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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...
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Genetic Drift Simulation - NetLogo
23 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...
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Modeling: A Primer - The crafty art of making, exploring, extending, transforming, tweaking, bending, disassembling, questioning, and breaking models
26 Feb 2016 | | Contributor(s):: William Wimsatt, Jeff Schank
This resource has been updated - find the current version here: https://qubeshub.org/publications/346Explore how to use, analyze, and criticize some important and historically influential models in biology in this text only module.
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Course materials for computational genomics using R
19 Nov 2015 | | Contributor(s):: Hong Qin
This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/907The R code and data are deposited at Github: https://github.com/hongqin/RCompBio
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SIMIODE - Systemic Initiative for Modeling Investigations and Opportunities with Differential Equations
20 Oct 2015 | | Contributor(s):: Brian Winkel
SIMIODE - Systemic Initiative for Modeling Investigations and Opportunities with Differential Equations is about teaching differential equations using modeling and technology upfront and throughout the learning process. You can learn more at our dynamic website, www.simiode.org, where we...
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Populus: Simulations of Population Biology
05 Oct 2015 | | Contributor(s):: D. N. Alstad
This resource has been updated - find the current version here: https://qubeshub.org/publications/352The Populus software contains a set of simulations that we use to teach population biology and evolutionary ecology at the University of Minnesota. Simulation models may be chosen from a...
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EvolSeq
14 Sep 2015 | | Contributor(s):: Tony Weisstein, John R Jungck
This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/776This worksheet simulates the molecular evolution of DNA sequences. The program begins with a single (random) sequence, then follows that sequence through time as it...
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Luria-Delbruck
14 Sep 2015 | | Contributor(s):: Tony Weisstein, John R Jungck, Doug Green
This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/777These two workbooks model the evolution of phage resistance in a bacterial population under two alternative hypotheses. Under the hypothesis of acquired immunity, mutation...
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Michaelis-Menten Enzyme Kinetics
14 Sep 2015 | | Contributor(s):: Tony Weisstein
This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/778In this simulation equations used in enzyme kinetics (Michaelis-Menten, Eadie-Hofstee, Dixon, and Lineweaver-Burk) are modeled under various conditions. The equations are...
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Disease Spread Simulation with M&M's and Information on the wider SIMIODE community
03 Jul 2015 | | Contributor(s):: Brian Winkel
This resource has been updated - find the current version here: https://qubeshub.org/publications/358This is a Student Version of a Modeling Scenario from the community, SIMIODE - Systemic Initiative for Modeling Investigations and Opportunities with Differential Equations at...
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BactVsPhage
27 Jun 2015 | | Contributor(s):: Drew LaMar
Simulates basic models in theoretical ecology, as well as three models of bacteria/bacteriophage interactions.
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ModelSim Population Biology Unit
18 May 2015 |
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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PPLANE
02 Apr 2015 |
PPLANE is a tool for Phase Plane Analysis of a System of Differential Equations of the form: x' = dx/dt = f(x,y), y' = dy/dt = g(x,y).
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QtOctave
19 Feb 2015 |
QtOctave is an open source GUI front-end application for GNU Octave.
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POPULUS Lotka - Volterra, the logistic equation & Isle Royale
13 Feb 2015 | | Contributor(s):: Stephen Malcolm
Laboratory exercise explores predator-prey dynamics using Populus.
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POPULUS Simulations of interspecific competition using the Lotka-Volterra model
13 Feb 2015 | | Contributor(s):: Scott Creel
Explores the Lotka-Volterra model of interspecific competition using Populus.
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COPASI
10 Feb 2015 |
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
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POPULUS Evolutionary forces
02 Feb 2015 | | Contributor(s):: Jonathan M. Brown
This lab is focused on understanding how evolutionary forces - including mutation, genetic drift, migration, and selection - result in changes in population allele frequencies.
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Population Growth
30 Jan 2015 | | Contributor(s):: Miles Silman
Lab exercise in which students model both discrete and continuous density-independent growth. Students also model discrete and time-lagged density-dependent growth. General questions are provided at the end.
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Lotka-Volterra, the logistic equation, and Isle Royale
30 Jan 2015 | | Contributor(s):: Stephen Malcolm
Students work through the basic Lotka-Volterra predator prey model using an example in which the prey exhibit density independence. Students then incorporate density dependence of prey items using several different features of Populus.