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WHAT IS IT?
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This is a model of the regulation of gene expression. It illustrates three genes
where an external signal initiates transcription of a gene, RNAs produced are
translated by ribosomes, and the proteins bind to other proteins to initiate
transcription of two other genes.
HOW IT WORKS
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The genes and promoters are patches. RNAs are circular turtles and proteins are
square turtles. Proteins can bind to the promoters to turn on production of RNAs.
RNAs diffuse to ribosomes, where they are converted into proteins. Proteins, in
turn, can initiate transcription of other genes.
HOW TO USE IT
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Click setup to create the genes and ribosomes. The promoters are the color of
proteins that will bind to them and are labeled 1, 2, and 3. A slider determines
the time until RNAs and proteins are degraded.
THINGS TO NOTICE
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There are a few simplifications in this version of the model. Once a protein
binds to a promoter, it stays bound until it degrades. A more accurate model
would have proteins have a chance of becoming unbound. Proteins move using a mechanism
that ensures that two don't occupy a patch at the same time -- otherwise it might
be possible for two to bind to the promoter. RNAs move using a different mechanism.
THINGS TO TRY
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This section could give some ideas of things for the user to try to do (move sliders, switches, etc.) with the model.
EXTENDING THE MODEL
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This section could give some ideas of things to add or change in the procedures tab to make the model more complicated, detailed, accurate, etc.
NETLOGO FEATURES
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This section could point out any especially interesting or unusual features of NetLogo that the model makes use of, particularly in the Procedures tab. It might also point out places where workarounds were needed because of missing features.
RELATED MODELS
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This section could give the names of models in the NetLogo Models Library or elsewhere which are of related interest.
CREDITS AND REFERENCES
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This model was created as part of the 2004 BioQUEST Curriculum Consortium
Summer Workshop.
Copyright 2004 by Steven Brewer and Pat Ehrman. All rights reserved.
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. and Ehrman, P. (2004). A Family of Models on the Regulation of
Gene Expression. http://bcrc.bio.umass.edu/netlogo/models/GeneExpression
Biology Computer Resource Center
In other publications, please use:
Copyright 2004 by Steven Brewer and Pat Ehrman. All rights reserved. See
http://bcrc.bio.umass.edu/netlogo/models/GeneExpression
for terms of use.