系统生物学

系统生物学（），是一个使用整体论（而非还原论）的方式， 整合不同学科、层次的信息，以研究、分析、理解（即多组学整合分析）生物系统如何行使功能的学术领域。系统生物学通过研究各个生物系统内部所有组成成分间，各分子层面上的相互关系和相互作用（例如，与细胞信号传送、代谢通路、细胞器、细胞、生理系统与生物等相关的基因和蛋白网络），期望最终能够建立整个系统的可理解模型，以及为有机体绘制完整图谱。系统生物学使用计算机模拟，数学分析的方法来构建复杂生物系统的模型。

系统生物学不同于以往只注意个别的基因和蛋白质的实验生物学，研究所有的基因、所有的蛋白质和组分间的所有相互关系；其目标是：对复杂的生物系统构建计算的数学模型，从总体上预测生物系统的真实性。特别是从2000年开始，这个概念在各种环境下被广泛用于生物学。人类基因组计划是生物学中应用系统思维的一个例子，它导致新的合作的方式来处理在遗传学生物学领域的问题。系统生物学的目标之一是模拟和发现涌现的特性，细胞的，组织的和生物体的特性，作为一个系统，其理论描述只能用系统生物学的技术进行。这些通常涉及代谢网络或细胞信号传送网络，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。

2008年美国NIH设立肿瘤的系统遗传学研究专项基金。

相關領域
途径概述]]
根據使用跨學科工具從多个實驗中獲得，整合和分析複雜數據集的能力的系統生物學解釋，一些典型的技術平台包括：
*
:在生物體表型變化，因為它在其壽命的變化。

• 基因組學
• 表觀遺傳學
• 轉錄組

:在有機體的，組織的或細胞水平上的基因表現的量測，通過DNA微陣列或。

• 蛋白質組學

:子領域包括，與。

• 代謝物組學

:在有機體的，組織的或細胞水平上的被稱為代謝產物的小分子的量測。

• 糖組學

:在有機體的，組織的或細胞水平上的醣類的量測。

• 脂类组学(Lipidomics)

:在有機體的，組織的或細胞水平上的脂质的量測。

• 多組學(Multiomics)

除了上述給定分子的識別和量化之外，進一步的技術還分析細胞內的動力學和相互作用。 這包括：

• （Interactomics）

:在有機體的，組織的或細胞水平上的分子間相互作用的研究。

• （Fluxomics）

:在有機體的，組織的或細胞水平上的分子隨時間變化的動態變化的量測。

• （Biomics）。

:生物群系的系統分析。

生物信息学和数据分析
计算机科学，信息学和统计学的其他方面也用于系统生物学。

参见

• 系统生物学置标语言（SBML）
• 人工生命
• 生物医学控制论
• 计算机仿真
• 基因调节网络
• 系统生态学
• 系統藥理學
• 系统生物学家
• 合成生物学
• 调节子

参考文献
引用
来源

• 曾湘文，以系統生物學方法探討細菌內毒素在大鼠胸主動脈內皮細胞所引發之反應。國立陽明大學藥理學研究所博士論文（2005），https://web.archive.org/web/20090426071139/http://etds.ncl.edu.tw/theabs/index.html]
• Hiroaki Kitano (editor),（2001）Foundations of Systems Biology, MIT Press;（October 15, 2001）ISBN 0-262-11266-3
• 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 [http://www.nature.com/nrg/journal/v5/n10/poster/omics/index.html From OMICS to systems biology]
• E. Klipp, R. Herwig, A. Kowald, C. Wierling, and H. Lehrach, Systems Biology in Practice, Wiley-VCH, 2005, ISBN 3-527-31078-9
• Werner, E., "The Future and Limits of Systems Biology", [http://stke.sciencemag.org/content/vol2005/issue278/ Science STKE] 2005, pe16 (2005).
• Bernhard ?. Palsson. 2006 "Systems Biology - Properties of Reconstructed Networks," Cambridge University Press. ISBN 978-0-521-85903-5.
• Cambien F.& Tiret L., Atherosclerosis: From genetic polymorphisms to system genetics. Cardiovascular Toxicology, Volume 5, Number 2, June 2005, pp. 143-152 (10).

外部链接

• [https://web.archive.org/web/20060403183230/http://www.biocircle.org/ 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.
• [https://web.archive.org/web/20060618095622/http://www.biochemweb.org/systems.shtml BioChemWeb.org] - The Virtual Library of Biochemistry and Cell Biology: A Guide to Biochemistry, Molecular Biology & Cell Biology on the Web
• [http://www.guardian.co.uk/life/science/story/0,12996,1477776,00.html 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）
• [https://web.archive.org/web/20060528171444/http://psimap.kaist.ac.kr/ PsiMap.kaist.ac.kr] - PSIbase Database: Protein Structure Interactome Map Database Server: Structural Interactome Map of all Proteins
• [http://www.sciencemag.org/content/vol295/issue5560/ ScienceMag.org] - Special Issue: Systems Biology, Science, Vol 295, No 5560, March 1, 2002
• [http://www.nature.com/msb/index.html Nature] - Molecular Systems Biology
• [http://www.scq.ubc.ca/?p=253 Systems Biology: An Overview] - a review from the Science Creative Quarterly

