Complex networks: Difference between revisions

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Keywords: '''complex networks''', complexity, robustness, biology, feedback, internet
Keywords: '''complex networks''', complexity, robustness, biology, feedback, internet


 
==Slides==
==Introductory slides 2002-2004==
===Introductory slides 2002-2004===
Introductory and review slides on complex networks, biological complexity and robustness.
Introductory and review slides on complex networks, biological complexity and robustness.


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*Introduction to HOT [http://www.cds.caltech.edu/~doyle/CmplxNets/HOT_intro.ppt (ppt)]
*Introduction to HOT [http://www.cds.caltech.edu/~doyle/CmplxNets/HOT_intro.ppt (ppt)]


==Review papers==
==Papers==
===Review papers===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''],<br>
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''],<br>
Carlson JM, Doyle J,<br>  
Carlson JM, Doyle J,<br>  
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Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB pdf)
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB pdf)


*See also introductory papers on [[Research|HOT]]
===Papers 2000-2005===
 
==Papers==
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''],<br>
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''],<br>
Csete M.E. and J.C. Doyle,<br>
Csete M.E. and J.C. Doyle,<br>
Line 58: Line 57:
Proc. Natl. Acad. Sci. USA 97(9):4649-4653, 2000.
Proc. Natl. Acad. Sci. USA 97(9):4649-4653, 2000.


===PhD theses & Drafts===
*''Feedback regulation of the heat shock response in E. coli''<br>
*''Robust Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence'',  
Kurata, H.  El-Samad, H.  Yi, T.-M.  Khammash, M.  Doyle, J. <br>
IEEE CDC Vol 1 pp 837-842; Orlando, FL, USA 2001


PhD thesis by Kumar Bobba [http://www.cds.caltech.edu/~doyle/CmplxNets/Bobba.pdf (pdf)]
''Highly optimized tolerance: A mechanism for power laws in designed systems''<br>
JM Carlson, J Doyle<br>
Phys Rev E 60(2), 1999


*''Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization'',
===Drafts===


Pablo Parrilo,
==Related topics==
*[[Network architecture and protocols]]
*[[General complexity]]
*[[Complexity and robustness]]
*[[Research|HOT]]


PhD Thesis, Control and Dynamical Systems, Caltech, [http://www.cds.caltech.edu/~pablo/thesis.ps.gz (Gzipped postscript)]
==Related reading==
 
===PhD theses===
*''Feedback regulation of the heat shock response in E. Coli'',  
*''Robust Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence'', <br>
 
PhD thesis at Caltech by Kumar Bobba, 2004 [http://www.cds.caltech.edu/~doyle/CmplxNets/Bobba.pdf (pdf)]
Kurata, El-Samad, Yi, Khammash, and Doyle, draft, [http://www.cds.caltech.edu/~doyle/CmplxNets/heat_shock.ps (PS 7MB) ] or [http://www.cds.caltech.edu/~doyle/CmplxNets/heat_shock.zip Zipped (300k)]


*''Highly Optimized Tolerance: A Mechanism for Power Laws in Designed Systems'', <br>
*''Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization'', <br>
Carlson and Doyle, <br>
PhD Thesis CDS, Caltech by Pablo Parrilo, 2000 [http://www.cds.caltech.edu/~pablo/thesis.ps.gz (Gzipped postscript)]
PRE, (pdf)


==Related reading==
===Supplementary material===
===Supplementary material===
*Biological examples [http://www.cds.caltech.edu/~doyle/CmplxNets/Bio1.pdf (pdf)]
*Biological examples [http://www.cds.caltech.edu/~doyle/CmplxNets/Bio1.pdf (pdf)]
*Feedback examples [http://www.cds.caltech.edu/~doyle/CmplxNets/Fdbk1.pdf (pdf)]
*Feedback examples [http://www.cds.caltech.edu/~doyle/CmplxNets/Fdbk1.pdf (pdf)]
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*Integral feedback pdf: [http://www.cds.caltech.edu/~doyle/CmplxNets/IntFdbck1.pdf Proofs] and [http://www.cds.caltech.edu/~doyle/CmplxNets/IntFdbck2.pdf Notes]  
*Integral feedback pdf: [http://www.cds.caltech.edu/~doyle/CmplxNets/IntFdbck1.pdf Proofs] and [http://www.cds.caltech.edu/~doyle/CmplxNets/IntFdbck2.pdf Notes]  


