Potential integration of multi-fitting, inverse problem and mechanistic modelling approaches to applied research in animal science: a review

Modern researchers working in applied animal science systems have faced issues with modelling huge quantities of data. Modelling approaches that have previously been used to model biological systems are having problems to adapt to increased number of publications and research. So as to develop new approaches that have the potential to deal with these fast-changing complex conditions, it is relevant to review modern modelling approaches that have been used successfully in other fields. Therefore, this paper reviews the potential capacity of new integrated applied animal-science approaches to discriminate parameters, interpret data and understand biological processes. The analysis shows that the principal challenge is handling ill-conditioned complex models, but an integrated approach can obtain meaningful information from complementary data that cannot be obtained from present applied animal-science approaches. Furthermore, it is shown that parameter sloppiness and data complementarity are key concepts during system behaviour restrictions and parameter discrimination. Additionally, model evaluation and implementation of the potential integrated approach are reviewed. Finally, the objective of an integral approach is discussed. Our conclusion is that these approaches have the potential to be used to deepen the understanding of applied animal systems, and that exist enough developed resources and methodologies to deal with the huge quantities of data associated with this science.

[1]  Jens Timmer,et al.  Dynamical modeling and multi-experiment fitting with PottersWheel , 2008, Bioinform..

[2]  R. Veerkamp,et al.  Systems biology in animal sciences. , 2011, Animal : an international journal of animal bioscience.

[3]  Bruce Tidor,et al.  Sloppy models, parameter uncertainty, and the role of experimental design. , 2010, Molecular bioSystems.

[4]  Bryan C. Daniels,et al.  Sloppiness, robustness, and evolvability in systems biology. , 2008, Current opinion in biotechnology.

[5]  K. S. Brown,et al.  Statistical mechanical approaches to models with many poorly known parameters. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[6]  Andreas Zell,et al.  Automating mathematical modeling of biochemical reaction networks , 2010 .

[7]  Charles W. Groetsch Inverse Problems and Torricelli's Law , 1993 .

[8]  Keith A. Woodbury,et al.  Inverse problems and parameter estimation: integration of measurements and analysis , 1998 .

[9]  A. Tarantola Popper, Bayes and the inverse problem , 2006 .

[10]  Diana B. Petitti,et al.  Meta-Analysis, Decision Analysis, and Cost-Effectiveness Analysis: Methods for Quantitative Synthesis in Medicine , 1994 .

[11]  E. Poeter,et al.  Inverse Models: A Necessary Next Step in Ground‐Water Modeling , 1997 .

[12]  Luis Gustavo Barioni,et al.  Mathematical models in ruminant nutrition , 2005 .

[13]  E. Avila-Vales,et al.  Turix, a dynamic mechanistic model for feed evaluation , 2013 .

[14]  H. Engl,et al.  Inverse problems in systems biology , 2009 .

[15]  J. Jacquez,et al.  Numerical parameter identifiability and estimability: Integrating identifiability, estimability, and optimal sampling design , 1985 .

[16]  Johannes Jaeger,et al.  Parameter estimation and determinability analysis applied to Drosophila gap gene circuits , 2008, BMC Systems Biology.

[17]  Guangquan Li,et al.  Parameter Identifiability and Redundancy: Theoretical Considerations , 2008, PloS one.

[18]  Christopher R. Myers,et al.  Universally Sloppy Parameter Sensitivities in Systems Biology Models , 2007, PLoS Comput. Biol..

[19]  J. Gunawardena Models in Systems Biology: The Parameter Problem and the Meanings of Robustness , 2010 .

[20]  Sebastian Bohl,et al.  Dynamic Pathway Modeling , 2007, Annals of the New York Academy of Sciences.

[21]  Tina Toni,et al.  Parameter inference and model selection in signaling pathway models. , 2009, Methods in molecular biology.

[22]  Ermias Kebreab,et al.  Empirical modelling through meta-analysis vs mechanistic modelling. , 2006 .

[23]  K. S. Brown,et al.  Sloppy-model universality class and the Vandermonde matrix. , 2006, Physical review letters.

[24]  Maria Pia Saccomani,et al.  Parameter identifiability of nonlinear systems: the role of initial conditions , 2003, Autom..

[25]  Kamil Erguler,et al.  Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models. , 2011, Molecular bioSystems.

[26]  Christopher R Myers,et al.  Extracting Falsifiable Predictions from Sloppy Models , 2007, Annals of the New York Academy of Sciences.

[27]  Peter C. Young,et al.  The data-based mechanistic approach to the modelling, forecasting and control of environmental systems , 2006, Annu. Rev. Control..

[28]  Luis Orlindo Tedeschi,et al.  Assessment of the adequacy of mathematical models , 2006 .