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Defining Systems Biology: A Brief Overview of the Term and Field

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In Silico Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1021))

Abstract

Here we provide a broad overview of the definition of the term “systems biology” as well as pinpoint specific events in biological research and beyond that are consistently cited to have contributed and led to the current science of in silico systems biology. Since there have been many reviews and historical accounts describing the term, it would be impossible to include all single references. However, we do attempt to provide a consensus vision of how the field has evolved and consequently the terminology that followed it. We also highlight the development and general acceptance, and use, of standards for model representations as being crucial to the continued success of the in silico systems biology field.

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References

  1. Noble D (1960) Cardiac action and pacemaker potentials based on the Hodgkin-Huxley equations. Nature 188:495–497

    Article  CAS  Google Scholar 

  2. Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduct and excitation in nerve. J Physiol II7:500–544

    Google Scholar 

  3. Auffray C, Noble D (2009) Origins of systems biology in William Harvey’s masterpiece on the movement of the heart and the blood in animals. Int J Mol Sci 10:1658–1669

    Article  PubMed  Google Scholar 

  4. Auffray C, Imbeaud S, Roux-Rouquie M, Hood L (2003) From functional genomics to systems biology: concepts and practices. C R Biol 326:879–892

    Article  PubMed  CAS  Google Scholar 

  5. Saks V, Monge C, Guzun R (2009) Philosophical basis and some historical aspects of systems biology: from Hegel to Noble—applications for bioenergetic research. Int J Mol Sci 10(3):1161–1192

    Article  PubMed  CAS  Google Scholar 

  6. Csete ME, Doyle JC (2002) Reverse engineering of biological complexity. Science 295:1664–1669

    Article  PubMed  CAS  Google Scholar 

  7. Cannon WB (1941) The body physiologic and the body politic. Science 93:1–10

    Article  PubMed  CAS  Google Scholar 

  8. Joyner MJ, Pedersen BK (2011) Ten questions about systems biology. J Physiol 589:1017–1030

    Article  PubMed  CAS  Google Scholar 

  9. Noble D (2010) Biophysics and systems biology. Philos Trans R Soc A 2010(368):1125–1139

    Article  Google Scholar 

  10. Selinger DW, Wright MA, Church GM (2003) On the complete determination of biological systems. Trends Biotechnol 21(6):251–254

    Article  PubMed  CAS  Google Scholar 

  11. Collins FS, Morgan M, Patrinos A (2003) The human genome project: lessons from large-scale biology. Science 300:286

    Article  PubMed  CAS  Google Scholar 

  12. Frazier ME, Johnson GM, Thomassen DG, Oliver CE, Patrinos A (2003) Realizing the potential of the genome revolution: the genomes to life program. Science 300:290

    Article  PubMed  CAS  Google Scholar 

  13. Schneider MV, Orchard S (2011) Omics technologies, data and bioinformatics principles. Methods Mol Biol 719:3–30

    Article  PubMed  CAS  Google Scholar 

  14. Jamers A, Blust R, De Coen W (2009) Omics in algae: paving the way for a systems biological understanding of algal stress phenomena? Aquat Toxicol 92(3):114–121

    Article  PubMed  CAS  Google Scholar 

  15. Gopalacharyulu PV, Lindfors E, Bounsaythip C, Kivioja T, Yetukuri L, Hollmén J, Orešic M (2005) Data integration and visualization system for enabling conceptual biology. Bioinformatics 21(suppl 1):i177–i185

    Article  PubMed  CAS  Google Scholar 

  16. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr J-H, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524–531

    Article  PubMed  CAS  Google Scholar 

  17. Finney A, Hucka M (2003) Systems biology markup language: level 2 and beyond. Biochem Soc Trans 31(6):1472–1473

    Article  PubMed  CAS  Google Scholar 

  18. Cuellar AA, Lloyd CM, Nielsen PF, Bullivant DP, Nickerson DP, Hunter PJ (2003) An overview of CellML 1.1, a biological model description language. Simulation 79(12):740–747

    Article  Google Scholar 

  19. Hedley WJ, Nielsen PMF, Hunter Seattle PJ (2000) XML languages for describing biological models. In: Proceeding of BMES 2000 (Biomedical Engineering Society Annual Meeting)

