OmniBio: an easy-to-use web app for kinetic growth parameter calculation from microplate reader data.

Area of Science:

• Microbiology
• Bioinformatics
• Computational Biology

Background:

• Microbial growth curve analysis is crucial for understanding bacterial physiology and optimizing bioprocesses.
• Manual analysis of microplate reader data is time-consuming and requires specialized bioinformatics skills.
• Existing tools often lack user-friendliness or require extensive data preprocessing.

Purpose of the Study:

• To develop a user-friendly web application, OmniBio, for streamlined analysis of microbial growth curves.
• To automate the computation of key kinetic parameters from microplate reader data.
• To provide intuitive visualization and data export capabilities for researchers.

Main Methods:

• Development of a web application using R, the gcplyr package, and the Shiny framework.
• Support for data outputs from common plate reader software (Gen5, iControl).
• Implementation of automated calculation for parameters like maximum growth rate, lag time, ODmax, and area under the curve.
• Inclusion of real-time plotting and heatmap analysis for comparative studies.

Main Results:

• OmniBio successfully processes data from various commercial plate readers, handling multiple sheets within a single file.
• The application computes and visualizes microbial growth kinetic parameters in real-time.
• Users can generate comparative heatmap analyses and download processed data in an Excel report.
• The tool offers an intuitive, step-by-step workflow, eliminating the need for coding or bioinformatics training.

Conclusions:

• OmniBio provides an efficient and accessible platform for high-throughput microbial growth curve analysis.
• The web application optimizes time and resource utilization for researchers.
• OmniBio democratizes microbial growth analysis, making it feasible for users without specialized computational expertise.