Complex networks: Difference between revisions

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NEED TO TRANSFER papers from old page to this page and also to other pages for sub-topics.
NEED TO TRANSFER papers from old page to this page and also to other pages for sub-topics.


Sub-topics:
Related topics:
*[[network architecture and protocols]]
*[[network architecture and protocols]]
*[[Internet topology]]
*[[General complexity
*[[HOT]]
*[[Robust yet fragile & biological networks]]
 


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


*Physics talk (slides) Nov 11, 2004
*Physics talk (slides) Nov 11, 2004
*Emergent complexity (slides) Nov 22, 2004 Georgia Tech
*Emergent complexity (slides) Nov 22, 2004 Georgia Tech
*Old IPAM slides  
*Old IPAM slides  
*Complexity and Robustness, JM Carlson and J Doyle, PNAS, 99, Suppl. 1, 2538-2545 (pdf)
 
*Reverse Engineering of Biological Complexity, ME Csete and J Doyle, Science, 295, 1664 (2002) (pdf)
*[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''],<br>
Carlson JM, Doyle J,<br>
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.
*[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/7a/Science1664-2002.pdf ''Reverse Engineering of Biological Complexity'']<br>
Csete M and Doyle J,<br>
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB pdf)
 
*See also introductory papers on [[Research|HOT]]
*See also introductory papers on [[Research|HOT]]


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*[Systems Biology Workbench (SBW) and Markup Language (SBML)]
*[Systems Biology Workbench (SBW) and Markup Language (SBML)]


==Selected additional references:==
==Related reading==
 
*''Robust Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence'',
 
PhD thesis by Kumar Bobba (pdf)
 
*''Bow ties, metabolism, and disease'',
 
Csete M.E. and J.C. Doyle, 
 
Trends in Biotechnology, 22(9):pp 446-450; 2004,(pdf).
 
*''Robustness of cellular functions'',


J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle,


Cell, October, 2004 (pdf).
[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>
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)


*''Surviving Heat Shock: Control Strategies for Robustness and Performance'',


H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash,  
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''Robustness of cellular functions''],<br>
J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle,<br>
Cell 118: 675–685, Sept 17 2004. (244K)


PNAS 2004,
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''Surviving Heat Shock: Control Strategies for Robustness and Performance''], <br>
 
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash,<br>
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/Topology-sigcomm04.pdf ''A First-principles Approach to Understanding the Internet's Router-level Topology''][http://www.acm.org/sigs/sigcomm/sigcomm2004/papers.html#A_First_Principles Abstract]
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)
 
Lun Li, David Alderson, W. Willinger and John C. Doyle


[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/Topology-sigcomm04.pdf ''A First-principles Approach to Understanding the Internet's Router-level Topology''][http://www.acm.org/sigs/sigcomm/sigcomm2004/papers.html#A_First_Principles Abstract]<br>
Lun Li, David Alderson, W. Willinger and John C. Doyle<br>
in Proceedings of ACM SIGCOMM, Portland, OR, Aug 2004 (1.5MB)
in Proceedings of ACM SIGCOMM, Portland, OR, Aug 2004 (1.5MB)


*''Mutation, specialization, and hypersensitivity in highly optimized tolerance''
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''Mutation, specialization, and hypersensitivity in highly optimized tolerance''],<br>
 
Zhou T, Carlson JM, Doyle J,<br>
Zhou, Carlson, and Doyle,  
Proc. Natl. Acad. Sci. USA 99 (4): 2049-2054 Feb 19, 2002.
 
PNAS 2002 99: 2049-2054;
 
*''Power laws, Highly Optimized Tolerance and generalized source coding'',  


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


PRL, (pdf)


*''Highly Optimized Tolerance: A Mechanism for Power Laws in Designed Systems'',  
*''Highly Optimized Tolerance: A Mechanism for Power Laws in Designed Systems'',  
Line 92: Line 82:


Kurata, El-Samad, Yi, Khammash, and Doyle, draft, (PS (7M) or Zipped (300k))
Kurata, El-Samad, Yi, Khammash, and Doyle, draft, (PS (7M) or Zipped (300k))
===Related reading: PhD theses===
*''Robust Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence'',
PhD thesis by Kumar Bobba (pdf)


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

Revision as of 17:36, 23 August 2008

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

This page copied from "http://www.cds.caltech.edu/~doyle/CmplxNets/"

NEED TO TRANSFER papers from old page to this page and also to other pages for sub-topics.

Related topics:

Introduction and review papers

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

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

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

  • See also introductory papers on HOT

Supplementary material

  • Biological examples (pdf)
  • Feedback examples (pdf)
  • Legos and protocols: Notes and Pictures
  • Biology and protocols: Slides
  • Integral feedback: Proofs and Notes

Links

  • [Feedback Control Theory, by Doyle, Francis and Tannenbaum]
  • [Internet Protocols, Evolution, and Theory]
  • [Systems Biology Workbench (SBW) and Markup Language (SBML)]

Related reading

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.


  • Highly Optimized Tolerance: A Mechanism for Power Laws in Designed Systems,

Carlson and Doyle,

PRE, (pdf)

  • Robust perfect adaptation in bacterial chemotaxis through integral feedback control,

Yi, Huang, Simon, and Doyle,

PNAS, (Link or PDF)

  • Feedback regulation of the heat shock response in E. Coli,

Kurata, El-Samad, Yi, Khammash, and Doyle, draft, (PS (7M) or Zipped (300k))

Related reading: PhD theses

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

PhD thesis by Kumar Bobba (pdf)

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

Pablo Parrilo,

PhD Thesis, Control and Dynamical Systems, Caltech, (Gzipped postscript)

Slides from old talks on Complexity and Robustness

1. CDC plenary slides (ppt)

2. Introduction to complex networks (ppt)

3. Allerton plenary (ppt)

4. Introduction to HOT (ppt)

Additional recommended books

A course in Robust Control Theory: A Convex Approach, Dullerud and Paganini, Springer

Essentials of Robust Control, Zhou, Prentice-Hall

Cells, Embryos, and Evolution, Gerhart and Kirschner

Related news and commentary items

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