    Google Scholar 

  20. Joyce AR, Palsson BØ (2006) The model organism as a system: integrating ‘omics’ data sets. Nature 7:198–210

    CAS  Google Scholar 

  21. Woodger JH (1929) Biological principles: a critical study, 2nd edn. Routledge, London

    Google Scholar 

  22. Whyte LL, Wilson AG, Wilson D (eds) (1969) Hierarchical structures. American Elsevier, New York

    Google Scholar 

  23. Pattee HH (1973) Hierarchy theory: the challenge of complex systems. Brazilier, New York

    Google Scholar 

  24. Trewavas A (2006) A brief history of systems biology. Plant Cell 18(10):2420–2430

    Article  PubMed  CAS  Google Scholar 

  25. Machado D et al (2011) Modelling formalisms in systems biology. AMB Exp 1:45

    Article  Google Scholar 

  26. Adelinde M Uhrmacher1, Daniela Degenring1, and Bernard Zeigler2 C Priami et al. (eds) (2005) Transactions on Computational Systems Biology, 3380:66–89

    Google Scholar 

  27. Bosl WL (2007) Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery. BMC Syst Biol 1:13

    Article  PubMed  Google Scholar 

  28. Fisher J, Piterman N (2010) The executable pathway to biological networks. Brief Funct Genomics 9(1):79–92

    Article  PubMed  Google Scholar 

  29. Laszlo A, Krippner S (1998) Systems theories: their origins, foundations, and development, ch. 3. In: Jordan JS (ed) Systems theories and a priori aspects of perception. Elsevier Science, Amsterdam, pp 47–74

    Chapter  Google Scholar 

  30. Yarden Y, Pines G (2012) The ERBB network: at last, cancer therapy meets systems biology. Nat Rev Cancer 12(8):553–563

    Article  PubMed  CAS  Google Scholar 

  31. Trautmann L, Sekaly RP (2011) Solving vaccine mysteries: a systems biology perspective. Nat Immunol 12(8):729–731

    Article  PubMed  CAS  Google Scholar 

  32. Kitano H (2002) Computational systems biology. Nature 420(6912):206–210

    Article  PubMed  CAS  Google Scholar 

  33. Liu Y-Y, Slotine J-J, Baraba’si A-L (2011) Controllability of complex networks. Nature 473:167–173

    Article  PubMed  CAS  Google Scholar 

  34. Chen L-L, Chung W-C, Lin C-P, Kuo C-H (2012) Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PLoS One 7(3):e34407. doi:10.1371/journal.pone.0034407

    Article  PubMed  CAS  Google Scholar 

  35. Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD (2008) Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol 19(3):228–234

    Article  PubMed  CAS  Google Scholar 

  36. de Jong B, Siewers V, Nielsen J (2012) Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels. Curr Opin Biotechnol 23(4):624–630

    Article  PubMed  Google Scholar 

  37. Nookaew I, Gabrielsson BG, Holmäng A, Sandberg A-S, Nielsen J (2010) Identifying molecular effects of diet through systems biology: influence of herring diet on sterol metabolism and protein turnover in mice. PLoS One 5(8):e12361. doi:10.1371/journal.pone.0012361

    Article  PubMed  Google Scholar 

  38. Uri A (2006) An introduction to systems biology: design principles of biological circuits, 2nd edn. (Chapman & Hall/CRC Mathematical & Computational Biology). http://www.amazon.com/Introduction-Systems-Biology-Mathematical-Computational/dp/1584886420

  39. Klipp E, Herwig R, Kowald A, Wierling C, Lehrach H (2005) Systems biology in practice: concepts, implementation and application. Wiley-VCH, Weinheim. ISBN 3-527-31078-9

    Book  Google Scholar 

  40. Falconer E, Hills M, Naumann U, Poon SS, Chavez EA, Sanders AD, Zhao Y, Hirst M, Lansdorp PM (2012) DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods 9:1107–1112. doi:10.1038/nmeth.2206

    Article  PubMed  CAS  Google Scholar 

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Acknowledgement

I am grateful to Boye Gricar for useful comments on earlier and final versions of this chapter. Thanks to Nicolas Le Novère for inspiration. Big thanks to Jacqueline Dreyer, Nick Juty and Julio Saez-Rodriguez for useful comments to the final version of this chapter.

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Schneider, M.V. (2013). Defining Systems Biology: A Brief Overview of the Term and Field. In: Schneider, M. (eds) In Silico Systems Biology. Methods in Molecular Biology, vol 1021. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-450-0_1

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  • DOI: https://doi.org/10.1007/978-1-62703-450-0_1

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-449-4

  • Online ISBN: 978-1-62703-450-0

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