===Additional recommended books===
===Books===
A course in Robust Control Theory: A Convex Approach, Dullerud and Paganini, Springer
[http://www.cds.caltech.edu/~doyle/SFI_robustness/books.htm Covers of some recommended books below]


Essentials of Robust Control, Zhou, Prentice-Hall
''Essentials of robust control''<br>
Kemin Zhou, John C. Doyle<br>
Prentice-Hall, Englewood Cliffs, NJ, 1998, (ISBN: 0-13-790874-1)


Cells, Embryos, and Evolution, Gerhart and Kirschner
''Feedback Control Theory'' ,<br>
[http://www.control.utoronto.ca/people/profs/francis/dft.pdf (free version in pdf 1.2MB)]<br>
[http://www.cds.caltech.edu/~macmardg/cds110b/dft.html (free version by chapter from CDS Caltech)]<br>
John Comstock Doyle, Bruce A. Francis and Allen R. Tannenbaum<br>
Macmillan Coll Div , USA 1992 (ISBN-13: 9780023300110)<br>
Also at:
[http://portalparts.acm.org/580000/574259/cover/1078912.gif ACM portal, Prentice Hall Professional Technical Reference, USA 1991 (ISBN:0023300116)]


===Related topics===
===Other books===
*[[network architecture and protocols]]
[http://www.springer.com/math/book/978-0-387-98945-7 ''A Course in Robust Control Theory: A Convex Approach'']<br>
*[[General complexity]]
Geir E. Dullerud and Fernando G. Paganini<br>
*[[Complexity and robustness]]
Springer, 2000 (ISBN 0387989455, 9780387989457)
===Links===
[http://www.control.utoronto.ca/people/profs/francis/dft.pdf ''Feedback Control Theory''] , (pdf 1.2MB )<br>
John Comstock Doyle, Bruce A. Francis and Allen R. Tannenbaum
Prentice Hall Professional Technical Reference, USA 1991<br>
(ISBN:0023300116)
[http://portalparts.acm.org/580000/574259/cover/1078912.gif front cover]


''Cells, Embryos, and Evolution'',<br>
J Gerhart and M Kirschner
Blackwell Sience, 1997 (ISBN 0-86542-574-4)


===Links===
*[http://netlab.caltech.edu/internet/ Netlab, Caltech on Internet Protocols, Evolution, and Theory]
*[http://netlab.caltech.edu/internet/ Netlab, Caltech on Internet Protocols, Evolution, and Theory]
*Systems Biology Workbench (SBW) and Markup Language [http://sbml.org/SBML.org:About (SBML)]
*Systems Biology Workbench (SBW) and Markup Language [http://sbml.org/SBML.org:About (SBML)]
[http://www.cds.caltech.edu/erato/ broken link for ERATO ]
[http://www.cds.caltech.edu/erato/ broken link for ERATO ]
 
===Related news and commentary items===
===Related news and commentary items===
[http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm ''Highly Optimized Tolerance]''<br>
[http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm ''Highly Optimized Tolerance]''<br>
Line 124: Line 132:


*This link is broken (Aug 2008) for ''International Science News'', as the author is deceased. [http://unisci.com/stories/20001/0314004.htm]
*This link is broken (Aug 2008) for ''International Science News'', as the author is deceased. [http://unisci.com/stories/20001/0314004.htm]
<! Hana unable to find original article for this link-->
<!-- Hana unable to find original article for this link-->


==See also==
==Note==
*This page copied and re-formatted from "http://www.cds.caltech.edu/~doyle/CmplxNets/"
*This page was copied from <http://www.cds.caltech.edu/~doyle/CmplxNets/> and re-formatted with updated citation details.
*On this page there are both internal wiki links, external links to <http://www.cds.caltech.edu/~doyle/CmplxNets/> and elsewhere .
*[[To Do]]
*[[To Do]]


Latest revision as of 02:13, 6 September 2008

Keywords: complex networks, complexity, robustness, biology, feedback, internet

Slides

Introductory slides 2002-2004

Introductory and review slides on complex networks, biological complexity and robustness.

