2003年4月14日，由6個國家的科學家共同宣佈人類基因體序列圖繪製成功，所完成的序列圖覆蓋人類基因體所含基因區域的99％，精確率達到99.99％，這一計畫的完成比原先估計的要提前兩年。自從1990年10月1日開始進行的人類基因體計畫是由美國能源部 (Department of Energy; DOE) 及國家衛生院 (National Institutes of Health; NIH) 共同主導展開的一項跨國計畫。計劃主旨是希望能將人類的基因體完全定序出來，並找出基因的相關位置，以便能夠進一步研究每個基因可能的生理功能及其與疾病發生之間的相關性。就在人類基因體計畫完成之前，由於計畫所產生的鉅量的資料，因此在90年代初，生物學家將電腦分析及微機電的方法大量引入生物學的研究，使得生物醫學的研究跳脫出傳統的研究方式，進入了一個新的研究領域：系統生物學 (systems biology)，帶動了生物學新研究方法的風潮。

2001年第二屆國際系統生物學會 (2nd International Conference on Systems Biology；ICSB 2001) 對 ”系統生物學” 的解釋為：Systems Biology is the quantitative study of biological processes as whole systems instead of isolate parts. The goal of Systems Biology is the construction and experimental validation of models that explain and predict the behavior of biological systems. (系統生物學是對生物體整個過程做一全面性的定量研究，並非以生物體的某一部分為對象。目的是要建立模式並以實驗來證實其可預測的生物體的表現)。簡單的說，這樣的研究方法就是利用資訊科學及微機電工程的技術來研究生物學的問題，最後並希望能夠利用電腦運算的結果，來預測細胞、器官、系統甚至完整生物體的表現。

最先把DNA测序 (sequencing) 自動化，同時也是1985年首先推動基因体計畫的科學家之一的Leroy Hood博士是最早提出「系統生物學」，並認為系統生物學是研究一個生物系統內所有組成份的構成，以及在特定條件下這些組成份相互關係的學科。並在2000年1月與Alan Aderem及Ruedi Aebersold等學者創立一個非營利性質的研究機構：Institute for Systems Biology，致力於系統生物學在生命科學相關領域的研究與應用。Leroy Hood博士在2001年3月來台訪問時，對系統生物學曾有以下的描述：系統生物學是將DNA、RNA、蛋白質以及三者彼此之間的交互作用等資訊加以整合，並運用這些資料去建立出數學計量模型，以期能掌握所有生物基因與組織間的關係及運作。因此系統生物學的研究過程是先取得一個生物、組織或細胞系統，辨識出各種內部因素，在獲得DNA、RNA及蛋白質相互作用及資訊網路方面整合所獲得的資訊，然後開發出能描述系統結構和行為的數學模型，最後可以藉由此一個模型系統，使這個系統可以自動執行所需的功能。因此系統生物學是結合許多不同學科的領域，透過彼此相互的網狀合作，針對一個生物現象所進行的研究。

而Hiroaki Kitano博士認為系統生物學的研究可以包含四大部分，分別利用資訊科學 (computation)、分析 (analysis)、技術 (technology)、基因组學 (genomics)、四者形成環型而連續的關係，建立出一個新的研究模式(Kitano, 2002)，並且利用這一模式所發展的一系列的工具來解決生物學家所面臨的研究問題。

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. Some traditionalists respond that the alleged dichotomy between holistic and reductionist approaches generally exists in the mind of observers, rather than practitioners, of science. Still others accuse systems biologists of setting vague and poorly articulated goals without proposing concrete strategies, while the projects that they actually end up working on fall so far short of the initial goals as to be reductionist according to system's biology's own terms, or simply insignificant.

Using knowledge from molecular biology, the systems biologist can propose hypotheses that explain a system's behavior. Importantly, these hypotheses can be used to mathematically model the system. Models are used to predict how different changes in the system's environment affect the system and can be iteratively tested for their validity. 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.

[编辑] 发展史

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.

系统生物学的概念由来已久。生物学家及生化学家早就意识到，纵向的单个分子及其通路〔如蛋白质，或更常见的酶〕细致研究仅仅是对于认识生命科学的可行的、必要的开始。当代生物科学的进展—生物信息学—即是对以往的个别研究的归纳和演绎。

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.

20世纪中期的研究手段只允许单个蛋白质分子的研究。以“高通量”为特色的研究工具的发展使得对整个细胞（单细胞生物如大肠杆菌 E. coli）以致对整个生物个体（多细胞生物如斑马鱼 D. rerio）的研究成为可能。

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.

评论：尽管生物学家很早就认为应该在细胞的水平研究单个蛋白质分子的功能，但也只有到最近人们才能得到这方面的信息。

[编辑] 应用

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. Even with today's resources and expertise, this goal is immeasurably distant.

[编辑] 著名机构

Organizations created to further systems biology in the United States include the Institute for Systems Biology (ISB) in Seattle, Washington, BioX at Stanford University, a new Department of Systems Biology at Harvard Medical School, and the Systems Biology research group at Pacific Northwest National Laboratory. 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. Work at PNNL is focused on a variety of research areas, including oxidative stress and radiation, cell signaling networks, and microbial communities. 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, the Institute for Molecular Systems Biology Zürich, Switzerland , SystemsX: the Swiss Initiative in Systems Biology, and the Center for the Study of Biological Complexity.

[编辑] 参见

[编辑] 参考书目

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 ?. Palsson. 2006 "Systems Biology - Properties of Reconstructed Networks," Cambridge University Press. ISBN 9780521859035

[编辑] 系统生物学机构网址

issb.org - The International Society for Systems Biology
InterActomics.org - Community for Interactomics: Editable hypertext pages (a systems biology Wiki)
omica.netf irms.com/ Celln omica.com - Research in multicellular developmental systems biology (US based)
SystemsBiology.org - Institute for Systems Biology (US based)
Systems-Biology.org - Systems Biology Institute (Japan based)
Ottawa Institute for Systems Biology (Canada)
Munich Systems Biology Forum - Systems biology groups in Munich and worldwide
CSBi :: Computational and Systems Biology at MIT
Biosystems Informatics Institute - Systems biology research institute in Newcastle upon Tyne, UK
YSBN.org - Yeast Systems Biology Network worldwide
Institute for Molecular Systems Biology
sysbio.org - Systems Biology at Pacific Northwest National Laboratory
SystemsX - The Swiss Initiative in Systems Biology
CSBC - Center for the Study of Biological Complexity
MCISB - The Manchester Centre for Integrative Systems Biology

[编辑] 系统生物学研究团体

请添加其它合适的团体。

[编辑] 系统生物学软件工具

[编辑] 国际会议

[编辑] 外部链接

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
Systems Biology: An Overview - a review from the Science Creative Quarterly