Abstract
The focus of this chapter is on steps 6–10 of Fig. 4.1. The first step involves adding the kinetics associated with each reaction. Once, the model has been assembled it can be simulated. Its output can then be explored, analysed, and interpreted. If the output is in agreement with its biological counterpart, then the hypothesis can be tested.
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References
Schomburg, I., et al. 2004. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Research 32 (Database issue): D431–D433.
Wittig, U., et al. 2012. SABIO-RK—database for biochemical reaction kinetics. Nucleic Acids Research 40 (Database issue): D790–D796.
Tanabe, M., and M. Kanehisa. 2012. Using the KEGG database resource. Current Protocols in Bioinformatics. Chapter 1: Unit 1.12.
Fabregat, A., et al. 2016. The Reactome pathway Knowledgebase. Nucleic Acids Research 44 (D1): D481–D487.
Caspi, R., et al. 2008. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research 36 (Database issue): D623–D631.
Chelliah, V., C. Laibe, and N. Le Novere. 2013. BioModels Database: a repository of mathematical models of biological processes. Methods in Molecular Biology 1021: 189–199.
Drager, A., et al. 2015. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Systems Biology 9: 68.
Goldberg, R.N., Y.B. Tewari, and T.N. Bhat. 2004. Thermodynamics of enzyme-catalyzed reactions—a database for quantitative biochemistry. Bioinformatics 20 (16): 2874–2877.
Kale, N.S., et al., MetaboLights: an open-access database repository for metabolomics data. Current Protocols in Bioinformatics 53: 14.13.1–14.13.18.
Vizcaino, J.A., et al. 2016. 2016 update of the PRIDE database and its related tools. Nucleic Acids Research 44 (D1): D447–D456.
Barrett, T., et al. 2013. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Research 41 (Database issue): D991–D995.
Schellenberger, J., et al. 2010. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11: 213.
Huang, Z., et al. 2011. ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Research 39 (Database issue): D663–D669.
Parkinson, H., et al. 2011. ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Research 39 (Database issue): D1002–D1004.
Wishart, D.S., et al. 2007. HMDB: the Human Metabolome Database. Nucleic Acids Research 35 (Database issue): D521–D526.
Costa, R.S., A. Verissimo, and S. Vinga. 2014. KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. BMC Systems Biology 8: 85.
Mc Auley, M.T., et al. 2012. A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Systems Biology 6 (1): 130.
Lin, D.S., and W.E. Connor. 1980. The long term effects of dietary cholesterol upon the plasma lipids, lipoproteins, cholesterol absorption, and the sterol balance in man: the demonstration of feedback inhibition of cholesterol biosynthesis and increased bile acid excretion. Journal of Lipid Research 21 (8): 1042–1052.
Paalvast, Y., J.A. Kuivenhoven, and A.K. Groen. 2015. Evaluating computational models of cholesterol metabolism. Biochimica et Biophysica Acta 1851 (10): 1360–1376.
Genser, B., et al. 2012. Plant sterols and cardiovascular disease: a systematic review and meta-analysis. European Heart Journal 33 (4): 444–451.
Law, M. 2000. Plant sterol and stanol margarines and health. BMJ 320 (7238): 861–864.
Katan, M.B., et al. 2003. Efficacy and safety of plant stanols and sterols in the management of blood cholesterol levels. Mayo Clinic Proceedings 78 (8): 965–978.
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Mc Auley, M.T. (2019). Model Building: Part Two. In: Computer Modelling for Nutritionists. Springer, Cham. https://doi.org/10.1007/978-3-319-39994-2_5
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