Phenotype Microarray - opm

The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. The phenotypic reaction of single-celled organisms such as bacteria, fungi, and animal cell cultures to up to 2,000 environmental challenges can be recorded on sets of 96-well microtiter plates. The opm package for the free statistical software environment R (available 
here) offers tools for storing the curve kinetics, aggregating the curve parameters, recording associated metadata of organisms and experimental settings as well as methods for analysing these highly complex data sets graphically and statistically. The package also includes 95% confidence plots, enhanced graphics and customized multiple comparisons of means procedures for comparing the estimated curve parameters. Parameters can be discretised and exported for generating reports for taxonomic journals such as IJSEM. Export and import in the YAML, JSON or CSV format facilitates the data exchange among labs. The CSV files produced by the OmniLog® reader can not only be easily imported but also batch-converted in large numbers.