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Systems biology

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Systems biology, a field of study in the biosciences, focuses on the systematic study of complex interactions in biological systems. Particularly from 2000 onwards, the term is used widely in the biosciences, and in a variety of contexts.

Overview Edit

Systems biology can be considered from a number of different aspects:

  • Some sources discuss systems biology as a field of study, particularly, the study of the interactions between the components of biological systems, and how these interactions give rise to the function and behavior of that system (for example, the enzymes and metabolites in a metabolic pathway)[1][2].
  • Other sources consider systems biology as a paradigm, usually defined in antithesis to the so-called reductionist paradigm, although fully consistent with the scientific method. The distinction between the two paradigms is referred to in these quotations:
  • Still other sources view systems biology in terms of the operational protocols used for performing research, namely a cycle composed of theory, computational modelling to propose specific testable hypotheses about a biological system, experimental validation, and then using the newly acquired quantitative description of cells or cell processes to refine the computational model or theory.[5][6]. Since the objective is a model of the interactions in a system, the experimental techniques that most suit systems biology are those that are system-wide and attempt to be as complete as possible. Therefore, transcriptomics, metabolomics, proteomics and high-throughput techniques are used to collect quantitative data for the construction and validation of models.
  • Finally, some sources see it as a socioscientific phenomenon defined by the strategy of pursuing integration of complex data about the interactions in biological systems from diverse experimental sources using interdisciplinary tools and personnel.



Systems biology finds its roots in:

One of the theorists who can be seen as a precursor of systems biology is Ludwig von Bertalanffy with his general systems theory. One of the first numerical simulations in biology was published in 1952 by the British neurophysiologists and nobel prize winners Alan Lloyd Hodgkin and Andrew Fielding Huxley, who constructed a mathematical model that explained the action potential propagating along the axon of a neuronal cell[7]. Their model described a cellular function emerging from the interaction between two different molecular components, a potassium and a sodium channels, and can therefore be seen as the beginning of computational systems biology[8]. In 1960, Denis Noble developed the first computer model of the heart pacemacker [9].




Techniques associated with systems biology Edit



  • Interactomics which is used mostly in the context of protein-protein interaction but in theory encompasses interactions between all molecules within a cell
  • Fluxomics, which deals with the dynamic changes of molecules within a cell over time
  • Biomics: systems analysis of the biome.

The investigations are frequently combined with large scale perturbation methods, including gene-based (RNAi, mis-expression of wild type and mutant genes) and chemical approaches using small molecule libraries. Robots and automated sensors enable such large-scale experimentation and data acquisition. These technologies are still emerging and many face problems that the larger the quantity of data produced, the lower the quality. A wide variety of quantitative scientists (computational biologists, statisticians, mathematicians, computer scientists, engineers, and physicists) are working to improve the quality of these approaches and to create, refine, and retest the models to accurately reflect observations.

The investigations of a single level of biological organization (such as those listed above) are usually referred to as Systematic Systems Biology. Other areas of Systems Biology includes Integrative Systems Biology, which seeks to integrate different types of information to advance the understanding the biological whole, and Dynamic Systems Biology, which aims to uncover how the biological whole changes over time (during evolution, for example, the onset of disease or in response to a perturbation). Functional Genomics may also be considered a sub-field of Systems Biology.

The systems biology approach often involves the development of mechanistic models, such as the reconstruction of dynamic systems from the quantitative properties of their elementary building blocks[11][12]. For instance, a cellular network can be modelled mathematically using methods coming from chemical kinetics and control theory. Due to the large number of parameters, variables and constraints in cellular networks, numerical and computational techniques are often used. Other aspects of computer science and informatics are also used in systems biology. These include new forms of computational model, such as the use of process calculi to model biological processes, the integration of information from the literature, using techniques of information extraction and text mining, the development of online databases and repositories for sharing data and models (such as BioModels Database), approaches to database integration and software interoperability via loose coupling of software, websites and databases (such as Gaggle [1]), and the development of syntactically and semantically sound ways of representing biological models, such as the Systems Biology Markup Language.

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Wiktionary: Systems biology

References Edit

  1. Snoep J.L. and Westerhoff H.V.; Alberghina L. and Westerhoff H.V. (Eds.) (2005.). "From isolation to integration, a systems biology approach for building the Silicon Cell". Systems Biology: Definitions and Perspectives: p7, Springer-Verlag. 
  2. Systems Biology - the 21st Century Science.
  3. Sauer, U. et al. "Getting Closer to the Whole Picture" Science (journal) 316 550 17 April 2007
  4. Denis Noble The Music of Life Oxford University Press (2006) p21
  5. Systems Biology: Modelling, Simulation and Experimental Validation.
  7. Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol, 117: 500-544.
  8. Le Novere (2007) The long journey to a Systems Biology of neuronal function. BMC Systems Biology, 1: 28
  9. Noble D (1960) Cardiac action and pacemaker potentials based on the Hodgkin-Huxley equations. Nature, 188: 495-497.
  10. Working the Systems.
  11. Gardner, TS, di Bernardo D, Lorenz D and Collins JJ (04 Jul 2003). Inferring genetic networks and identifying compound of action via expression profiling. Science 301: 102-1005.
  12. di Bernardo, D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliot SJ, Schaus SE and Collins JJ (Mar 2005). Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology 23: 377-383.
  13. Werner, E., "All systems go"., Naturevol 446, pp 493-494, March 29, 2007.
Genomics topics
Genome project | Glycomics | Human Genome Project | Proteomics
Chemogenomics | Structural genomics | Pharmacogenetics | Pharmacogenomics | Toxicogenomics
Bioinformatics | Cheminformatics | Systems biology

Category systems theory
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