title: How computational models can help unlock biological systems.
abstract: With computation models playing an ever increasing role in the advancement of science, it is important that researchers understand what it means to model something; recognize the implications of the conceptual, mathematical and algorithmic steps of model construction; and comprehend what models can and cannot do. Here, we use examples to show that models can serve a wide variety of roles, including hypothesis testing, generating new insights, deepening understanding, suggesting and interpreting experiments, tracing chains of causation, doing sensitivity analyses, integrating knowledge, and inspiring new approaches. We show that models can bring together information of different kinds and do so across a range of length scales, as they do in multi-scale, multi-faceted embryogenesis models, some of which connect gene expression, the cytoskeleton, cell properties, tissue mechanics, morphogenetic movements and phenotypes. Models cannot replace experiments nor can they prove that particular mechanisms are at work in a given situation. But they can demonstrate whether or not a proposed mechanism is sufficient to produce an observed phenomenon. Although the examples in this article are taken primarily from the field of embryo mechanics, most of the arguments and discussion are applicable to any form of computational modelling.
authors.affiliation: Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada. Electronic address: brodland@uwaterloo.ca.
authors.forename: G Wayne
authors.initials: GW
authors.lastname: Brodland
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D047108:Embryonic Development / Q000235:genetics / Q000502:physiology*; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D008954:Models, Biological; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D049490:Systems Biology / Q000379:methods
keywords: Biological systems; Cell mechanics; Computational modelling; Developmental mechanisms; Embryo mechanics; Embryogenesis; Models; Morphogenetic movements; Review; Tissue mechanics