grofit: Fitting Biological Growth Curves withR

Abstract

The grofit package was developed to fit many growth curves obtained under different conditions in order to derive a conclusive dose-response curve, for instance for a compound that potentially affects growth. grofit fits data to different parametric models and in addition provides a model free spline method to circumvent systematic errors that might occur within application of parametric methods. This amendment increases the reliability of the characteristic parameters (e.g.,lag phase, maximal growth rate, stationary phase) derived from a single growth curve. By relating obtained parameters to the respective condition (e.g.,concentration of a compound) a dose response curve can be derived that enables the calculation of descriptive pharma-/toxicological values like half maximum effective concentration (EC50). Bootstrap and cross-validation techniques are used for estimating confidence intervals of all derived parameters.

Simple and Versatile Turbidimetric Monitoring of Bacterial Growth in Liquid Cultures Using a Customized 3D Printed Culture Tube Holder and a Miniaturized Spectrophotometer: Application to Facultative and Strictly Anaerobic Bacteria

“…Hence, we evaluated the feasibility of our methodology to monitor the growth of three anaerobic ruminal species - B. fibrisolvens , B. proteoclasticus , and P. acnes – in Hungate culture tubes. After measuring the OD values for 48 h, we modeled the growth curves using the gcFit function (part of the grofit R package; Kahm et al, 2010) that estimated the abovementioned parameters of the growth curves: μ, λ, A ( Table 3 ). In this case, we found a high repeatability between the two different culture tubes prepared from the same inoculum.…”

“…Bacterial growth curves were analyzed using the grofit R software package (Kahm et al, 2010). For E. coli , S. aureus , and McFarland standards, the relationship between the growth rate values from the growth curves (slope of calibration curve in the case of McFarland standards) obtained from the measurement using either the experimental device or the benchtop spectrophotometer were evaluated by using the PROC MIXED procedure of SAS (version 9.1, SAS Institute, Inc., Cary, NC, USA).…”

Morphometry and growth of sea pen species from dense habitats in the Gulf of St. Lawrence, eastern Canada

“…Age-length data for A. grandiflorum and P. aculeata were fitted using the 'grofit' package (Kahm et al 2010) from the statistical computing software R (R Development Core Team 2015). Three parametric models (logistic, Gompertz and Richards; Table SIV) were considered to estimate the growth parameters (λ-lag phase, μ-maximum growth rate and Amaximum growth).…”

Insect antimicrobial peptides act synergistically to inhibit a trypanosome parasite

“…For each peptide combination treatment, cell numbers were measured at 0, 24, 48, 72 and 96 h from the start of the experiment. From this, the growth curve for each combination and replicate was estimated with R package grofit [57] by fitting a spline [57], for each replicate growth series, which yields three parametersthe lag phase (l), maximum growth rate (r obs ), and maximum cell concentration (A max ) (figure 1). Here, we focus on this observed growth rate (r obs ); the analysis of the other parameters would have resulted in similar results and conclusions.…”