  • Physics talk (slides) Nov 11, 2004
  • Emergent complexity (slides) Nov 22, 2004 Georgia Tech
  • Old IPAM slides 2002

Slides from old talks on Complexity and Robustness

  • Introduction to complex networks (ppt)
  • Introduction to HOT (ppt)

Papers

Review papers

Complexity and robustness,
Carlson JM, Doyle J,
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

Reverse Engineering of Biological Complexity
Csete M and Doyle J,
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB pdf)

Papers 2000-2005

Bow ties, metabolism, and disease,
Csete M.E. and J.C. Doyle,
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

Robustness of cellular functions,
J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle,
Cell 118: 675–685, Sept 17 2004. (244K)

Surviving Heat Shock: Control Strategies for Robustness and Performance,
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash,
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

A First-principles Approach to Understanding the Internet's Router-level TopologyAbstract
Lun Li, David Alderson, W. Willinger and John C. Doyle
in Proceedings of ACM SIGCOMM, Portland, OR, Aug 2004 (1.5MB)

Mutation, specialization, and hypersensitivity in highly optimized tolerance,
Zhou T, Carlson JM, Doyle J,
Proc. Natl. Acad. Sci. USA 99 (4): 2049-2054 Feb 19, 2002.

Power Laws, Highly Optimized Tolerance and Generalized Source Coding,
J. Doyle and J.M. Carlson,
Phys. Rev. Let., 84(24):5656-5659, 2000.

Robust perfect adaptation in bacterial chemotaxis through integral feedback control.
Yi T-M, Huang Y, Simon MI, Doyle J.
Proc. Natl. Acad. Sci. USA 97(9):4649-4653, 2000.

  • Feedback regulation of the heat shock response in E. coli

Kurata, H. El-Samad, H. Yi, T.-M. Khammash, M. Doyle, J.
IEEE CDC Vol 1 pp 837-842; Orlando, FL, USA 2001

Highly optimized tolerance: A mechanism for power laws in designed systems
JM Carlson, J Doyle
Phys Rev E 60(2), 1999

Drafts

Related topics

Related reading

PhD theses

  • Robust Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence,

PhD thesis at Caltech by Kumar Bobba, 2004 (pdf)

  • Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization,

PhD Thesis CDS, Caltech by Pablo Parrilo, 2000 (Gzipped postscript)

Supplementary material

Books

Covers of some recommended books below

Essentials of robust control
Kemin Zhou, John C. Doyle
Prentice-Hall, Englewood Cliffs, NJ, 1998, (ISBN: 0-13-790874-1)

Feedback Control Theory ,
(free version in pdf 1.2MB)
(free version by chapter from CDS Caltech)
John Comstock Doyle, Bruce A. Francis and Allen R. Tannenbaum
Macmillan Coll Div , USA 1992 (ISBN-13: 9780023300110)
Also at: ACM portal, Prentice Hall Professional Technical Reference, USA 1991 (ISBN:0023300116)

Other books

A Course in Robust Control Theory: A Convex Approach
Geir E. Dullerud and Fernando G. Paganini
Springer, 2000 (ISBN 0387989455, 9780387989457)

Cells, Embryos, and Evolution,
J Gerhart and M Kirschner Blackwell Sience, 1997 (ISBN 0-86542-574-4)

Links

broken link for ERATO

Related news and commentary items

Highly Optimized Tolerance
by Phillip F. Schewe and Ben Stein
in American Institute of Physics (AIP) Physics News Update
Number 474 (Story #1), March 10, 2000

Applied mathematics: The power of design
Mark Newman
Nature 405, 6785, pp 412-413 (25 May 2000)

Cell signaling pathways as control modules: Complexity for simplicity?
Douglas A. Lauffenburger,
Proc. Natl. Acad. Sc. May 9, 2000 vol. 97 no. 10 5031-5033

  • This link is broken (Aug 2008) for International Science News, as the author is deceased. [1]

Note

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