Grofit: Fitting biological growth curves

Matthias Kahm,Maik Kschischo,Guido Hasenbrink,Jost Ludwig,Hella Lichtenberg-Frate

doi:10.1038/npre.2010.4508.1

Matthias Kahm, Maik Kschischo + Show 3 more

Open Access

https://doi.org/10.1038/npre.2010.4508.1

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Abstract

AbstractGrowth experiments are routinely used to analyze basic properties of a given organism or cellular model. Similarly, within the TRANSLUCENT project the characterization of cellular growth and particularly under conditions of high extra cellular potassium or sodium is an important task. Any growth analysis should ideally reveal a relationship between the concentration of a compound/substrate and its effect on a particular growth parameter. In view of the quite labor intensive analysis of hundreds of growth curves - sometimes not revealing ideal relationships - the Grofit-software was developed to support biologists and such approaches. Within the software package, specifically tailored regression and bootstrapping techniques are utilized to statistically estimate the effect of different growth conditions. Grofit was implemented in R, an open source statistical software environment. A complete description of the Grofit software and information about the implemented methods is given in a manuscript published by the Journal of Statistical Software. In addition the software is available from CRAN repositories or the developers homepage http://www.rheinahrcampus.de/Research-Group-of-Maik-Kschisc.2452.0.html

Highlights

Growth experiments are routinely used to analyze basic properties of a given organism or cellular model
Grofit was implemented in R, an open source statistical software environment
A complete description of the Grofit software and information about the implemented methods is given in a manuscript submitted to the Journal of Statistical Software

Summary

Introduction

Growth experiments are routinely used to analyze basic properties of a given organism or cellular model. Any growth analysis should ideally reveal a relationship between the concentration of a compound/substrate and its effect on a particular growth parameter. In view of the quite labor intensive analysis of hundreds of growth curves - sometimes not revealing ideal relationships - the Grofit-software was developed to support biologists and such approaches. Tailored regression and bootstrapping techniques are utilized to statistically estimate the effect of different growth conditions.

Results

Conclusion