title: How computational models contribute to our understanding of the germ line.
abstract: Computational models are an invaluable tool in modern biology. They provide a framework within which to summarize existing knowledge, enable competing hypotheses to be compared qualitatively and quantitatively, and to facilitate the interpretation of complex data. Moreover, models allow questions to be investigated that are difficult to approach experimentally. Theories can be tested in context, identifying the gaps in our understanding and potentially leading to new hypotheses. Models can be developed on a variety of scales and with different levels of mechanistic detail, depending on the available data, the biological questions of interest, and the available mathematical and computational tools. The goal of this review is to provide a broad picture of how modeling has been applied to reproductive biology. Specifically, we look at four uses of modeling: (i) comparing hypotheses; (ii) interpreting data; (iii) exploring experimentally challenging questions; and (iv) hypothesis evaluation and generation. We present examples of each of these applications in reproductive biology, drawing from a range of organisms-including Drosophila, Caenorhabditis elegans, mouse, and humans. We aim to describe the data and techniques used to construct each model, and to highlight the benefits of modeling to the field, as complementary to experimental work. Mol. Reprod. Dev. 83: 944-957, 2016 © 2016 Wiley Periodicals, Inc.
authors.affiliation: Computational Biology Group, Department of Computer Science, University of Oxford, Oxford, United Kingdom.|Biological Computation, Microsoft Research, Cambridge, United Kingdom.
authors.forename: Kathryn
authors.initials: K
authors.lastname: Atwell
authors.affiliation: Biological Computation, Microsoft Research, Cambridge, United Kingdom.
authors.forename: Sara-Jane
authors.initials: SJ
authors.lastname: Dunn
authors.affiliation: School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.
authors.forename: James M
authors.initials: JM
authors.lastname: Osborne
authors.affiliation: Biological Computation, Microsoft Research, Cambridge, United Kingdom.|Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel.
authors.forename: Hillel
authors.initials: H
authors.lastname: Kugler
authors.affiliation: Skirball Institute of Biomolecular Medicine, Department of Cell Biology, and Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, New York.
authors.forename: E Jane Albert
authors.initials: EJ
authors.lastname: Hubbard
mesh_terms: D000818:Animals; D003198:Computer Simulation; D005854:Germ Cells / Q000502:physiology*; D006801:Humans; D008954:Models, Biological; D012098:Reproduction / Q000502:physiology*