Bull: Data Literacy and Information Science Course Slides
    Slides that accompany the Course DCS 105 Calling Bull: Data Literacy and Information Science from Bates College

    Keywords: datamisinformationslidesCalling BullshitBates CollegeCourse Material

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    Modeling Crop Rotation with Discrete Mathematics
    The module develops discrete mathematics models that allow for creation of crop rotation schedules meeting a variety of needs.

    Keywords: modulesustainabilitydiscrete mathematicsagricultureResources @ DIMACSResources @ QUBES - Teaching & Referencescienceexperiment

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    2015-Cano-EtAl-Bringing partial differential equations to life for students
    This work describes how to use an authoring tool, Easy Java Simulations, to build interactive simulations using FreeFem++ (Hecht F 2012 J. Numer. Math. 20 251) as a PDE solver engine.

    Keywords: Java SimulationFreeFemauthoring toolsauthoring methodsphysical modellingclassroom teaching

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    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

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    Teaching Data Viz and Communication as an Undergraduate Biology Course: Assignments and Projects
    Teaching materials co-developed for a new upper-level undergraduate biology course to teach data exploration and communication without requiring previous coding experience.

    Keywords: data visualizationR programming languagedata literacycalling bulldata viztidy dataOur World in DataDear Data

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    NEON Data in the Classroom: Using the QUBES Platform and Faculty Mentoring Networks to Build, Adapt, and Publish Data­-Driven Teaching Resources
    The NEON FMN has been offered for three semesters with 37 faculty participating, resulted in a wide variety of new and adapted modules being publicly available.

    Keywords: NEON FMN

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    Community Conversation: OER for Diversity, Equity and Inclusion in STEM Classrooms
    Follow the link to the webinar video, "OER for Diversity, Equity and Inclusion in STEM Classrooms". In this conversation, bringing in Diversity, Equity, and Inclusion to the classroom was discussed...
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    STEM Inclusive Teaching Practices Webinar Series: Universal Design for Learning Recording
    Video recordings (with captions), transcript, and chat for the STEM Inclusive Teaching Practices Webinar Series: Universal Design for Learning.
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    Incubators: A community based model for improving the usability of bioinformatics learning resources
    Poster on Incubators, a NIBLSE and QUBES collaboration presented at Great Lakes Bioinformatics Conference - Chicago, IL

    Keywords: NIBLSEincubators

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    Understanding Gene Prediction Programs
    Introduces students to the key biological concepts underlying computational gene prediction. Outcomes include ability to analyze and evaluate output of gene prediction programs, and reflect on...

    Keywords: Genome annotationSEA-PHAGESgene predictiongenemarkcoding potentialcodon biassix frame translation

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    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

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    Avida-ED Lab Book
    Avida-ED activities, modified for the Argentina 2019 Avida-ED Workshop, presented at the 2019 BioQUEST & QUBES Summer Workshop

    Keywords: Evolutionavida-ed

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    Balancing Chemical Equations Using Matrix Algebra
    This Excel workbook introduces using matrix algebra to balance chemical reactions. The workbook allows the user to set up their own matrices for chemical reactions involving 2-7 elements.

    Keywords: chemical reactionsInverse matrix methodmatrix algebra

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    EvolSeq
    An Excel worksheet that simulates the molecular evolution of DNA sequences.

    Keywords: molecular evolutionDNA

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    Luria-Delbruck
    These two workbooks model the evolution of phage resistance in a bacterial population under two alternative hypotheses.

    Keywords: phageLuria-Delbruckresistance

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    Michaelis-Menten Enzyme Kinetics
    In this simulation, equations used in enzyme kinetics (Michaelis-Menten, Eadie-Hofstee, Dixon, and Lineweaver-Burk) are modeled under various conditions.

    Keywords: Michaelis-Mentenenzymesenzyme kinetics

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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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