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Small-world models
02 Jun 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender
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...
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BIO2010: Transforming Undergraduate Education for Future Research Biologists
25 May 2015 | Teaching & Reference Material | Contributor(s): Committee on Undergraduate Biology Education to Prepare Research Scientists for the 21st Century, Board on Life Sciences, Division on Earth and Life Studies, National Research Council
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...
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BIO2010: Transforming Undergraduate Education for Future Research Biologists
25 May 2015 | Teaching & Reference Material | Contributor(s): Committee on Undergraduate Biology Education to Prepare Research Scientists for the 21st Century, Board on Life Sciences, Division on Earth and Life Studies, National Research Council
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...
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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...
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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...
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BioRadiant
19 May 2015 | Software (On-site) | Contributor(s): Drew LaMar
Interactive statistics package using R and Shiny.
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Statistical Power for One-Sample t-Test
18 May 2015 | Software (On-site) | Contributor(s): Drew LaMar
Interactive visualization of statistical power for a one-sample t-test.
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R for biologists
18 May 2015 | Teaching & Reference Material | Contributor(s): Marco Martinez
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.
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R for biologists
18 May 2015 | Teaching & Reference Material | Contributor(s): Marco Martinez
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.
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R for biologists
18 May 2015 | Teaching & Reference Material | Contributor(s): Marco Martinez
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.
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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....
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The preferential attachment model
10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar, Ying Xin
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...
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Exploring distances with IONTW
10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar
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...
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The friendship paradox
10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar
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...
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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...
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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...
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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...
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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...
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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...
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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...