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Systems biology

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Systems biology is an academic field that seeks to integrate different levels of information to understand how biological systems function. By studying the relationships and interactions between various parts of a biological system (e.g. metabolic pathways, organelles, cells, physiological systems, organisms etc.) it is hoped that eventually an understandable model of the whole system can be developed.


Systems biology begins with the knowledge of possible genes and proteins in an organism, and then either uses high-throughput techniques such as microarrays to measure the changes in all mRNAs, or uses proteomics methods and mass spectrometry to measure the change in protein concentration, in response to a given perturbation. A crucial part of this process is to model the inherent stochasticity of the system.

In contrast to much of molecular biology, systems biology does not seek to break down a system into all of its parts and study one part of the process at a time, with the hope of being able to reassemble all the parts into a whole. Some systems biologists argue that this reductionist approach to biology must always fail, either because of nature's redundancy and complexity, or because we have not understood all the parts of the processes.

Using knowledge from molecular biology, the systems biologist can propose a hypothesis that explains these changes, and importantly, these hypotheses can be used to mathematically model the system. This model is used to predict how different changes affect the phenotype of a cell, and can be iteratively tested to prove or disprove the model. New approaches are being developed by quantitative scientists such as computational biologists, statisticians, mathematicians, computer scientists, engineers, and physicists to improve our ability to make these high-throughput measurements and create, refine, and retest the models until the predicted behavior accurately reflects the phenotype seen.

History

Many of the concepts of systems biology are not new. Biologists and biochemists have long known that the detailed (reductionist) study of individual proteins is just the first step toward an understanding of the overall (integrated) life process. The current advances in biology (coming from bioinformatics in the post genomic era) are a direct result of the success of this reductionist approach.

The available experimental procedures necessarily forced a 'one protein at a time' analysis during the middle of the 20th century. Advances in experimental methodology (high-throughput screening technologies) have made the 'global' view accessible for the first time, allowing scientific research at the overall level of the cell or the organism possible.

The point is: while biologists have always known a protein must function within the context of the whole cell, it has only recently become possible to obtain data about this functional level.

Applications

Many predictions concerning the impact of genomics on health care have been proposed. For example, the development of novel therapeutics and the introduction of personalised treatments are conjectured and may become reality as a small number of biotechnology companies are using this cell-biology driven approach to the development of therapeutics. However, these predictions rely upon our ability to understand and quantify the roles that specific genes possess in the context of human and pathogen physiologies. The ultimate goal of systems biology is to derive the prerequisite knowledge and tools.

Notable organizations

Organizations created to further systems biology in the United States include the Institute for Systems Biology (ISB) in Seattle, Washington and a new Department of Systems Biology at Harvard Medical School. The ISB is a non-profit research institute with a goal to identify strategies for predicting and preventing diseases such as cancer, diabetes and AIDS. There also exists the Systems Biology Institute based in Tokyo; the Institute for Systems Biology at St Petersburg, Russia, the Biosystems Informatics Institute in the UK, the Ottawa Institute of Systems Biology and the Institute for Molecular Systems Biology Zürich, Switzerland .

See also

Bibliography

  • Hiroaki Kitano (editor), (2001) Foundations of Systems Biology, MIT Press; (October 15, 2001) ISBN 0262112663
  • Gregory Bock and Jamie A. Goode (eds), (2002) "In Silico" Simulation of Biological Processes, Novartis Foundation Symposium 247, John Wiley & Sons Ltd,, ISBN 0-470-84480-9
  • Marc Vidal and Eileen E. M. Furlong. Nature Reviews Genetics 2004 From OMICS to systems biology
  • E. Klipp, R. Herwig, A. Kowald, C. Wierling, and H. Lehrach, Systems Biology in Practice, Wiley-VCH, 2005, ISBN 3527310789
  • Werner, E., "The Future and Limits of Systems Biology", Science STKE 2005, pe16 (2005).
  • Bernhard Ø. Palsson. 2006 "Systems Biology - Properties of Reconstructed Networks," Cambridge University Press. ISBN 9780521859035

Systems biology organization websites

Systems Biology Research Groups

Please add other groups as appropriate

Software Tools for Systems Biology

International Conference

  • BioCircle.org - The Open Source Systems Biology Portal dedicated to computational aspects of Systems Biology. Visit us for the first community wide Systems Biology Tools & Resources - Survey - 2005 results.
  • BioChemWeb.org - The Virtual Library of Biochemistry and Cell Biology: A Guide to Biochemistry, Molecular Biology & Cell Biology on the Web
  • Guardian.co.uk - 'The unselfish gene: The new biology is reasserting the primacy of the whole organism - the individual - over the behaviour of isolated genes', Johnjoe McFadden, The Guardian (May 6, 2005)
  • PsiMap.kaist.ac.kr - PSIbase Database: Protein Structure Interactome Map Database Server: Structural Interactome Map of all Proteins
  • ScienceMag.org - Special Issue: Systems Biology, Science, Vol 295, No 5560, March 1, 2002
  • Nature - Molecular Systems Biology


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