created with NetLogo
view/download model file: unknown.nlogo
WHAT IS IT?
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This is a model that offers a series of "unknown" problems for students to explore
in learning about gene expression systems.
Genes are represented by colored patches labeled A, B, C, D and E. Transcription-factor binding sites are numbered 1-10. Genes are transcribed to produce RNAs (represented as lines) which are translated by ribosomes (cyan patches) to produce proteins (irregular polygons).
HOW IT WORKS
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In this simulation, there are 5 genes: A-E. Each gene has two promoters and can
be knocked out (turned-off) using a switch.
HOW TO USE IT
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A pop-up menu allows the user to select a problem.
Click "setup" to create the genes and ribosomes.
Click "go" to start the model.
Switches allow the user to turn genes A-E on and off.
Two plots show current and historical concentrations of proteins.
THINGS TO NOTICE
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You can tell which proteins bind to which sites. Notice under what conditions genes turn on and off. Does the system become fixed at some point, or does it oscillate?
THINGS TO TRY
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For each gene, determine what roles the binding sites are playing in the system (enhancer or silencer).
How does the behavior of the system change when genes are knocked out? Can you predict
these changes based on what you know by observing the system?
EXTENDING THE MODEL
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To simplify this model, a number of factors have been de-paramaterized, including the rates of each gene and the coefficients of binding and dissociation (KB and Kd). By adding sliders, you could extend this model and explore the behavior of the system with different values. By changing these values you can try to decrease the leakiness of the system and increase the speed of the system turning on or off.
CREDITS AND REFERENCES
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This model is based on work completed during the 2004 BioQUEST Curriculum Consortium
Summer Workshop.
Copyright 2004 by Steven Brewer. All rights reserved.
This model was inspired by many of the sample Netlogo models and parts were based on functions from the Enzyme Kinetics model. (Wilensky, U. (2001). NetLogo Enzyme Kinetics model. http://ccl.northwestern.edu/netlogo/models/EnzymeKinetics. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.)
Permission to use, modify or redistribute this model is hereby granted,
provided that both of the following requirements are followed:
a) this copyright notice is included.
b) this model will not be redistributed for profit without permission
from the authors.
Contact the authors for appropriate licenses for redistribution for
profit.
To refer to this model in academic publications, please use:
Brewer, S.D. (2004). Unknown Gene Expression: Problems for Students. http://bcrc.bio.umass.edu/netlogo/models/Unknown
Biology Computer Resource Center
In other publications, please use:
Copyright 2004 by Steven Brewer. All rights reserved. See
http://bcrc.bio.umass.edu/netlogo/models/Unknown