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Updated: Jan 16, 2026

The Use of Chemostats in Microbial Systems Biology
Published on: October 14, 2013
Protocol to detect dilution cycles in chemostat experiments and estimate growth rate slopes with linear modeling with
Samuel I Koehler1, Jennifer T Pentz1, Earl A Middlebrook1
1Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87509, USA.
Abstract:
Chemostat growth chambers measure optical density over time and require manual calculation of growth rates. Here, we present chemostat_regression, R software that enables users to automatically identify chemostat cycles and estimate growth rate using a linear regression approach. We describe steps for creating requisite software environment(s), formatting input data, executing the software via command line/RStudio/R-Shiny, interpreting results, assessing the validity of results, and modifying input parameters.
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