The Origins of the GrowthRates Program

At a Society for Molecular Biology and Evolution meeting in 2012, Dr. Hall met a graduate student named Hande Acar ( and spent some time discussing her work in the lab at the Institute of Science & Technology Austria. She described the wonderful new microplate reader they were using to monitor the growth of bacterial cultures. The reader could automatically follow the growth of 96 cultures for hours, or overnight, and report the density of each culture at specified reading intervals.  

The problem that Hande encountered was that it took days to do the calculations that would turn the resulting raw data into useful growth rates. Dr. Hall suggested that it should be possible to write a computer program that would automate the calculation process. He encouraged Hande to send him some output files from growth experiments to use as the basis for writing such a computer program.

Hande followed up with the data. At the same time, Prof. Miriam Barlow of the University of California at Merced, a colleague of Dr. Hall, was facing exactly the same problem with similar data on an even larger scale, with a microplate reader that read 384-well plates at once. Prof. Barlow’s plate reader output the data in an entirely different format, which required writing a special formatter to convert the data to the format that GrowthRates could understand. Since that time an additional ten formats have been added to the program to accommodate different plate readers.

Hande Acar fills wells with a solution to be read by a microplate reader

Dr. Hall wrote the first version of GrowthRates using those first two data sets. In 2014 they published a paper describing the work and the GrowthRates program (Hall, B. G., H. Acar, A. Nandipati and M. Barlow 2014  Growth Rates Made Easy.  Mol. Biol. Evol. 31: 232-238doi:10.1093/molbev/mst197).

GrowthRates has continued to evolve with improvements to the algorithm that allows the program to identify the optimum time points to use for the calculation. GrowthRates 4.5 can now be used with twelve different makes and models of microplate readers to improve the analysis of their output data. The original paper has been cited more than 300 times and versions 4.x have been downloaded more than 1600 times. Hande has finished her Ph.D. and is thriving as a post-doctoral researcher at the University of Oklahoma.

#GrowthRates #HandeAcar #microplatereader #SMBE #molecularbiology #microbiology

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