Application of Bioinformatics in Chronobiology Research

Abstract

Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

“…Scarcity is first. We attempted to be as inclusive as possible and added resources far beyond the focus of our study on core clock genes in flies; recent reviews (L opes et al . 2013; L i et al .…”

“…2016). A recent review of additional bioinformatics resources pointed out that tools cannot replace researchers, because it is “often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability” (L opes et al . 2013).…”

“…EUCLIS (http://www.bioinfo.mpg.de/euclis/) is the ‘EU Clock Information System’. It adapted an advanced database architecture from another systems biology project for circadian clock researchers in order to combine modules for experimental data, clock models, and a related digital library (B atista et al 2007) L opes , 2013 #3694}.…”

“…The underlying issues have not yet been solved on a broader scale (NIH et al 2012; NIH 2015; NIH 2016; W ilkinson et al 2016). A recent review of additional bioinformatics resources pointed out that tools cannot replace researchers, because it is “often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability” (L opes et al 2013). We argue that much of this low- level work could be transparently handled by a compiler that acts as an assistant (see comments in: http://elm-lang.org/blog/compilers-as-assistants).…”

“…However, FlyClockbase is not the first biological information repository sharing observations about circadian oscillations in gene expression. We will next discuss some examples of related efforts; a review of additional bioinformatics resources relevant for clock research can be found elsewhere (L opes et al . 2013; L i et al .…”