QUBES will have scheduled maintenance work beginning on Wednesday, June 26, 2024, 4pm ET/1pm PT. The platform will operate normally for most of the day, except for an extended outage period lasting no more than 4 hours. All running tool sessions will expire during the maintenance window. Please plan accordingly and we do apologize for any inconvenience. close

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-The European Bioinformatics Institute-BioModels Database
    BioModels Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references.

    Keywords: computational biologyBioModels Databasebio databaselife science experiments

    109

    views

    62

    downloads

    0

    comments

    0

    adaptations

    Developing hands-on activities linking plankton and computational thinking
    Poster on computational thinking as a method to help address complex problems, create systems, and understand behaviors presented at the 2018 QUBES/BioQUEST Summer Workshop

    Keywords: computational thinkingplanktonSummer Workshop 2018

    1374

    views

    262

    downloads

    0

    comments

    0

    adaptations

    2009-Eriksson- Estep-Hansho-Johnson-Computational Differential Equations
    Differential Equations and Advanced Computational Differential Equations, presents a unified approach to computational mathematical modeling using differential equations based on a principle of a...

    Keywords: Galerkin

    93

    views

    42

    downloads

    0

    comments

    0

    adaptations

    Cell Collective
    Session presentation on an easy-to-use software, that makes this computational modeling approach accessible to any student and instructor

    Keywords: computational modelSummer Workshop 2018

    1744

    views

    1629

    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

    1004

    views

    2072

    downloads

    0

    comments

    0

    adaptations

    2017-Bonin-EtAl-Mathematical modeling based on ordinary differential equations - promising approach to vaccinology
    As a proof of concept, we developed a model of the immune response to vaccination against the yellow fever. Our simulations have shown consistent results when compared with experimental data...

    Keywords: immune systemyellow fevercomputational immunologycomputational vaccinology

    107

    views

    38

    downloads

    0

    comments

    0

    adaptations

    2015-European_Bioinformatics_Institute-Bio-Models-Database
    Bio Models Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references. All models are...

    Keywords: biologydatabasebioinformaticsModelscomputational models

    116

    views

    59

    downloads

    0

    comments

    0

    adaptations

    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

    1104

    views

    461

    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

    4524

    views

    797

    downloads

    1

    comments

    8

    adaptations

    2013-Fathalla_Rihan-Delay Differential Equations in Biosciences - Parameter estimation and sensitivity analysis
    This is a review article to show that delay differential models have a richer mathematical framework (compared with models without memory or after-effects) and a better consistency with biological...

    Keywords: epidemiologysensitivityImmunologyphysiologyRK-methodstime-lags

    563

    views

    60

    downloads

    0

    comments

    0

    adaptations

    2012-Brian_Ingalls-Mathematical_Modelling_in_Systems_Biology
    This text provides an introduction to dynamic mathematical modeling of cellular processes. The emphasis is on using computational tools to investigate models of cellular phenomena.

    Keywords: biologygene regulatory networksModelsmetabolic networkssignal transduction pathwayselectrophysiology

    100

    views

    36

    downloads

    0

    comments

    0

    adaptations

    2016-Bonin-EtAl-Mathematical modeling based on ordinary differential equations-vaccinology
    We developed a model of the immune response to vaccination against the yellow fever. Our simulations have shown consistent results when compared with experimental data available in the literature.

    Keywords: Immunologyimmune systemAntigenvaccinologyyellow fever

    107

    views

    59

    downloads

    0

    comments

    0

    adaptations

    2015-H_Sayama-Intro to Modeling and Analysis of Complex Systems
    Introduces students to mathematical/computational modeling and analysis developed in the emerging interdisciplinary field of Complex Systems Science.

    Keywords: textbooktext

    98

    views

    41

    downloads

    0

    comments

    0

    adaptations

    Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes
    This lesson is a five-week series of laboratory activities designed to help students transition from applying lower order thinking skills to the central dogma to applying higher-order thinking skills.

    Keywords: bioinformaticsNIBLSEProtein StructureDNAmolecular modelinggenotypephenotypeCourseSourcecomputational modelingcentral dogmaplant leaf structure

    1306

    views

    290

    downloads

    0

    comments

    0

    adaptations

    2007-Bellomo-De_Angelis-Delitala-Lecture Notes on Mathematical Modelling in Applied Sciences
    The Lectures Notes correspond to the first part of the course devoted to modelling issues to show how the application of models to describe real world phenomena generates mathematical problems to...

    Keywords: spring massLegendre polynomialsintegro-differential equationskinetic theory

    81

    views

    35

    downloads

    0

    comments

    0

    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

    1218

    views

    289

    downloads

    0

    comments

    0

    adaptations

    Populus: Simulations of Population Biology
    Link to Populus Software

    Keywords: simulationpopulation growthpopulus

    2087

    views

    317

    downloads

    0

    comments

    0

    adaptations

    2017-Brandi-Garcia-Motivating engineering students to math classes - Practical experience teaching ODEs
    In this paper we propose an approach to teaching-learning process of mathematical concepts to engineering students with a motivational factor: a practical problem to be modeled in which students...

    Keywords: computational toolsteachingengineering studentspractical problem

    91

    views

    52

    downloads

    0

    comments

    0

    adaptations

    Discrete Modeling and Structures (Course Materials)
    These are the materials for DCS course offered at Bates College. This is a sampler of structures and ways they are used to model biological and social phenomena.

    Keywords: labsagent-based modelingoctavematlabDiscrete Difference Equationsmatrix modelscoursezombiesbiomath courseeconomicsdemonstrationin-class activitylab protocolproblem sethamlet

    1549

    views

    670

    downloads

    0

    comments

    0

    adaptations

    2012-Brian_Ingalls-Mathematical Modelling in Systems Biology An Introduction
    This is a comprehensive text with much biology background to motivate the mathematical modeling, exercises and answers, and many rich examples.

    Keywords: spatialsensitivity analysisgene regulatory networksstochasticbifurcationmetabolic networkselectrophysiologytransductionrate lawsbiochemical reactions

    359

    views

    78

    downloads

    0

    comments

    0

    adaptations

    Close

    Home

    Search