Systems biology: Difference between revisions

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imported>Anthony.Sebastian
m (Added external link: Systems Biology Medicine Symposium 2006 - Webcasts)
imported>Chris day
(→‎Systems biology people and places: we dn't need alll these links to labs and people. Not sure we even need the links to the conferences)
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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.
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.


==Systems biology people and places==
== International conferences ==
A large number of organizations have been created to further the study of systems biology.
Some notable systems biology organizations
include Japan's [http://www.sbi.jp/ Systems Biology Institute] headed by Hiroaki Kitano;
Canada's [http://mededu.med.uottawa.ca/oisb/ Ottawa Institute of Systems Biology]; United States' [[Institute for Systems Biology]] (ISB), the [http://biox.stanford.edu/ BioX] program at [[Stanford University]], the [http://sysbio.med.harvard.edu/ Department of Systems Biology] at [[Harvard Medical School]], the [http://www.sysbio.org/ Systems Biology Research Group] at the [[Pacific Northwest National Laboratory]], and the [http://www.vcu.edu/csbc/ Center for the Study of Biological Complexity]. The ISB is headed by [[Leroy Hood]] and 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. 
In Europe: UK's Biosystems Informatics Institute; Swizerland's [http://www.imsb.ethz.ch Institute for Molecular Systems Biology] and [http://www.systemsx.ch SystemsX], Ireland's [http://www.systemsbiologyireland.org/ Systems Biology Ireland], and Russia's Institute for Systems Biology.
 
 
=== Systems biology societies and projects ===
<!--Please do not place any ads in this section-->
* [http://www.issb.org International Society for Systems Biology] - the international systems biology society
* [http://www.msbf.mpg.de/ Munich Systems Biology Forum] - systems biology collaboration portal
* [http://www.ysbn.org Yeast Systems Biology Network] - systems biology researchers working in yeast
* [http://www.e-cell.org/ E-Cell Project] - international effort to model the cell in silico
* [http://www.physiome.org/ National Simulation Research Physiome Project] - international effort to model biology administered by the [[University of Washington]]
* [http://www.interaction-proteome.org/index.html Proteome Interaction Project]
 
=== Independent systems biology research centers ===
<!--Ordered by institute name -->
* [http://www.biiuk.com Biosystems Informatics Institute] (United Kingdom)
* [http://www.systemsbiology.org/ Institute for Systems Biology] (United States)
* [http://www.oisb.ca Ottawa Institute for Systems Biology] (Canada)
* [http://www.sbi.jp/ Systems Biology Institute] (Japan)
* [http://www.systemsx.ch/ SystemsX] (Switzerland)
* {{cite web | title = The Molecular Sciences Institute (MSI) [Berkeley] | work = “The flagship activity of the MSI is the Alpha Project at the Center for Quantitative Genome Function that aims to predict the quantitative behavior of a eukaryotic regulatory network in individual cells over time and in response to defined perturbations. “  | url = http://www.molsci.org/ | accessdate = 2006-12-17 }}
* [http://www.vcell.org/ Virtual Cell Group] (United States)
 
=== Systems biology research groups ===
<!--Ordered by country then university -->
* [http://www.sysbiolab.uottawa.ca/ Kaern Dynamical Systems Biology Lab] at [[University of Ottawa]] (Canada)
* [http://www.systemsbiology.ie/ Systems Biology] at Hamilton Institute in the [[National University of Ireland, Maynooth]] (Ireland)
* [http://www.systemsbiologyireland.org/ Systems Biology Ireland] at [[Trinity College, Dublin]] (Ireland)
* [http://www.weizmann.ac.il/centers/system_biology.html Systems Biology at the Weizmann institute] at [[Weizmann Institute of Science]], Rehovot (Israel)
* [http://www.imsb.ethz.ch Institute for Molecular Systems Biology] at [[ETH Zürich]] (Switzerland)
* [http://cssb.icmb.utexas.edu Center for Systems and Synthetic Biology] at [[University of Texas at Austin]] (United States)
* [http://www.ebi.ac.uk/compneur/ Computational Neurobiology Group] at [[European Bioinformatics Institute]] (United Kingdom)
* [http://www.bioinformatics.ed.ac.uk/csb Computational Systems Biology] at [[University of Edinburgh]] (United Kingdom)
* [http://www.mcisb.org/ Manchester Centre for Integrative Systems Biology] at [[University of Manchester]] (United Kingdom)
* [http://www.shef.ac.uk/dcs/research/groups/compbio/ Computational Systems Biology] at [[University of Sheffield]] (United Kingdom)
* [http://www.cellnomica.netfirms.com/ Multicellular Systems Research at Cellnomica] (United States)
* [http://www.cellnomica.netfirms.com/ Cancer Modeling Project at Cellnomica] (United States)
* [http://www.phil.cmu.edu/projects/genegroup/ Computational Systems Biology Group] at [[Carnegie Mellon University]]
* [http://sysbio.med.harvard.edu/ Department of Systems Biology] at [[Harvard Medical School]] (United States)
* [http://vcp.med.harvard.edu/ Virtual Cell Program] at [[Harvard University]] (United States)
* [http://www.sys-bio.org Computational Systems Biology] at the Keck Institute (United States)
* [http://bionetgen.lanl.gov/ Cell Signaling Team] at [[Los Alamos National Laboratory]] (United States)
* [http://csbi.mit.edu/ Computational and Systems Biology Initiative] at [[MIT]] (United States)
* [http://www.computationalmedicine.se/ Computational Medicine] at [[LiU & KI]] (Sweden)
* [http://www.sysbio.org/ Systems Biology] at [[Pacific Northwest National Laboratory]] (United States)
* [http://systemsbiology.ucsd.edu/ Systems Biology Research Group] at [[UCSD]] (United States)
* [http://bme.virginia.edu/csbl/ Computational Systems Biology Lab] at [[University of Virginia]] (United States)
* [http://www.vcu.edu/csbc/ Center for the Study of Biological Complexity] at [[Virginia Commonwealth University]] (United States)
* [http://www.genomedynamics.org Center for Genome Dynamics] at [[The Jackson Laboratory]] (United States)
 
