Background
Thanks to technological innovations in the last decade, modern biology has gain the ability to describe biological phenomena more precisely using quantitatively techniques. This is particularly true in the area of Phenomics – a field focused on understanding an organism’s physical and molecular responses to changes to its genetic makeup and the influence of its environment – which has evolved rapidly and expanded from analysing qualitative traits to also include quantitative traits.
Phenotyping micro-organisms is particularly challenging because of its microscopic size. An array of techniques has been in use for many years each tackling different aspects of the phenome. One of such approaches is uses the quantification of an organism’s culture growth. This technique offers high resolution and decent throughput and has proven valuable for precisely quantifying growth alterations in the model organism S. Cerevisiae, (recorded by measuring changes in optical density over time) as a consequence of the loss of every individual gene in the yeast genome during various physiological states, i.e. the growth variables adaptation time, growth rate and growth efficiency.
Quantifying the growth phenotypes of microorganisms in high throughput requires two main components. First, an instrument that can effectively record the proliferation of cultures in bulk. Second, a framework to extract the quantitative traits of the data and report the results in a convenient format. The Bioscreen C is a computer-controlled incubator/reader/ shaker that measures the growth of a culture in a micro-plate well. This instrument is successfully used to study and characterized micro-organisms like E. coli and S. Cerevisiae. The Bioscreen C outputs a text file with growth data (OD / Time) for each of the 200 wells it can process. It is up the user to analyse this data and extract any useful information. To this end, we developed a tool aimed to facilitate the trait extraction of growth data named PRECOG (PREsentation and Characterization of Growth-data).
PRECOG
PRECOG is an application developed to not only extract growth traits, but also to present the data usefully, in a matter that allows the user to interact, explore, and validate the experimental data, to further facilitate the discovery of knowledge. PRECOG is also experiment agnostic, meaning that it requires not prior knowledge of the experimental setup to produce results. This enables the user to quickly start working on the data analysis almost immediately after obtaining the data from the instrument.
We developed PRECOG (PREsentation and Characterization Of Growth-data) as a standardised and flexible tool for the characterization (quantitative traits) and visualization of high-throughput microbial growth curves.
PRECOG is built to process the data produced by the Bioscreen C instrument. The system is also tuned for the model organism Saccharomyces cerevisiae. It is important to note that the Bioscreen simply records and outputs OD over time measurements and that any similar measurements from a different machine could easily be adapted as an additional input. Also PRECOG can be tuned to other microbial organisms easily by simply adding a different “calibration function”.