Microbial lag calculator: A shiny‐based application and an R package for calculating the duration of microbial lag phase

The duration of lag phase can be used as an organismal fitness marker; however, it is often underreported as its estimation may be challenging and method and parameters dependent. Moreover, there are no publicly available tools to calculate lag duration by different methods. We developed a shiny‐bas...

Full description

Saved in:

Bibliographic Details
Published in:	Methods in ecology and evolution Vol. 15; no. 2; pp. 301 - 307
Main Authors:	Smug, Bogna J., Opalek, Monika, Necki, Maks, Wloch‐Salamon, Dominika
Format:	Journal Article
Language:	English
Published:	London John Wiley & Sons, Inc 01-02-2024 Wiley
Subjects:	Applications programs bacterial growth models Decision trees fitness Lag phase lag phase length lag time Mathematical analysis microbial growth curve Microorganisms Parameters
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	The duration of lag phase can be used as an organismal fitness marker; however, it is often underreported as its estimation may be challenging and method and parameters dependent. Moreover, there are no publicly available tools to calculate lag duration by different methods. We developed a shiny‐based web application (https://microbialgrowth.shinyapps.io/lag_calulator/) where the lag duration can be calculated based on the user‐specified growth curve data, and for various explicitly specified methods, parameters and data preprocessing techniques. Additionally, we release an R package ‘miLAG’ that can be further customised and developed. We also describe in short the assumptions, advantages and disadvantages of the most popular lag calculation methods and propose a decision tree to choose a method most suited to one's data. Finally, we show some working examples of how to calculate lag duration using our shiny server.
ISSN:	2041-210X 2041-210X
DOI:	10.1111/2041-210X.14269