=== Systems biology researchers ===
<!-- organized by researcher last name -->
* [http://www.weizmann.ac.il/mcb/UriAlon/ Alon, Uri] at [[Weizmann Institute of Science]]
* [http://genomics.lbl.gov/ Arkin, Adam] at [[Lawrence Berkeley National Laboratory]]
* [http://www.phys.huji.ac.il/bio_physics/nathalie/ Balaban, Nathalie Questembert] at [[Hebrew University of Jerusalem]]
* [http://www.public.asu.edu/~cbaral/ Baral, Chatta] at [[Arizona State University]]
* [http://barkai-serv.weizmann.ac.il/GroupPage/ Barkai, Naama] at [[Weizmann Institute of Science]]
* [http://www.utoronto.ca/boonelab/ Boone, Charlie] at [[University of Toronto]]
* [http://cluzel.uchicago.edu/ Cluzel, Phillippe] at [[University of Chicago]]
* [http://www.bu.edu/abl Collins, Jim] at [[Boston University]]
* [http://www.molbio2.princeton.edu/index.php?option=content&task=view&id=206/ Cox, Edward] at [[Princeton University]]
* [http://www.its.caltech.edu/~mirsky/ Davidson, Eric] at [[CalTech]]
* [http://www.elowitz.caltech.edu/ Elowitz, Michael] at [[CalTech]]
* [http://web.mit.edu/be/people/endy.htm Endy, Drew] at [[MIT]]
* [http://www.stanford.edu/group/ferrelllab/ Ferrell, Jim] at [[Stanford University]]
* [http://www.immunologia.unibo.it/ Franceschi, Claudio] at [[University of Bologna]]
* [http://hugheslab.med.utoronto.ca/ Hughes, Tim] at [[University of Toronto]]
* [http://chianti.ucsd.edu/idekerlab/index.html Ideker, Trey] at [[UCSD]]
* [http://www.mssm.edu/labs/iyengar/ Iyengar, Ravi] at [[Mount Sinai School of Medicine]]
* [http://microarray.icmb.utexas.edu/ Iyer, Vishwanath] at [[University of Texas]]
* [http://www.ee.kth.se/~jacobsen Jacobsen, Elling W.] at [[KTH]]
* [http://www.molgen.mpg.de/~ag_klipp/ Klipp, Edda] at [[Max Planck Institute]]
* [http://www.rockefeller.edu/labheads/leibler/leibler-lab.php/ Leibler, Stanislas] at [[Rockefeller University]]
* [http://polaris.icmb.utexas.edu/home.html Marcotte, Edward] at [[University of Texas]]
* [http://caulo.stanford.edu/usr/hm/ McAdams, Harley] at [[Stanford University]]
* [http://mendes.vbi.vt.edu/tiki-index.php Mendes, Pedro] at [[Virginia Tech]]
* [http://mcb.harvard.edu/o%27shea/ O'Shea, Erin] at [[Harvard]]
* [http://math.berkeley.edu/~lpachter/ Pachter, Lior] at [[UC Berkeley]]
* [http://systemsbiology.ucsd.edu/ Palsson, Bernhard Ø.] at [[UCSD]]
* [http://thebigone.stanford.edu/ Quake, Stephen] at [[Stanford University]]
* [http://www.cubic.uni-koeln.de/ Schomburg, Dietmar] at [[Cologne University]]
* [http://mendel.stanford.edu/SidowLab/ Sidow, Arend] at [[Stanford University]]
* [http://www.ornl.gov/ment/ Simpson, Michael] at [[Oak Ridge National Laboratory]]
* [http://www.yale.edu/snyder/ Snyder, Michael] at [[Yale University]]
* [http://biology.caltech.edu/Members/Stathopoulos Stathopoulos, Angelike] at [[CalTech]]
* [http://www.karlavagen90.se/ Tegnér, Jesper] at [[Liu & KI]] 
* [http://www.ncbs.res.in/mukund/groups_mukund.htm Thattai, Mukund] at [[Tata Institute of Fundamental Research]]
* [http://mit.edu/tidor/ Tidor, Bruce] at [[MIT]]
* [http://mpf.biol.vt.edu/ Tyson, John] at [[Virginia Tech]]
* [http://web.mit.edu/biophysics van Oudenaarden, Alexander] at [[MIT]]
* [http://vidal.dfci.harvard.edu/ Vidal, Marc] at [[Dana Farber Cancer Institute]]
* [http://www.ucsf.edu/jswlab/ Weissman, Jonathan] at [[UCSF]]
* [http://www.cellnomica.netfirms.com/ Werner, Eric] at [http://cellnomica.netfirms.com/ Cellnomica]
* [http://web.wi.mit.edu/young/ Young, Richard] at [[MIT]]
 
