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Simulating Gene Expression using Netlogo
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secondary and undergraduate |
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Using a modelling environment that simulates the behavior of DNA, RNA, protein, transcription, and translation, a system can emerge that shows properties qualitatively similar to gene expression models. Two models were created: one simulates the lac operon, one of the classical models in gene expression. Another model illustrates how a gene expression system can behave like any logical gate (AND, OR, NAND, NOR). |
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Regulation of lac operon Gene Expression. Logical Promoter: Simulating Logical Gates Using Gene Expression |
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Brewer, S.D. Ehrman, P., and Koop, A. (2004). Regulation of lac operon Brewer, S.D. (2004). Logical Promoter: Simulating Logical Gates Using Gene Expression. http://bcrc.bio.umass.edu/netlogo/models/LogicalPromoter Biology Computer Resource Center; UMass Amherst, Amherst, MA. 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. Other links: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/LacOperon.html NCBI structural program http://www.ncbi.nlm.nih.gov/ http://www.webbooks.com/MoBio/Free/Ch4D3.htm |
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We plan to create other models and have created a wiki page with our curricular goals: http://bcrc.bio.umass.edu/coursewiki/index.php/GeneExpressionModel |
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