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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Noble D (1960) Cardiac action and pacemaker potentials based on the Hodgkin-Huxley equations. Nature 188:495–497
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
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
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
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
Csete ME, Doyle JC (2002) Reverse engineering of biological complexity. Science 295:1664–1669
Cannon WB (1941) The body physiologic and the body politic. Science 93:1–10
Joyner MJ, Pedersen BK (2011) Ten questions about systems biology. J Physiol 589:1017–1030
Noble D (2010) Biophysics and systems biology. Philos Trans R Soc A 2010(368):1125–1139
Selinger DW, Wright MA, Church GM (2003) On the complete determination of biological systems. Trends Biotechnol 21(6):251–254
Collins FS, Morgan M, Patrinos A (2003) The human genome project: lessons from large-scale biology. Science 300:286
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
Schneider MV, Orchard S (2011) Omics technologies, data and bioinformatics principles. Methods Mol Biol 719:3–30
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
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
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
Finney A, Hucka M (2003) Systems biology markup language: level 2 and beyond. Biochem Soc Trans 31(6):1472–1473
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
Hedley WJ, Nielsen PMF, Hunter Seattle PJ (2000) XML languages for describing biological models. In: Proceeding of BMES 2000 (Biomedical Engineering Society Annual Meeting)
Joyce AR, Palsson BØ (2006) The model organism as a system: integrating ‘omics’ data sets. Nature 7:198–210
Woodger JH (1929) Biological principles: a critical study, 2nd edn. Routledge, London
Whyte LL, Wilson AG, Wilson D (eds) (1969) Hierarchical structures. American Elsevier, New York
Pattee HH (1973) Hierarchy theory: the challenge of complex systems. Brazilier, New York
Trewavas A (2006) A brief history of systems biology. Plant Cell 18(10):2420–2430
Machado D et al (2011) Modelling formalisms in systems biology. AMB Exp 1:45
Adelinde M Uhrmacher1, Daniela Degenring1, and Bernard Zeigler2 C Priami et al. (eds) (2005) Transactions on Computational Systems Biology, 3380:66–89
Bosl WL (2007) Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery. BMC Syst Biol 1:13
Fisher J, Piterman N (2010) The executable pathway to biological networks. Brief Funct Genomics 9(1):79–92
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
Yarden Y, Pines G (2012) The ERBB network: at last, cancer therapy meets systems biology. Nat Rev Cancer 12(8):553–563
Trautmann L, Sekaly RP (2011) Solving vaccine mysteries: a systems biology perspective. Nat Immunol 12(8):729–731
Kitano H (2002) Computational systems biology. Nature 420(6912):206–210
Liu Y-Y, Slotine J-J, Baraba’si A-L (2011) Controllability of complex networks. Nature 473:167–173
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
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
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
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
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
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
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
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.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
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
Download citation
DOI: https://doi.org/10.1007/978-1-62703-450-0_1
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-449-4
Online ISBN: 978-1-62703-450-0
eBook Packages: Springer Protocols