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Team:Illinois/Modelingteam
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Contents |
Modeling Team
Goals: Our team will be creating mathematical models of our bacterial decoder and of the various biological processes involved. More specifically, we will be modeling:
- simple sRNA regulation of one gene
- multiple sRNAs regulating one gene
- one sRNA regulating multiple genes
- promoter activity as a function of input concentration
- our bacterial decoder as a whole
We will be using Matlab and SimBiology often as tools to help us model various systems. Our team will also be taking measurements and recording data in order to compare our actual decoder with the models we have constructed.
For more information, please view the Modeling page.
June 23
We made a Matlab program that models simple sRNA regulation of a single gene. The program takes a vector containing times and numbers of sRNA, mRNA, and protein molecules and outputs a vector of solutions to the differential equations used for each time.
We will be measuring fluorescence of E. coli cells with pXG-0, pXG-1
June 24
We made a program in SimBiology that models simple sRNA regulation of a single gene. The equations and constant values used were taken from a paper on sRNA regulation (please see the Research page).
We attempted to measure fluorescence of our cells today using a plate reader, but we ran into some technical problems. We may have to use a different plate reader, or we may be able to fix the problems on the current plate reader.
June 25
We created a working program in SimBiology that roughly models our decoder. In the program, each gene is regulated by two sRNAs. The sRNA synthesis rates are assumed to be constant for now, whereas in reality these rates will depend on input concentrations and promoter activity. We verified by changing sRNA synthesis rates that combinations of two sRNAs resulted in production of the correct fluorescent protein.
We cultured cells overnight in anticipation that we will be able to perform a fluorescence reading tomorrow.
