iPedia Free Information Center

Information about Systems Biology

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

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:
"The reductionist approach has successfully identified most of the components and many of the interactions but, unfortunately, offers no convincing concepts or methods to understand how system properties emerge...the pluralism of causes and effects in biological networks is better addressed by observing, through quantitiative measures, multiple components simultaneously and by rigorous data integration with mathematical models" Science[3]


"Systems biology...is about putting together rather than taking apart, integration rather than reduction. It requires that we develop ways of thinking about integration that are as rigorous as our reductionist programmes, but different....It means changing our philosophy, in the full sense of the term" Denis Noble[4]
  • 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.
This variety of viewpoints is illustrative of the fact that systems biology refers to a cluster of peripherally overlapping concepts rather than a single well-delineated field. However the term has widespread currency and popularity as of 2007, with chairs and institutes of systems biology proliferating worldwide.

History

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. In 1952, the British neurophysiologists and nobel prize winners Alan Lloyd Hodgkin and Andrew Fielding Huxley constructed a mathematical model explaining the action potential propagating along the axon of a neuronal cell. In 1960, Denis Noble developed the first computer model of a beating heart.

The 1960s and 1970s saw the development of several approaches to study complex molecular systems, such as the Metabolic Control Analysis and the biochemical systems theory. The successes of molecular biology throughout the 1980s, coupled with a skepticism toward theoretical biology, that then promised more than it achieved, caused the quantitative modelling of biological processes to become a somewhat minor field.

However the birth of functional genomics in the 1990s meant that large quantities of high quality data became available, while the computing power exploded, making more realistic models possible. In 1997, the group of Masaru Tomita published the first quantitative model of the metabolism of a whole (hypothetical) cell.

Around the year 2000, when Institutes of Systems Biology were established in Seattle and Tokyo, systems biology emerged as a movement in its own right, spurred on by the completion of various genome projects, the large increase in data from the omics (e.g. genomics and proteomics) and the accompanying advances in high-throughput experiments and bioinformatics. Since then, various research institutes dedicated to systems biology have been developed. As of summer 2006, due to a shortage of people in systems biology[7] several doctoral training centres in systems biology have been established in many parts of the world.

Techniques associated with systems biology

According to the interpretation of System Biology as the ability to obtain, integrate and analyze complex data from multiple experimental sources using interdisciplinary tools, some typical technology platforms are: In addition to the identification and quantification of the above given molecules further techniques analyze the dynamics and interactions within a cell. This includes:
  • 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
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. 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.

See also

References

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.
6. ^ Kholodenko B.N., Bruggeman F.J., Sauro H.M.; Alberghina L. and Westerhoff H.V.(Eds.) (2005.). "Mechanistic and modular approaches to modeling and inference of cellular regulatory networks". Systems Biology: Definitions and Perspectives: p143, Springer-Verlag. 
7. ^ Working the Systems.
8. ^ Werner, E., "All systems go"., Naturevol 446, pp 493-494, March 29, 2007.

Bibliography

Books

  • H Kitano (editor). Foundations of Systems Biology. MIT Press: 2001. ISBN 0-262-11266-3
  • CP Fall, E Marland, J Wagner and JJ Tyson (Editors). "Computational Cell Biology." Springer Verlag: 2002 ISBN 0-387-95369-8
  • G Bock and JA Goode (eds).In Silico" Simulation of Biological Processes, Novartis Foundation Symposium 247. John Wiley & Sons: 2002. ISBN 0-470-84480-9
  • E Klipp, R Herwig, A Kowald, C Wierling, and H Lehrach. Systems Biology in Practice. Wiley-VCH: 2005. ISBN 3-527-31078-9
  • L. Alberghina and H. Westerhoff (Editors) – Systems Biology: Definitions and Perspectives, Topics in Current Genetics 13, Springer Verlag (2005), ISBN 13: 978-3540229681
  • A Kriete, R Eils. Computational Systems Biology., Elsevier - Academic Press: 2005. ISBN 0-12-088786-X
  • K. Sneppen and G. Zocchi, (2005) Physics in Molecular Biology, Cambridge University Press, ISBN 0-521-84419-3
  • D. Noble, The Music of life. Biology beyond the genome Oxford University Press 2006. ISBN-10: 0199295735, ISBN-13: 978-0199295739
  • Z. Szallasi, J. Stelling, and V.Periwal (eds.) System Modeling in Cellular Biology: From Concepts to Nuts and Bolts (Hardcover), MIT Press: 2006, ISBN 0-262-19548-8
  • B Palsson, Systems Biology - Properties of Reconstructed Networks. Cambridge University Press: 2006. ISBN 978-0-521-85903-5
  • K Kaneko. Life: An Introduction to Complex Systems Biology. Springer: 2006. ISBN: 3540326669
  • U Alon. An Introduction to Systems Biology: Design Principles of Biological Circuits. CRC Press: 2006. ISBN 1-58488-642-0 - emphasis on Network Biology (For a comparative review of Alon, Kaneko and Palsson see[8] )

