During analyzing experiment data, we've found that many data analysis processes are identical. In an effort to save time and labor, we've written down some scripts to deal with large data sets of a similar group or from a similar experiment. We're posting our codes here in the hope that when someone else in the future has to deal with data sets from a similar experiment, our codes would help to make such processes easier. Moreover, we believe that tools can make synthetic biology more standardized than ever.

  Characterization is undoubtedly both common and important in synthetic biology. Though there're more than one way to characterize promoter activity, the usage of fluorescence protein (such as GFP, YFP, RFP and CFP) is quick and convenient. One can attach the coding region of GFP for instance to the promoter (including RBS) and measure the fluorescence intensity.

  The tools we offer here can be used to analyze the data collected (OD and fluorescence time profile) and compute the transcription rate (PoPS). We've written one function file for matlab and another Macro for Excel. The codes have been thoroughly documented, making it much easier to use and modify. For more information on detailed experiment steps for characterization, please refer to our biobrick characterization page and protocol.

Algorithm

  The transcription rate can be calculated by the following function (Leveau and Lindow, 2001):

  P=transcription rate(PoPS); μ=growth rate; m=XFP maturation; D=XFP degradation; fss=steady-state fluorophore concentration at exponential phase. The default vaules for m (1.5h-1, Andersen et al.,1998) and D (0.23h-1, Cormack et al.,1996) are for GFP as the reporter.

Input

  Users should prepare data from the exponential phase in three rows, for example:

Output

  The output consists of 1 value of PoPS and 4 figures automatically saved under the current directory. The output for the example is as follows:

1. P=2.3546e4

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