专业组织/研究机构

• [https://web.archive.org/web/20090106134929/http://www.sysbioeng.com/wabse/index.html SysBioEng.com] - The (World) Associates for Biosystem Science and Engingeering（Jan. 1999~）
• [http://www.issb.org issb.org] - The International Society for Systems Biology
• [http://interactomics.org InterActomics.org] - Community for Interactomics: Editable hypertext pages (a systems biology Wiki)
• [http://celln omica.netf irms.com/ Celln omica.com] - Research in multicellular developmental systems biology (US based)
• [http://www.systemsbiology.org/ SystemsBiology.org] - Institute for Systems Biology (US based)
• [http://www.systems-biology.org/ Systems-Biology.org] - Systems Biology Institute (Japan based)
• [http://www.oisb.ca Ottawa Institute for Systems Biology] （Canada）
• [https://web.archive.org/web/20190123034228/http://www.genbrain.org/ Benjoe Institute] - Systems Genetics Lab., Benjoe Institute of Systems Bio-Engineering (China)
• [https://web.archive.org/web/20060210022659/http://www.msbf.mpg.de/ Munich Systems Biology Forum] - Systems biology groups in Munich and worldwide
• [http://csbi.mit.edu/ CSBi :: Computational and Systems Biology at MIT]
• [http://www.biiuk.com Biosystems Informatics Institute] - Systems biology research institute in Newcastle upon Tyne, UK
• [http://www.ysbn.org YSBN.org] - Yeast Systems Biology Network worldwide
• [http://www.imsb.ethz.ch Institute for Molecular Systems Biology]
• [https://web.archive.org/web/20100516155832/http://www.sysbio.org/ sysbio.org] - Systems Biology at Pacific Northwest National Laboratory
• [http://www.systemsx.ch/ SystemsX] - The Swiss Initiative in Systems Biology
• [http://www.vcu.edu/csbc CSBC] - Center for the Study of Biological Complexity
• [http://www.mcisb.org/ MCISB] - The Manchester Centre for Integrative Systems Biology
• [https://web.archive.org/web/20100403055610/http://bioinfo.nctu.edu.tw/departmentinfo/pages.php?ID=about Institute of Bioinformatics and Systems Biology] - Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Taiwan

研究团队/实验室

• [https://web.archive.org/web/20060619182718/http://biology.caltech.edu/Members/Stathopoulos Stathopoulos Lab]
• [http://www.elowitz.caltech.edu/ Elowitz Lab]
• [https://web.archive.org/web/20061030203907/http://www.its.caltech.edu/~mirsky/ Davidson Lab]
• [https://web.archive.org/web/20060615042520/http://caulo.stanford.edu/usr/hm/ McAdams Lab]
• [https://web.archive.org/web/20070629154706/http://www.sysbiolab.uottawa.ca/ Kaern Dynamical Systems Biology Lab]
• [http://thebigone.stanford.edu/ Quake Lab]
• [http://mendel.stanford.edu/SidowLab/ Sidow Lab]
• [https://web.archive.org/web/20060830060718/http://cmgm.stanford.edu/~kimlab/ Kim Lab]
• [http://www.stanford.edu/group/ferrelllab/ Ferrell Lab]
• [http://www.weizmann.ac.il/mcb/UriAlon/ Alon Lab]
• [https://web.archive.org/web/20060616194202/http://www.systemsbiology.org/Scientists_and_Research/Faculty_Groups/Baliga_Group Baliga Lab]
• [http://www.imsb.ethz.ch/ Systems Biology ETH Zürich]
• [http://csb.inf.ethz.ch/ Computational Systems Biology ETH Zürich]
• [https://web.archive.org/web/20060206085853/http://gobi.lbl.gov/~aparkin/ Arkin Lab]
• [https://web.archive.org/web/20080120193506/http://www.bu.edu/abl/ Collins Lab]
• [https://web.archive.org/web/20051219010529/http://systemsbiology.org/Scientists_and_Research/Faculty_Groups/Bolouri_Group Bolouri Lab]
• [http://www.e-cell.org/ E-Cell group]
• [https://web.archive.org/web/20060614195517/http://www.symbio.jst.go.jp/symbio2/ Kitano Lab]
• [https://web.archive.org/web/20060616071103/http://www.systemsbiology.org/Scientists_and_Research/Faculty_Groups/Hood_Group Hood Lab]
• [https://web.archive.org/web/20060924000508/http://www.ebi.ac.uk/compneur/ Le Novere Group]
• [https://web.archive.org/web/20060803151137/http://mendes.vbi.vt.edu/tiki-index.php Pedro Mendes Lab]
• [http://www.sys-bio.org Sauro Lab]
• [http://mpf.biol.vt.edu/ John Tyson Lab]
• [http://www.vcell.org Virtual Cell Group]
• [https://web.archive.org/web/20100516155832/http://www.sysbio.org/ Systems Biology at PNNL]
• [http://systemsbiology.ucsd.edu/ Systems Biology Research Group - UCSD]
• [https://web.archive.org/web/20060828194855/http://bme.virginia.edu/csbl/ CSBL - University of Virginia]
• [http://www.shef.ac.uk/dcs/research/groups/compbio/ Computational Systems Biology - University of Sheffield, UK]
• [https://web.archive.org/web/20050411020205/http://www.systemsbiology.ie/ Systems biology research group - Hamilton Institute, NUY Maynooth, Ireland.]
• [http://www.physiome.org/Models National Simulation Research, University of Washington]
• [http://www.vcu.edu/csbc/ Center for the Study of Biological Complexity, Virginia Commonwealth University]
• [https://web.archive.org/web/20061001065035/http://www.bioinformatics.ed.ac.uk/csb/ Computational Systems Biology] at University of Edinburgh
• [http://openwetware.org/wiki/Endy_Lab Endy Lab]
• [http://mit.edu/tidor/ Tidor Lab]
• [http://web.mit.edu/biophysics van Oudenaarden Systems Biology Lab]
• [http://vcp.med.harvard.edu/ Harvard Virtual Cell Program]
• [https://web.archive.org/web/20060508172624/http://www.ncbs.res.in/~faculty/thattai.html Thattai Lab]
• [http://www.sbi.uni-rostock.de/ Wolkenhauer Group, University of Rostock, Germany]
• [http://www.phil.cmu.edu/projects/genegroup/ Computational Systems Biology Group at Carnegie Mellon University]
• [https://web.archive.org/web/20060604075959/http://www.molgen.mpg.de/~ag_klipp/ Kinetic Modelling Group at the Max Planck Institute for Molecular Genetics, Klipp Group]
• [https://web.archive.org/web/20100701183442/http://tang.ucsf.edu/ Tang Lab]