Articles

External links

Genomics topics
Genome project | Paleopolyploidy | Glycomics | Human Genome Project | Proteomics
Chemogenomics | Structural genomics | Pharmacogenetics | Pharmacogenomics | Toxicogenomics | Computational genomics
Bioinformatics | Cheminformatics | Systems biology


 •  • [ e]
Global structure in Systems, Systems sciences and Systems scientists
Categories
SystemsBiological system Complex system Complex adaptive system Conceptual system Cultural system Dynamical system Economic system Ecosystem Formal system Global Positioning System Human organ systems Information systems Legal system Metric system Nervous system Non-linear system Operating system Physical system Political system Sensory system Social system Solar System System Systems of measurement
Fields of theoryChaos theory Complex systems Control theory Cybernetics Holism in science Sociotechnical systems theory Systems biology Systems dynamics Systems ecology Systems engineering Systems theory Systems science
Systems scientistsRussell L. Ackoff William Ross Ashby Gregory Bateson Ludwig von Bertalanffy Kenneth E. Boulding C. West Churchman Heinz von Foerster Charles Franois Jay Wright Forrester Ralph W. Gerard Debora Hammond George Klir Niklas Luhmann Humberto Maturana Donella Meadows Mihajlo D. Mesarovic Howard T. Odum Talcott Parsons Ilya Prigogine Anatol Rapoport Francisco Varela John N. Warfield Norbert Wiener
Biology (from Greek: βίος, bio, "life"; and λόγος, logos, "knowledge"), also referred to as the biological sciences, is the scientific study of life.
..... Click the link for more information.
A complex is a whole that comprehends a number of parts, especially one with interconnected or mutually related parts. It may refer to:
  • Complex (chemistry), also called a "coordination compound" or "metal complex", is a structure consisting of a central atom or molecule

..... Click the link for more information.
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.
..... Click the link for more information.
20th century - 21st century
1970s  1980s  1990s  - 2000s -  2010s  2020s  2030s
1997 1998 1999 - 2000 - 2001 2002 2003

2000 by topic:
News by month
Jan - Feb - Mar - Apr - May - Jun
..... Click the link for more information.
Biology (from Greek: βίος, bio, "life"; and λόγος, logos, "knowledge"), also referred to as the biological sciences, is the scientific study of life.
..... Click the link for more information.
Enzymes are proteins that catalyze (i.e. accelerate) chemical reactions.[1] In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, the products.
..... Click the link for more information.
Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" - specifically, the study of their small-molecule metabolite profiles.
..... Click the link for more information.
In biochemistry, a metabolic pathway is a series of chemical reactions occurring within a cell. In each pathway a principal chemical is modified by chemical reactions. These reactions are accelerated, more accurately catalyzed, by enzymes.
..... Click the link for more information.
Since the late 1960s, the word paradigm (IPA: /ˈpærədaɪm/) has referred to a thought pattern in any scientific discipline or other epistemological context.
..... Click the link for more information.
reductionism is a theory that asserts that the nature of complex things is reduced to the nature of sums of simpler or more fundamental things. This can be said of objects, phenomena, explanations, theories, and meanings.
..... Click the link for more information.
Scientific method is a body of techniques for investigating phenomena, acquiring new knowledge, or correcting and integrating previous knowledge. It is based on gathering observable, empirical and measurable evidence subject to specific principles of reasoning,[1]
..... Click the link for more information.
Science is the academic journal of the American Association for the Advancement of Science and is considered one of the world's most prestigious scientific journals. The journal is peer-reviewed, is published weekly, and has a print subscriber base of around 130,000.
..... Click the link for more information.
Denis Noble
Born November 16 1936 (1936--) (age 72)

