Analysis of OmniLog® Phenotype Microarray data
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 offers tools for storing the curve kinetics, aggregating the curve parameters, recording associated metadata of organisms and experimental settings as well as methods for analyzing these highly complex data sets graphically and statistically. The package also includes 95% confidence plots, enhanced heatmap graphics and customized multiple comparisons of means procedures for comparing the estimated curve parameters. It is also possible to discretize these parameters and to export them for investigations with other programs and 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.
Download and Installation
- the package at a dedicated site with up-to-date versions, source code and installation instructions for all systems
- the package at R-Forge (up-to-date versions, source code and binaries for Windows; click on "R Packages" in the upper right corner)
- the package at CRAN (outdated stable release; source code and binaries for Windows)
- Hofner et al. (2015) Controlling false discoveries in high-dimensional situations: Boosting with stability selection. BMC Bioinformatics 16: 144, 2015.
- Vaas et al. (2013) opm: An R package for analysing OmniLog® Phenotype MicroArray Data. Bioinformatics 29: 1823-1824.
- Vaas et al. (2012) Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE 7: e34846.
- support mailing list (on which all opm announcements are posted)
- user-friendly main tutorial
- user-friendly tutorial on using substrate information
- user friendly tutorial on applying opm to growth curves
- extensive HTML online documentation (also including
the helper packages pkgutils and opmdata)
- the same comprehensive manual comes as PDF file with the package
- step-by-step introduction in slide-show format
- fact sheet summarizing the main features of opm
- our introduction to the opm workshop at the 2015 Phenotype Microarray conference in Florence
- a paper on the underlying approaches for visualisation and quantitative comparison
- requests should be sent to the support mailing list
- a bug tracker is available at R-Forge
The opm package is developed in a cooperation between the DSMZ and the IMBE Erlangen.
Note that the DSMZ also offers in-house generations and analysis of Phenotype MicroArray data; please have a look at the the phenotypic characterization page for details.