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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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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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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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Disease Spread Simulation with M&M's and Information on the wider SIMIODE community
13 Feb 2018 | Teaching Materials | Contributor(s):
By Brian Winkel
SIMIODE - Systemic Initiative for Modeling Investigations and Opportunities with Differential Equations
This is a Student Version of a Modeling Scenario from the community, SIMIODE - Systemic Initiative for Modeling Investigations and Opportunities with Differential Equations at www.simiode.org
https://qubeshub.org/publications/358/?v=1
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Ehren Whigham
https://qubeshub.org/community/members/15679
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Erin Kiley
https://qubeshub.org/community/members/12062
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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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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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Help! I'm getting a Java error!
Users may experience a Java error on Mac OS X if they are using Java version 1.3 and below. Please ensure your Java install is up to date.NOTE! For gecko browsers (Mozilla, Firefox, Camino), the...
https://qubeshub.org/kb/software/javaerr
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jae Roh
https://qubeshub.org/community/members/15576
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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.
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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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Modeling the lac Operon to Understand the Regulation of Gene Expression in Prokaryotes
27 Sep 2019 | Teaching Materials | Contributor(s):
By Sam S Donovan
University of Pittsburgh
This resource is a recitation activity designed for an introductory biology course in which students explore a lac operon simulation (https://qubeshub.org/resources/phetlacoperon).
https://qubeshub.org/publications/1427/?v=1
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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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Modeling: A Primer - The crafty art of making, exploring, extending, transforming, tweaking, bending, disassembling, questioning, and breaking models
29 Jan 2018 | Teaching Materials | Contributor(s):
By William Wimsatt1, Jeff Schank2
1. University of Chicago 2. Indiana University
Explore how to use, analyze, and criticize some important and historically influential models in biology in this text only module.
https://qubeshub.org/publications/346/?v=1
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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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ModelSim Population Biology Unit
30 Oct 2018 | Teaching Materials | Contributor(s):
By Uri Wilensky1, Paulo Blikstein2, Corey Brady3, David Figlio1, Pratim Sengupta4, Jason Bertsche1, Yu (Bryan) Guo1, Nathan Holbert1, Michael Novak1, Firat Soylu1, Aditi Wagh1, Gokul Krishnan4, Brogan Miller2, Shima Salehi2
1. Northwestern University 2. Stanford University 3. Inquire Learning 4. Vanderbilt University
This resource provides rich student modeling activities and materials, teacher resources, and much more, in the realm of agent based models applied to population biology.
https://qubeshub.org/publications/902/?v=1
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Nick Galt
https://qubeshub.org/community/members/7728
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Oliver Alaijos
https://qubeshub.org/community/members/42150