Residence UK
Nationality British
..... Click the link for more information.
The transcriptome is the set of all messenger RNA (mRNA) molecules, or "transcripts", produced in one or a population of cells. The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type.
..... Click the link for more information.
Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" - specifically, the study of their small-molecule metabolite profiles.
..... Click the link for more information.
Proteomics is the large-scale study of proteins, particularly their structures and functions.[1][2] Proteins are vital parts of living organisms, as they are the main components of the physiological pathways of cells.
..... Click the link for more information.
20th century - 21st century - 22nd century
1970s  1980s  1990s  - 2000s -  2010s  2020s  2030s
2004 2005 2006 - 2007 - 2008 2009 2010

2007 by topic:
News by month
Jan - Feb - Mar - Apr - May - Jun
..... Click the link for more information.
Enzyme kinetics is the study of the rates of chemical reactions that are catalysed by enzymes. The study of an enzyme's kinetics provides insights into the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled in the cell and how drugs and
..... Click the link for more information.
19th century - 20th century
1870s  1880s  1890s  - 1900s -  1910s  1920s  1930s
1897 1898 1899 - 1900 - 1901 1902 1903

Year 1900 (MCM
..... Click the link for more information.
19th century - 20th century - 21st century
1940s  1950s  1960s  - 1970s -  1980s  1990s  2000s
1967 1968 1969 - 1970 - 1971 1972 1973

Year 1970 (MCMLXX
..... Click the link for more information.
For control theory in psychology and sociology, see .


Control theory is an interdisciplinary branch of engineering and mathematics, that deals with the behavior of dynamical systems. The desired output of a system is called the reference.
..... Click the link for more information.
Cybernetics was defined by Norbert Wiener, in his book of that title, as the study of control and communication in the animal and the machine. Stafford Beer called it the science of effective organization and Gordon Pask extended it to include information flows "in all
..... Click the link for more information.
Karl Ludwig von Bertalanffy (September 19, 1901, Vienna, Austria – June 12, 1972, New York, USA) was an Austrian-born biologist known as one of the founders of general systems theory. He finished his PhD thesis about physicist and philosopher Gustav Theodor Fechner in 1926.
..... Click the link for more information.
Systems theory is an interdisciplinary field of science. It studies the nature of complex systems in nature, society, and science. More specificially, it is a framework by which one can analyze and/or describe any group of objects that work in concert to produce some result.
..... Click the link for more information.
Sir Alan Lloyd Hodgkin, OM, KBE, FRS (born February 5, 1914, Banbury, Oxfordshire, England [1]; died December 20, 1998 Cambridge [2]) was a British physiologist and biophysicist, who won the 1963 Nobel Prize in Physiology or Medicine for his work with Andrew
..... Click the link for more information.
Sir Andrew Fielding Huxley, OM, FRS (born 22 November 1917, Hampstead, London [1]) is an English physiologist and biophysicist, who won the 1963 Nobel Prize in Physiology or Medicine for his work with Alan Lloyd Hodgkin on the basis of nerve action potentials, the
..... Click the link for more information.
Denis Noble
Born November 16 1936 (1936--) (age 72)

Residence UK
Nationality British
..... Click the link for more information.
19th century - 20th century - 21st century
1930s  1940s  1950s  - 1960s -  1970s  1980s  1990s
1957 1958 1959 - 1960 - 1961 1962 1963

Year 1960 (MCMLX
..... Click the link for more information.
19th century - 20th century - 21st century
1940s  1950s  1960s  - 1970s -  1980s  1990s  2000s
1967 1968 1969 - 1970 - 1971 1972 1973

Year 1970 (MCMLXX
..... Click the link for more information.
Metabolic control analysis (MCA) is a mathematical framework for describing metabolic, signaling and genetic pathways. MCA quantifies how variables, such as fluxes and species concentrations, depend on network parameters.
..... Click the link for more information.


This article is copied from an article on Wikipedia.org - the free encyclopedia created and edited by online user community. The text was not checked or edited by anyone on our staff. Although the vast majority of the wikipedia encyclopedia articles provide accurate and timely information please do not assume the accuracy of any particular article. This article is distributed under the terms of GNU Free Documentation License.
Herod_Archelaus


page counter