软件工具

• [http://simtk.org/xml/index.xml SimTK]
• [http://gaggle.systemsbiology.net Gaggle]
• [http://www.sys-bio.org Systems Biology Workbench]
• [http://www.sbml.org Systems Biology Markup Language]
• [http://www.cellml.org The CellML language]
• [http://www.littleb.org The little b Modeling Language]
• [http://www.copasi.org Copasi (Version 4 of Gepasi)]
• [http://ecell.sourceforge.net/ E-Cell System]
• [https://web.archive.org/web/20061031143659/http://www.pdn.cam.ac.uk/groups/comp-cell/StochSim.html StochSim]
• [http://www.vcell.org Virtual Cell]
• [http://jigcell.biol.vt.edu/ JigCell (John Tyson Lab)]
• [http://pysces.sourceforge.net/ Python Simulator for Cellular Systems]
• [https://web.archive.org/web/19990125100225/http://www.ingenuity.com/ Ingenuity Pathways Analysis]
• [https://web.archive.org/web/20060907074456/http://mips.gsf.de/proj/biorel/ BIOREL is a web-based resource for quantitative estimation of the gene network bias in relation to available database information about gene activity/function/properties/associations/interactions.]
• [http://www.mssm.edu/labs/iyengar/resources/software/SAVI/ SAVI Signaling Analysis and Visualization]
• [https://web.archive.org/web/20060914165111/http://nsr.bioeng.washington.edu/Software/JSIM JSim]
• [https://web.archive.org/web/20141119095756/http://bionetgen.lanl.gov/ BioNetGen]
• [https://web.archive.org/web/20061101140948/http://sysbio.molgen.mpg.de/SBML-PET/ SBML-PET is a Systems Biology Markup Language (SBML) based Parameter Estimation Tool. This tool has been designed to do parameter estimation work for biological models.]
• [https://web.archive.org/web/20100330144253/http://bioinfo.life.nctu.edu.tw/ Systems Biology Software Databases developed by Molecular Bioinformatics Center, National Chiao Tung University, Taiwan ]

国际会议

• International Conference on Systems Theory and Biology, 1968.
• [https://web.archive.org/web/20120730202554/http://www.picb.ac.cn/icmsb2009/submission.html ICMSB 2009 - 11th International Conference on Molecualr Systems Biology]
• [https://web.archive.org/web/20090916161433/http://ittc.up.edu.ph/icmsb08.htm ICMSB 2008 - 10th International Conference on Molecualr Systems Biology]
• [https://web.archive.org/web/20060701192018/http://www.necsi.org/events/iccs6/ ICCS 2006 - International Conference on Complex Systems]
• [http://www.icsb-2006.org/ ICSB 2006 - 7th International Conference on Systems Biology]
• [http://www.icsb-2005.org/ ICSB 2005 - 6th International Conference on Systems Biology]
• [http://www.icsb2004.org/ ICSB 2004 - 5th International Conference on Systems Biology]
• [https://web.archive.org/web/20060618045756/http://icsb2003.molecool.wustl.edu/ ICSB 2003 - 4th International Conference on Systems Biology]
• [http://www.icsb2001.org/ ICSB 2001 - The 2nd International Conference on Systems Biology]
• [https://web.archive.org/web/20060302153419/http://www.symbio.jst.go.jp/systemsbiology/news/icsb/ The First International Conference on Systems Biology (ICSB)]