Support

Support Options

  • Knowledge Base

    Find information on common questions and issues.

  • Support Messages

    Check on the status of your correspondences with members of the QUBES team.

Contact Us

About you
About the problem

Resources: All

Find a resource
  1. presentation x
  2. referencematerial x
  3. teachingmaterial x
  1. Avida-ED User Manual

    07 Jun 2015 | Teaching & Reference Material

    Basic User manual to use Avida-ED

  2. Agent-based and Individual-based Modeling: A Practical Introduction

    03 Jun 2015 | Teaching & Reference Material

    From the authors website:  "We designed this book to fill the need for an introductory text on agent-based modeling for scientists, for use both in university courses (graduate or upper level undergraduate) and by people teaching themselves. The book is not specific to any particular...

  3. HHMI-AAMC Scientific Foundations for Future Physicians report

    03 Jun 2015 | Teaching & Reference Material

    The AAMC and HHMI convened a group of scientists, physicians, and science educators from small colleges, large universities, and medical schools around the United States to determine the most important scientific competencies required of students graduating from college prior to matriculating...

  4. A Quick Guide to Teaching R Programming to Computational Biology Students

    03 Jun 2015 | Teaching & Reference Material

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/838An introduction from an experienced educator in teaching R to computational biology graduate students. Contains information that is relevant for the undergraduate classroom...

  5. Exploring generic scale-free networks

    02 Jun 2015 | Teaching & Reference Material

    This module is a companion module to Module [[Resource(384)]]. Here we study in more detail networks that are generic for a given network size and a given exponent of a power-law degree distribution. We explore predicted structural properties of such networks both mathematically and with...

  6. Clustering coefficients

    02 Jun 2015 | Teaching & Reference Material

    In this module we introduce several definitions of so-called clustering coefficients. A motivating example shows how these characteristics of the contact network may influence the spread of an infectious disease. In later sections we explore, both with the help of IONTW and theoretically,...

  7. Small-world models

    02 Jun 2015 | Teaching & Reference Material

    Small-world networks are classes of networks that have both the small-world property and exhibit strong clustering. Two constructions of such networks are implemented in IONTW. Here we study, both theoretically and with simulation experiments, the structure of these networks and how it influences...

  8. BIO2010: Transforming Undergraduate Education for Future Research Biologists

    25 May 2015 | Teaching & Reference Material

    Biological sciences have been revolutionized, not only in the way research is conducted -- with the introduction of techniques such as recombinant DNA and digital technology -- but also in how research findings are communicated among professionals and to the public. Yet, the undergraduate...

  9. Vision and Change in Undergraduate Biology Education: A Call to Action

    25 May 2015 | Teaching & Reference Material

    This is the final report of a national conference organized by the American Association for the Advancement of Science with support from the National Science Foundation in an effort to show how the undergraduate biology education system needs to be improved: "Given the radical changes in the...

  10. R for biologists

    18 May 2015 | Teaching & Reference Material

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/815An introductory guide to data analysis in R for life sciences researchers.

  11. ModelSim Population Biology Unit

    18 May 2015 | Teaching & Reference Material | Contributor(s): David Donoho

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/902This resource provides rich student modeling activities and materials, teacher resources, and much more, in the realm of agent based models applied to population biology....

  12. ModelSim Population Biology Unit

    18 May 2015 | Teaching & Reference Material

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/902This resource provides rich student modeling activities and materials, teacher resources, and much more, in the realm of agent based models applied to population biology....

  13. The preferential attachment model

    10 May 2015 | Teaching & Reference Material

    Many empirically studied networks have approximately so-called power-law or scale-free degree distributions. In Section 1 we formally define such distributions and explore some of their properties. We also introduce and briefly compare two methods for constructing random...

  14. Exploring distances with IONTW

    10 May 2015 | Teaching & Reference Material

    Section 1 is purely conceptual and invites readers to critically evaluate popular claims based on Stanley Milgram's famous experiment that gave birth to the phrases small-world property and six degrees of separation. In Section 2 we use IONTW to explore distances between nodes in several...

  15. The friendship paradox

    10 May 2015 | Teaching & Reference Material

    In this module we introduce the so-called friendship paradox and illustrate how it affects disease transmission on networks that exhibit this phenomenon.You also need to download the input file degreesFP.txt that will be used in this module.Level: Advanced undergraduate and graduate...

  16. The replacement number

    10 May 2015 | Teaching & Reference Material

    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...

  17. Differential equation models of disease transmission

    10 May 2015 | Teaching & Reference Material

    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...

  18. Exploring random regular graphs with IONTW

    10 May 2015 | Teaching & Reference Material

    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...

  19. Exploring Erdős-Rényi random graphs with IONTW

    10 May 2015 | Teaching & Reference Material

    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...

  20. Exploring contact patterns between two subpopulations

    10 May 2015 | Teaching & Reference Material

    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...