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. 2017 Jun 15;33(12):1905-1906.
doi: 10.1093/bioinformatics/btx084.

PMAnalyzer: a new web interface for bacterial growth curve analysis

Daniel A Cuevas  1 , Robert A Edwards  1   2
Affiliations

PMAnalyzer: a new web interface for bacterial growth curve analysis

Daniel A Cuevas et al. Bioinformatics. .

Abstract

Summary: Bacterial growth curves are essential representations for characterizing bacteria metabolism within a variety of media compositions. Using high-throughput, spectrophotometers capable of processing tens of 96-well plates, quantitative phenotypic information can be easily integrated into the current data structures that describe a bacterial organism. The PMAnalyzer pipeline performs a growth curve analysis to parameterize the unique features occurring within microtiter wells containing specific growth media sources. We have expanded the pipeline capabilities and provide a user-friendly, online implementation of this automated pipeline. PMAnalyzer version 2.0 provides fast automatic growth curve parameter analysis, growth identification and high resolution figures of sample-replicate growth curves and several statistical analyses.

Availability and implementation: PMAnalyzer v2.0 can be found at https://edwards.sdsu.edu/pmanalyzer/ . Source code for the pipeline can be found on GitHub at https://github.com/dacuevas/PMAnalyzer . Source code for the online implementation can be found on GitHub at https://github.com/dacuevas/PMAnalyzerWeb .

Contact: dcuevas08@gmail.com.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1
Fig. 1
PMAnalyzer figure outputs. Figures generated after processing four different samples. (a) Comparative growth level heatmap between four samples. (b) Average growth curves of a Citrobacter sedlakii sample with standard error intervals. (c) Box and density plots of several metrics reported by the pipeline. Intervals indicate ±1 standard deviation
See this image and copyright information in PMC

References

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    1. Cuevas D.A. et al. (2016b) From DNA to FBA: how to build your own genome-scale metabolic model. Front. Microbiol., 7, 907.. - PMC - PubMed
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