=== Systems biology companies ===
<!--Please do not place any ads in this section-->
* [http://www.bgmedicine.com BG Medicine]
* [http://cellnomica.netfirms.com/ Cellnomica]
* [http://www.entelos.com Entelos]
* [http://www.genego.com GeneGo]
* [http://www.genomatica.com Genomatica]
* [http://www.genstruct.com Genstruct] ([[Genstruct|wiki entry]])
* [http://www.ingenuity.com Ingenuity Systems]
* [http://www.clinicalgenenetworks.com Clinical Gene Networks]
 
=== International conferences ===
* [http://necsi.org/events/iccs6/ ICCS 2006 - 6th International Conference on Complex Systems]
* [http://necsi.org/events/iccs6/ ICCS 2006 - 6th International Conference on Complex Systems]
* [http://necsi.org/events/iccs/iccscover.html ICCS 2004 - 5th International Conference on Complex Systems]
* [http://necsi.org/events/iccs/iccscover.html ICCS 2004 - 5th International Conference on Complex Systems]

Revision as of 23:54, 17 December 2006

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., gene and protein networks involved in cell signaling, metabolic pathways, organelles, cells, physiological systems, organisms, etc.) it is hoped that eventually an understandable model of the whole system can be developed. Since the mathematical and analytical foundation of systems biology is far from being perfect, computer simulation and heuristics are often used as research methods.

History

In 1952, the British neurophysiologists and nobel prize winners Alan Lloyd Hodgkin and Andrew Fielding Huxley constructed a mathematical model of the nerve cell. In 1960, Denis Noble developed the first computer model of a beating heart. Systems biologists invoke these pioneering pieces of work as illustrative of the systems biology project. The possibility of performing systems biology increased around the year 2000 with the completion of various genome projects and the proliferation of genomic and proteomic data, and the accompanying advances in experimental methodology.

The experimental procedures available during the 20th century necessitated 'one protein at a time' projects which have been the mainstay of molecular biology since its inception. Some biologists and biochemists believe that this approach of individual biomolecules has fostered a reductionist perspective, and that it is just the first step toward an understanding of the overall (integrated) life process, which can only be properly addressed from a systems biology persepective.

Approaches

There are two major and complementary focuses in systems biology:

  • Quantitative Systems Biology - otherwise known as "systems biology measurement", it focuses on measuring and monitoring biological systems on the system level.
  • Systems Biology Modeling - focuses on mapping, explaining and predicting systemic biological processes and events through the building of computational and visualization models.

Quantitative systems biology

This subfield is concerned with quantifying molecular reponses in a biological system to a given perturbation.

Some typical technology platforms are:

These are frequently combined with large scale perturbation methods, including gene-based (RNAi, misexpression 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 until the predicted behavior accurately reflects the phenotype seen.

Systems biology modeling

Using knowledge from molecular biology, the systems biologist can causally model the biological system of interest and propose hypotheses that explain a system's behavior. These hypotheses can then be confirmed and be used as a basis for mathematically model the system. The difference between the two modeling approaches is that causal models are used to explain the effects of a biological perturbations while mathematical models are used to predict how different perturbations in the system's environment affect the system.

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

International conferences

Tools for systems biology

Bibliography

Books

  • H Kitano (editor). Foundations of Systems Biology. MIT Press: 2001. ISBN 0-262-11266-3
  • 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
  • B Palsson. Systems Biology - Properties of Reconstructed Networks. Cambridge University Press: 2006. ISBN 9780521859035

Articles

  • Werner, E., "The Future and Limits of Systems Biology", Science STKE 2005, pe16 (2005).
  • 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
  • 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)

External links

See also

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