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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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    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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    The Molecular CaseNet Pipeline for Authoring, Piloting, and Evaluating Molecular Case Studies
    This poster provides an overview of the pipeline for authoring, piloting, and reviewing molecular case studies for publication in Molecular CaseNet.

    Keywords: resources @ Molecular CaseNet

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    Turning ecological research into engaging online modules for undergraduates through Gala/OCELOTS
    Learn how to create and implement online modules in tropical ecology for undergraduates. In an NSF-funded network, researchers and specialists in 4DEE, pedagogy, interactive data tools, and media...

    Keywords: tropical biologyOCELOTSLDC2023

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    Students Authoring Molecular Case Studies
    Poster on using case studies to help students develop their skills in reading primary literature and identifying authentic scientific problems by authoring their own case studies. Presented at the...

    Keywords: case studiesProtein StructureProtein Data BankMolecular Case Study2021 BIOME

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    BioMolViz - Development of an Inclusive Community for the Instruction of Visualizing Biomolecules (RCN-Introduction)
    BioMolViz is a community dedicated to advancing biomolecular visualization education. We provide training, teaching tools and validated visual literacy assessments. The BioMolViz Library—our online...

    Keywords: RCN-UBE Introduction

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    Use of PeerWise - an open digital question authoring tool
    Session on PeerWise presented at BioQUEST Workshop 2018

    Keywords: Summer Workshop 2018

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    Central Dogma, Dictionaries, and Functions: Using Programming Concepts to Simulate Biological Processes
    Technologies like next-generation sequencing, proteomics, and high-throughput phenotyping have transformed the way we do biology. There is a continued need for scientists with computational skills...

    Keywords: computationpythonJupyter notebookFunctionscentral dogmaDictionaries

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    Tools: New tools for new science
    A collection of computational, modeling and data analysis tools developed at Microsoft Research Labs.

    Keywords: modelingdata analysisdatacomputational toolsdata visualization

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    Phage Comparative Genomics Lab Manual
    A lab manual containing detailed instructions for several bioinformatics tools (dot plots, Phamerator maps, phylogenetic trees, and gene content similarity), all of which enable students to perform...

    Keywords: phageCUREcourse-based research experiences (CUREs)Comparative genomicsSEA-PHAGES

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    A Student's Guide to Tropical Marine Biology
    A Student's Guide to Tropical Marine Biology was curated and written entirely by students, and mostly edited by students at Keene State College that were enrolled in the course taught by Dr. Karen...

    Keywords: Student-Created

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    Serenity now! Keep calm and do science with real data in the classroom
    Session presented at NABT 2018 in San Diego, CA

    Keywords: NABTdata scienceeducational technologytool:serenitydata acumendata life cycle

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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

    1237

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    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

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    Learn tropical biodiversity through integration of artificial intelligence, data science, leadership roles, google tools and HHMI-Biointeractive tools. Implications for Tropical Medicine.
    Scientific skills, context & literacy, leadership roles, data science, data tools, simulations and artificial intelligence are important skills to be included in the course curriculum. Integrating...

    Keywords: ecologybiologydata scienceBiodiversityUndergraduateGraduate studentsgoogle toolsinstructor guidetropical medicineartficial intelligencehhmi toolsleadership roles

    551

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    Hidden Markov Model
    Hidden Markov models are a set of mathematical tools that can be used to draw inferences about genomic and evolutionary processes.

    Keywords: hidden markov models

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    AI Tools in Pedagogy
    Overview of ideas to discuss when it comes to usage of artificial intelligence in pedagogy

    Keywords: Artificial Intelligence

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    Biostatistical Tools
    This Excel collection of workbooks has tools for: 1. Linear regression through the origin 2. Linear regression not through the origin 3. Polynomial fit 4. A simple chi-square analysis to test...

    Keywords: linear regressionchi-square analysisHardy-Weinberg equilibriumpolynomial regression

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    Sequence Similarity: Introducing Biological Databases to Community College Biology Students
    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

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    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

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    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

    4829

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