3D FractaL-Tree

24 Aug 2015 | Teaching & Reference Material | Contributor(s): John R Jungck, Jennifer A Spangenberg, Noppadon Khiripet, Rawin Viruchpinta, Jutarat Maneewattanapluk

This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/775Artistid Lindemayer (1975, 1989, 1990) invented a mathematics based on graph grammar rewriting systems to describe iteratively branching structures; these were named in...

50 years of Data Science

23 Feb 2016 | Teaching & Reference Material | Contributor(s): David Donoho

This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/912More than 50 years ago, John Tukey called for a reformation of academic statistics. In ‘The Future of Data Analysis’, he pointed to the existence of an as-yet...

A BioGraphy of Life: How Graph Theory Makes Mathematics Recognizable, Relevant, and Research-Rich in Biology Education

11 Oct 2016 | Teaching & Reference Material | Contributor(s): John R Jungck

This resource has been updated - find the current version here: https://qubeshub.org/publications/241Biologists use graphs extensively in ecology, evolution, genetics, developmental biology, and biochemistry: phylogenetic trees, food webs, pedigrees, genetic networks, metabolic pathways,...

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...

A collaborative approach to quantitative biology course reform: It's better than doing it all by yourself

19 Jul 2015 | Teaching & Reference Material | Contributor(s): Jeremy M Wojdak

This resource has been updated - find the current version here: https://qubeshub.org/publications/233This is the abstract of an oral presentation given at the Society for Mathematical Biology Annual Meeting in Atlanta, GA in 2015. "Faculty often experience two distinct problems as...

A Framework for Modeling to Encourage Interdisciplinary Conversations

11 Oct 2016 | Teaching & Reference Material | Contributor(s): Carrie Diaz Eaton

This resource has been updated - find the current version here: https://qubeshub.org/publications/209Here we present a framework for thinking about what models and modeling are, particularly to other disciplines. We encourage that differing disciplinary approaches are seen as part of a...

A Framework for Teaching Modeling to Biologists

10 Oct 2016 | Teaching & Reference Material | Contributor(s): Drew LaMar

This resource has been updated - find the current version here: https://qubeshub.org/publications/210What are the modeling skills and metacognitive strategies of importance for the life sciences? In this talk, we describe a teaching and learning framework around modeling...

A Growing Concern: Sustaining Soil Resources through Local Decision Making

24 Aug 2015 | Teaching & Reference Material | Contributor(s): Sarah Fortner, Martha Murphy, Hannah Scherer

This resource has been updated - find the current version here: https://qubeshub.org/publications/291This module addresses agricultural productivity by providing students with the opportunity to examine the differences between intensively managed agricultural landscapes (e.g. grazelands,...

A Laboratory Class Exploring Microbial Diversity and Evolution Using Online Databases, the Biology Workbench, and Phylogenetics Software

29 Sep 2015 | Teaching & Reference Material | Contributor(s): Sarah Boomer, Kelly Shipley, Bryan Dutton, Daniel Lodge

Students assemble and align bacterial datasets using DNA information downloaded from the National Center for Biotechnology Information website and Biology Workbench.  Specifically, they compare unknown original DNA sequences (from, in our case, hot spring communities) to a backbone of...

A New Hub for QUBES based on the HUBzero Platform

26 Jul 2015 | Teaching & Reference Material | Contributor(s): Michael McLennan

This resource has been updated - find the current version here: https://qubeshub.org/publications/248The Quantitative Undergraduate Biology Education and Synthesis (QUBES) Consortium has a mission to connect educators across biology and mathematics with each other and with the latest...

A Quick Guide to Teaching R Programming to Computational Biology Students

03 Jun 2015 | Teaching & Reference Material | Contributor(s): Stephen Eglen

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...

A quick tour of IONTW

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

In this module we guide you through some of the capabilities of IONTW. Highlights include the types of networks supported, setting up various types of models of disease transmission, observing the resulting dynamics, and collecting statistics on the outcomes. Along the way, the module also...

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...

A Walk Through the Woods

09 Jul 2015 | Teaching & Reference Material | Contributor(s): Jerome Chave, David Coomes, Steven Jansen, Simon L. Lewis, Nathan G. Swenson, Amy E. Zanne, Gaby Lopez-gonzales, J Illic, RB Miller, MC Wiemann, Samantha Swauger

This resource has been updated - find the current version here: https://qubeshub.org/publications/274/Wood density data used in this activity are derived from: Zanne AE, Lopez-Gonzalez G, Coomes DA, Ilic J, Jansen S, Lewis SL, Miller RB, Swenson NG, Wiemann MC, Chave J (2009) Data from:...

Advancing population ecology with integral projection models: a practical guide

23 Jan 2015 | Teaching & Reference Material | Contributor(s): Cory Merow, Johan Dahlgren, Jessica Metcalf, Dylan Childs, Margaret Evans, Eelke Jongejans, Sydne Record, Mark Rees, Roberto Salguero-Gómez, Sean McMahon

This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/824Integral projection models (IPMs) use information on how an individual's state influences its vital rates – survival, growth and reproduction – to...

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

03 Jun 2015 | Teaching & Reference Material | Contributor(s): Steven F Railsback, Volker Grimm

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...

AIM-UP! (Advancing Integration of Museums into Undergraduate Programs)

13 Mar 2015 | Teaching & Reference Material | Contributor(s): Joseph A. Cook, Scott Edwards, Stefanie Ickert-Bond, Eileen Lacy

An NSF-funded Research Coordination Network, the goal of AIM-UP! is to bring museum archives and natural history collections to the forefront of biology education.  From the website:  "We are developing these themes through meetings, on-line discussions and workshops at scientific...

AIM-UP! Coal balls lesson

28 Mar 2015 | Teaching & Reference Material | Contributor(s): Monte Garroutte, Jordan Metzgar, Hirotsugu Mori

This resource has been updated - find the current version here: https://qubeshub.org/publications/334In this activity, students learn about ancient plant life and climate change by examining coal balls. In addition to the lesson itself, information is provided on where to purchase coal ball...

AIM-UP! GIS and bats lesson

28 Mar 2015 | Teaching & Reference Material

This resource has been updated - find the current version here: https://qubeshub.org/publications/335This lesson introduces the use of GIS (geographic information systems) in the study of biological questions, using bats as the model organism. This activity requires access to GIS...

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.