The 21st century finds us entering an age in which our understanding of evolutionary processes and molecular mechanisms has become sophisticated enough for us modify organisms in predictable ways. 

Phylogenetic comparisons at the genomic level are being used to examine the regulative and homeostatic dynamics that maintain and control the living state. 

At the same time, molecular signaling systems are being understood in the content of rigorous, data-dependent regulatory circuits |   (the arrow icon marks outside links!)

In Gene Machines, we are constructing virtual laboratory where students can learn how to work with bacteria and plasmids, and then how to design, build and test their own molecular circuits and, through the use of mathematical / computational models predict the behavior of their plasmid in a simulated cellular environment. 

 

Gene Machines consists of three distinct experimental modules. 

  • On Growth - where students learn the basics of working with bacteria, characterize their behavior as a function of temperature and time. 
  • the Plasmid Builder where students design and build their own plasmids, with the goal of producing specific behaviors, and ...  
  • virtual Coli, a simulated population of E.coli into which the plasmids can be transformed. Students are then called upon to analyze the behavior of their genetic circuit and determine whether their predicted models matches the experimental outcome.  
Because it is open-ended, students can design as simple or as complex a system of plasmids as they wish, making custom "independent study projects" possible.