AUTHOR=Wolkenhauer Olaf TITLE=Why model? JOURNAL=Frontiers in Physiology VOLUME=5 YEAR=2014 URL=https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2014.00021 DOI=10.3389/fphys.2014.00021 ISSN=1664-042X ABSTRACT=

Next generation sequencing technologies are bringing about a renaissance of mining approaches. A comprehensive picture of the genetic landscape of an individual patient will be useful, for example, to identify groups of patients that do or do not respond to certain therapies. The high expectations may however not be satisfied if the number of patient groups with similar characteristics is going to be very large. I therefore doubt that mining sequence data will give us an understanding of why and when therapies work. For understanding the mechanisms underlying diseases, an alternative approach is to model small networks in quantitative mechanistic detail, to elucidate the role of gene and proteins in dynamically changing the functioning of cells. Here an obvious critique is that these models consider too few components, compared to what might be relevant for any particular cell function. I show here that mining approaches and dynamical systems theory are two ends of a spectrum of methodologies to choose from. Drawing upon personal experience in numerous interdisciplinary collaborations, I provide guidance on how to model by discussing the question “Why model?”