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  1. The replacement number

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar, Ying Xin

    In this module we introduce the important notion of the replacement number, which generalizes the basic reproductive number R0. We investigate how this number behaves near the start of an outbreak in models based on the uniform mixing assumption and in models that assume a contact network that is...

  2. Differential equation models of disease transmission

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender

    In this module we explore ODE models of disease transmission and compare some of their predictions with those of agent-based models. Parts of this material will be referenced in later modules.Level: Advanced undergraduate and graduate students of mathematics or biology.DownloadStudent copy (no...

  3. Exploring random regular graphs with IONTW

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar

    In this module we introduce and explore the structure of random regular graphs. Moreover, we compare the predictions of SIR-models on random regular contact networks with the predictions of corresponding models on Erdős-Rényi networks.Level: Undergraduate students of biology or...

  4. Exploring Erdős-Rényi random graphs with IONTW

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar

    In this module we explore in detail the distribution of the sizes of connected components of Erdős-Rényi random graphs and discover the reasons for the similarities and differences between disease transmission on Erdős-Rényi networks and complete graphs that were observed in...

  5. Exploring contact patterns between two subpopulations

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar

    In this module we introduce a construction of generic random graphs for a given degree sequence or degree distribution and explore whether mixing between hosts who belong to different subpopulations is assortative or disassortative.Level: Undergraduate students of biology or...

  6. A brief review of basic probability theory

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just

    The spread of infectious diseases is inherently a stochastic process and the materials posted at this web site heavily rely on probability theory. Here we review some basic concepts of probability theory for easy reference. The material is restricted to notions that are used in teaching...

  7. Network-based models of transmission of infectious diseases: a brief overview

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar

    The main purpose of this document is to give a brief but mathematically rigorous description of the network-based models of transmission of infectious diseases that are studied on this web site. Readers will be able to find a much more detailed development of this material in our book chapters...

  8. Exploring Disease Transmission on Networks with NetLogo

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Ying Xin

  9. Ecology and Epidemiology in R

    09 May 2015 | Teaching & Reference Material

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/837

  10. Pre-Health Students' Attitudes towards the Relative Importance of Biology and Statistics for their Preparation for Professional School

    07 May 2015 | Teaching & Reference Material | Contributor(s): Atteh Akoto, Michelle Garber-Talamo, Sam S Donovan, Alison N Hale

    This resource has been updated - find the current version here: https://qubeshub.org/publications/235During a recent review of the MCAT exam, the American Association of Medical Colleges (AAMC) surveyed medical school faculty to determine the relative importance of basic science and...

  11. Characterizing the Quantitative Biology Curricula from Institutions Across the United States

    29 Apr 2015 | Teaching & Reference Material | Contributor(s): Wendy Jo Levenson, Monika Norea Herbst, Sam S Donovan, Alison N Hale

    This resource has been updated - find the current version here: https://qubeshub.org/publications/236Due to the increasingly quantitative nature of the biological sciences, many schools now offer majors in mathematical biology. As this is a new major, there is no standard for how the program...

  12. A very basic tutorial for performing linear mixed effects analyses: Tutorial 2

    24 Apr 2015 | Teaching & Reference Material | Contributor(s): Bodo Winter

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/833This tutorial serves as a quick boot camp to jump-start your own analyses with linear mixed effects models. This text is different from other introductions by being decidedly...

  13. Linear models and linear mixed effects models in R: Tutorial 1

    24 Apr 2015 | Teaching & Reference Material | Contributor(s): Bodo Winter

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/832Linear models and linear mixed models are an impressively powerful and flexible tool for understanding the world. This tutorial is the first of two tutorials that introduce...

  14. QUBES How-to: Make a New Group

    21 Apr 2015 | Teaching & Reference Material | Contributor(s): Rina Matsuda, QUBES Team

    This resource has been updated, view the Knowledge Base article here: https://qubeshub.org/kb/groups/newgroup

  15. QUBES How-to: Change Notification Settings

    21 Apr 2015 | Teaching & Reference Material | Contributor(s): Rina Matsuda, QUBES Team

    This resource has been updated, view the Knowledge Base article here: https://qubeshub.org/kb/misc/how-do-i-change-my-notification-settings

  16. QUBES How-to: Post on a Forum

    21 Apr 2015 | Teaching & Reference Material | Contributor(s): Rina Matsuda, QUBES Team

    This resource has been updated, view the Knowledge Base article here: https://qubeshub.org/kb/forums/how-to-post-to-a-forum

  17. QUBES How-to: Dashboard

    21 Apr 2015 | Teaching & Reference Material | Contributor(s): Rina Matsuda, QUBES Team

    This resource has been updated, view the Knowledge Base article here: https://qubeshub.org/kb/registration/dashboard

  18. The Effect of Instructor Communication on Student Perceptions of Mathematics in Biology

    19 Apr 2015 | Teaching & Reference Material | Contributor(s): Sam S Donovan, Alison N Hale, Hayley Orndorf

    This resource has been updated - find the current version here: https://qubeshub.org/publications/237Student perceptions of the importance of mathematics in biology are context dependent. While students often view math as unnecessary to understanding biology, certain conditions can promote...

  19. T2R38 taste receptor polymorphisms underlie susceptibility to upper respiratory infection

    01 Apr 2015 | Teaching & Reference Material

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/846Innate and adaptive defense mechanisms protect the respiratory system from attack by microbes. Here, we present evidence that the bitter taste receptor T2R38 regulates the...

  20. AIM-UP! Reading scientific literature module

    28 Mar 2015 | Teaching & Reference Material | Contributor(s): Galen Rask

    This resource has been updated - find the current version here: https://qubeshub.org/publications/336Designed to span 4 one-hour lectures, this module focuses upon developing the skill of thorough and critical reading of scientific literature.