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Tags: Resources @ QUBES - Software

All Categories (1-20 of 43)

  1. Predator-prey models as XPP files

    12 Nov 2018 | | Contributor(s):: Eli E Goldwyn

    These are the .ode files that XPP takes as input.  lv.ode is the Lotka-Volterra predator-prey model rm.ode is the Rosenzweig-MacArthur model rm3.ode is the Rosnezweig-MacArthur model but with predation following a Holling Type III functional response. The file rm.ode is...

  2. Avida-ED

    25 Oct 2018 | Teaching Materials | Contributor(s):

    By Robert T Pennock1, Diane Blackwood1

    Michigan State University

    Avida-ED is an award-winning educational application developed at Michigan State University for undergraduate biology courses to help students learn about evolution and scientific method.

    https://qubeshub.org/qubesresources/publications/874/?v=1

  3. Outstanding Oaks: Quercus phenology at NEON sites

    09 Oct 2018 | | Contributor(s):: Jackie Matthes

    This app visualizes data from the National Ecological Observatory Network (NEON) observations of oak phenology at three different sites.

  4. IPMpack: an R package for Integral Projection Models

    11 Sep 2018 | Teaching Materials | Contributor(s):

    By C. Jessica E. Metcalf1, Sean M. McMahon2, Roberto Salguero-Gómez3, Eelke Jongejans4, Cory Merow5

    1. University of Oxford 2. Smithsonian Tropical Research Institute 3. University of Queensland 4. Radbound University Nijmegen 5. STRI and University of Connecticut

    IPMpack is an R package (R Development Core Team 2013) that allows users to build and analyse Integral Projection Models.

    https://qubeshub.org/qubesresources/publications/779/?v=1

  5. Gene Machine: The Lac Operon

    08 Sep 2018 |

    Explore the effects of mutations within the lac operon by adding or removing genes from the DNA.

  6. Jupyter Lab

    13 Jul 2018 | | Contributor(s):: Erich Huebner

    An extensible environment for interactive and reproducible computing, based on the Jupyter Notebook and Architecture.

  7. Cultivating Your Growth Mindset

    22 Jun 2018 | | Contributor(s):: Kika Tuff, Jeremy M Wojdak, Arietta Fleming-Davies

    Learn what a growth mindset is and how it improves learning

  8. Investigating Trade-offs among Mammal Traits

    07 Jun 2018 | | Contributor(s):: Jackie Matthes

    This app draws on a large species-level dataset with metabolic, life history, and ecological traits of most living and recently extinct mammal species. Users can select and plot traits, fit linear models to the data, and query displayed datapoints.

  9. Modeling the Mechanisms of Evolution

    25 May 2018 | | Contributor(s):: Jackie Matthes

    Simulate population-level mechanisms of evolution: genetic drift, gene flow, and natural selection.

  10. R Shiny App Example

    09 May 2018 | | Contributor(s):: Drew LaMar

    This is a simple example used to demonstrate what is needed to host your R Shiny app on QUBESHub.

  11. Avida-ED

    06 Oct 2017 | | Contributor(s):: Robert T Pennock, Diane Blackwood

         This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/874Avida-ED is an award-winning educational application developed at Michigan State University...

  12. Radiant

    16 Sep 2015 |

    Business analytics using R and Shiny.

  13. Serenity

    25 Jun 2017 | | Contributor(s):: Drew LaMar

    A platform-independent browser-based interface to data science tools for the classroom.

  14. Web Popgen

    11 Jun 2017 | | Contributor(s):: Bob Sheehy

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/842A Hardy-Weinberg based population genetics simulator. This program assumes a single gene and two alleles. Simulation of allele frequency changes similar to...

  15. Jupyter Notebook

    05 May 2017 | | Contributor(s):: Martin Hunt

    Starts the Jupyter notebook server in your "notebooks" directory in your home directory.

  16. Genetic Drift Simulation - NetLogo

    22 Jun 2016 | | Contributor(s):: Tony Weisstein

    This model simulates genetic drift in a population.  The user can control the population size, whether the population is subdivided into separate local populations, and the amount of gene flow (if any) between local populations.  Phenotype frequency in each subpopulation is plotted as a...

  17. Wood Density

    15 Oct 2015 |

    Wood density shiny app

  18. GENI-ACT

    24 Jan 2016 |

    GENI-ACT allows collaborative genome annotation. Researchers or students can collectively suggest changes to an existing genome with supporting evidence. Changes can be ported back to genbank by exporting to a sequin file format. GENI-ACT also has ported the education components from IMG-ACT....

  19. OpenRefine

    18 Jan 2016 |

    OpenRefine (formerly Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.

  20. DFIELD

    19 Oct 2015 |

    DFIELD is an interactive tool that graphs a direction field for a given differential equation.

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