This project was prepared as part of a BioQUEST faculty development workshop entitled BioQUEST 2004 Summer Workshop for Undergraduate Faculty: Systems Biology at Beloit College in June 2004. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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Simulating Gene Expression using Netlogo
 
 
Authors          Audiences          Overview           Materials          Resources           Future Directions
 

 


Authors


Steven Brewer
University of Massachusetts


Allen Koop
Grand Valley State University


Patrick Ehrman
Institute for Systems Biology

 
   
 


Possible Audiences:

secondary and undergraduate  

 
 


Brief Overview:

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).  

 
   
 


Project Materials:

Regulation of lac operon Gene Expression.

Logical Promoter: Simulating Logical Gates Using Gene Expression  

 
 


Resources and References:

Brewer, S.D. Ehrman, P., and Koop, A. (2004). Regulation of lac operon
Gene Expression. http://bcrc.bio.umass.edu/netlogo/models/LacOperon Biology Computer Resource Center

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  

 
   
 


Future Directions:

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  

 
 


Attachments


- BQ.ppt