Predictive modelling of complex agronomic and biological systems.

Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead.

[1]  Luonan Chen Guest editorial. Computational systems biology. , 2013, IET systems biology.

[2]  C. Glasbey,et al.  Genetic and QTL analyses of yield and a set of physiological traits in pepper , 2013, Euphytica.

[3]  H. de Jong,et al.  Towards multiscale plant models: integrating cellular networks. , 2012, Trends in plant science.

[4]  Christophe Godin,et al.  Multiscale Systems Analysis of Root Growth and Development: Modeling Beyond the Network and Cellular Scales , 2012, Plant Cell.

[5]  Rui-Sheng Wang,et al.  Boolean modeling in systems biology: an overview of methodology and applications , 2012, Physical biology.

[6]  J. Molenaar,et al.  A Mathematical Model for BRASSINOSTEROID INSENSITIVE1-Mediated Signaling in Root Growth and Hypocotyl Elongation1[W] , 2012, Plant Physiology.

[7]  M. Apri,et al.  Complexity reduction preserving dynamical behavior of biochemical networks. , 2012, Journal of theoretical biology.

[8]  Andrew D Higginson,et al.  Heavy use of equations impedes communication among biologists , 2012, Proceedings of the National Academy of Sciences.

[9]  C. Buell,et al.  Advances in plant genome sequencing. , 2012, The Plant journal : for cell and molecular biology.

[10]  C. Reuzeau,et al.  Boosting Crop Yields with Plant Steroids[W] , 2012, Plant Cell.

[11]  S. Sabatini,et al.  Growth and development of the root apical meristem. , 2012, Current opinion in plant biology.

[12]  C. Bachem,et al.  Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality1[W][OA] , 2012, Plant Physiology.

[13]  Robert Finger,et al.  Food security: Close crop yield gap , 2011, Nature.

[14]  Marian Groenenboom,et al.  Metabolic Pathway Inference from Time Series Data: A Non Iterative Approach , 2011, PRIB.

[15]  Lei Li,et al.  Recent advances in the regulation of brassinosteroid signaling and biosynthesis pathways. , 2011, Journal of integrative plant biology.

[16]  Heather A. Piwowar,et al.  Data archiving is a good investment , 2011, Nature.

[17]  P. D. de Ruiter,et al.  Redefining plant systems biology: from cell to ecosystem. , 2011, Trends in plant science.

[18]  M. Lucas,et al.  Plant systems biology: network matters. , 2011, Plant, cell & environment.

[19]  F. V. van Eeuwijk,et al.  Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs , 2011, Theoretical and Applied Genetics.

[20]  Yiannis Kourmpetis,et al.  Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge , 2010, PloS one.

[21]  Richard Bonneau,et al.  DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models , 2010, PloS one.

[22]  Riet De Smet,et al.  Advantages and limitations of current network inference methods , 2010, Nature Reviews Microbiology.

[23]  Roeland C. H. J. van Ham,et al.  Continuous-time modeling of cell fate determination in Arabidopsis flowers , 2010, BMC Systems Biology.

[24]  Tom Beeckman,et al.  Auxin control of root development. , 2010, Cold Spring Harbor perspectives in biology.

[25]  F. V. van Eeuwijk,et al.  Detection and use of QTL for complex traits in multiple environments. , 2010, Current opinion in plant biology.

[26]  Peter Bühlmann,et al.  Predicting causal effects in large-scale systems from observational data , 2010, Nature Methods.

[27]  Mark Stitt,et al.  Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth1 , 2009, Plant Physiology.

[28]  J. Selbig,et al.  Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers , 2009, Theoretical and Applied Genetics.

[29]  Imre Blank,et al.  Identification of ethyl formate as a quality marker of the fermented off-note in coffee by a nontargeted chemometric approach. , 2009, Journal of agricultural and food chemistry.

[30]  Paul C. Struik,et al.  Modelling the crop: from system dynamics to systems biology. , 2009, Journal of experimental botany.

[31]  Dominique Chu,et al.  Models of transcription factor binding: sensitivity of activation functions to model assumptions. , 2009, Journal of theoretical biology.

[32]  Jingyuan Fu,et al.  System-wide molecular evidence for phenotypic buffering in Arabidopsis , 2009, Nature Genetics.

[33]  Jingyuan Fu,et al.  Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana , 2008, Genome Biology.

[34]  Xiaofeng Wang,et al.  Sequential transphosphorylation of the BRI1/BAK1 receptor kinase complex impacts early events in brassinosteroid signaling. , 2008, Developmental cell.

[35]  G. Slafer,et al.  Agronomy and plant breeding are key to combating food crisis , 2008, Nature.

[36]  J. Keurentjes,et al.  Quantitative genetics in the age of omics. , 2008, Current opinion in plant biology.

[37]  C. Batt Thinking small is not easy. , 2008, Nature nanotechnology.

[38]  H. Thomas Systems biology and the biology of systems: how, if at all, are they related? , 2007, The New phytologist.

[39]  P. Hogeweg,et al.  Auxin transport is sufficient to generate a maximum and gradient guiding root growth , 2007, Nature.

[40]  J Jaap Molenaar,et al.  Continuum modeling in the physical sciences , 2007, Mathematical modeling and computation.

[41]  K. Cassman,et al.  A dialogue on interdisciplinary collaboration to bridge the gap between plant genomics and crop sciences , 2007 .

[42]  Jingyuan Fu,et al.  Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci , 2007, Proceedings of the National Academy of Sciences.

[43]  J. Collins,et al.  Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles , 2007, PLoS biology.

[44]  P. Schoenemann Evolution of the Size and Functional Areas of the Human Brain , 2006 .

[45]  Adam A. Margolin,et al.  Reverse engineering cellular networks , 2006, Nature Protocols.

[46]  Richard Bonneau,et al.  The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo , 2006, Genome Biology.

[47]  Volkmar Wolters,et al.  Food Web Ecology: Playing Jenga and Beyond , 2005, Science.

[48]  L. Edelstein-Keshet Mathematical models in biology , 2005, Classics in applied mathematics.

[49]  Z. Oltvai,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[50]  Hirotada Mori,et al.  From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli. , 2004, Journal of biochemistry and molecular biology.

[51]  Katherine C. Chen,et al.  Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. , 2003, Current opinion in cell biology.

[52]  J. Goudriaan,et al.  Developments in modelling crop growth, cropping systems and production systems in the Wageningen school , 2003 .

[53]  H. Kitano Systems Biology: A Brief Overview , 2002, Science.

[54]  Tim Brown,et al.  High-resolution, time-lapse imaging for ecosystem-scale phenotyping in the field. , 2012, Methods in molecular biology.

[55]  M. Tester,et al.  High-throughput phenotyping of plant shoots. , 2012, Methods in molecular biology.

[56]  Dawn C. Walker,et al.  The virtual cellça candidate co-ordinator for ‘middle-out’ modelling of biological systems , 2009 .

[57]  M. Maurin,et al.  REVIEW ARTICLE doi: 10.1111/j.1472-8206.2008.00633.x The Hill equation: a review of its capabilities in pharmacological modelling , 2008 .

[58]  J. Goudriaan,et al.  ON APPROACHES AND APPLICATIONS OF THE WAGENINGEN CROP MODELS , 2003 .

[59]  F.W.T. Penning de Vries,et al.  A dynamic model of plant and crop growth , 1971 .

[60]  Chi Zhang,et al.  The mechanisms of brassinosteroids' action: from signal transduction to plant development. , 2011, Molecular plant.