Complex networks: Difference between revisions

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Network theory - study of graphs, representing symmetric or asymmetric relations between discrete objects.
Keywords: '''complex networks''', complexity, robustness, biology, feedback, internet


In network theory, complex networks - have ....???? attributes compared to simple networks.
==Slides==
===Introductory slides 2002-2004===
Introductory and review slides on complex networks, biological complexity and robustness.


Examples: World Wide Web, the Internet, gene regulatory networks, metabolic networks, social networks, epistemological networks, etc.
*Physics talk [http://www.cds.caltech.edu/~doyle/CmplxNets/PhysicsIntro.ppt (slides)] Nov 11, 2004
*Emergent complexity [http://www.cds.caltech.edu/~doyle/CmplxNets/Emergent.ppt (slides)] Nov 22, 2004 Georgia Tech
*Old IPAM [http://www.cds.caltech.edu/~doyle/IPAM slides] 2002


==Introduction and review papers==
===Slides from old talks on Complexity and Robustness===
Introductory and review papers on complex networks, biological complexity and robustness.
*CDC plenary slides [http://www.cds.caltech.edu/~doyle/CmplxNets/CDC_plenary.ppt (ppt)]


Copied from "http://www.cds.caltech.edu/~doyle/CmplxNets/"
*Introduction to complex networks [http://www.cds.caltech.edu/~doyle/CmplxNets/intro_cmplx_net.ppt (ppt)]


*Physics talk (slides) Nov 11, 2004
*Allerton plenary [http://www.cds.caltech.edu/~doyle/CmplxNets/allerton.ppt (ppt)]
*Emergent complexity (slides) Nov 22, 2004 Georgia Tech
*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)
*See also introductory papers on [[Research|HOT]]


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


*Biological examples (pdf)
==Papers==
*Feedback examples (pdf)
===Review papers===
*Legos and protocols: Notes and Pictures
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''],<br>
*Biology and protocols: Slides
Carlson JM, Doyle J,<br>
*Integral feedback: Proofs and Notes
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.


==Links==
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/7a/Science1664-2002.pdf ''Reverse Engineering of Biological Complexity'']<br>
*[Feedback Control Theory, by Doyle, Francis and Tannenbaum]
Csete M and Doyle J,<br>
*[Internet Protocols, Evolution, and Theory]
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB pdf)
*[Systems Biology Workbench (SBW) and Markup Language (SBML)]


==Selected additional references:==
===Papers 2000-2005===
[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)


Robust Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence, PhD thesis by Kumar Bobba (pdf)
[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)


Csete M.E. and J.C. Doyle, 2004, Bow ties, metabolism, and disease, Trends in Biotechnology, Vol 22, Issue 9, pg. 446-450 (pdf)
[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>
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)  


J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle, 2004, Robustness of cellular functions, Cell, October, 2004 (pdf)
[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)


H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash, 2004, Surviving Heat Shock: Control Strategies for Robustness and Performance, PNAS. Accepted, to appear.
[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>
Proc. Natl. Acad. Sci. USA 99 (4): 2049-2054 Feb 19, 2002.


[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/c/c5/PRLPLR2000.pdf  ''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.


Li, L., D. Alderson, J. Doyle, and W. Willinger. 2004. A First-Principles Approach to Understanding the Internet's Router-level Topology. Proc. ACM SIGCOMM
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''Robust perfect adaptation in bacterial chemotaxis through integral feedback control.]''<br>
Yi T-M, Huang Y, Simon MI, Doyle J.<br>
Proc. Natl. Acad. Sci. USA 97(9):4649-4653, 2000.


http://www.acm.org/sigs/sigcomm/sigcomm2004/papers.html#A_First_Principles
*''Feedback regulation of the heat shock response in E. coli''<br>
Kurata, H.   El-Samad, H.   Yi, T.-M.  Khammash, M.  Doyle, J. <br>
IEEE CDC Vol 1 pp 837-842; Orlando, FL, USA 2001


Mutation, specialization, and hypersensitivity in highly optimized tolerance, Zhou, Carlson, and Doyle, PNAS (pdf)
''Highly optimized tolerance: A mechanism for power laws in designed systems''<br>
PNAS 2002 99: 2049-2054; published online before print February 12 2002, 10.1073/pnas.261714399
JM Carlson, J Doyle<br>
Phys Rev E 60(2), 1999


Power laws, Highly Optimized Tolerance and generalized source coding, Doyle and Carlson, PRL, (pdf)
===Drafts===


Highly Optimized Tolerance: A Mechanism for Power Laws in Designed Systems, Carlson and Doyle, PRE, (pdf)
==Related topics==
*[[Network architecture and protocols]]
*[[General complexity]]
*[[Complexity and robustness]]
*[[Research|HOT]]


Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Yi, Huang, Simon, and Doyle, PNAS, (Link or PDF)
==Related reading==
===PhD theses===
*''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)]


Feedback regulation of the heat shock response in E. Coli, Kurata, El-Samad, Yi, Khammash, and Doyle, draft, (PS (7M) or Zipped (300k))
*''Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization'', <br>
PhD Thesis CDS, Caltech by Pablo Parrilo, 2000 [http://www.cds.caltech.edu/~pablo/thesis.ps.gz (Gzipped postscript)]


Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization, Pablo Parrilo, PhD Thesis, Control and Dynamical Systems, Caltech, (Gzipped postscript)
===Supplementary material===
*Biological examples [http://www.cds.caltech.edu/~doyle/CmplxNets/Bio1.pdf (pdf)]
*Feedback examples [http://www.cds.caltech.edu/~doyle/CmplxNets/Fdbk1.pdf (pdf)]
*Legos and protocols: [http://www.cds.caltech.edu/~doyle/CmplxNets/Protocols1.pdf (Notes pdf)] and [http://www.cds.caltech.edu/~doyle/CmplxNets/LegoPics.pdf (Pictures)]
*Biology and protocols: [http://www.cds.caltech.edu/~doyle/CmplxNets/BioPics.ppt Slides ppt]
*Integral feedback pdf: [http://www.cds.caltech.edu/~doyle/CmplxNets/IntFdbck1.pdf Proofs] and [http://www.cds.caltech.edu/~doyle/CmplxNets/IntFdbck2.pdf Notes]


==Slides from old talks on Complexity and Robustness==
===Books===
[http://www.cds.caltech.edu/~doyle/SFI_robustness/books.htm Covers of some recommended books below]


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


2.     Introduction to complex networks (ppt)
''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)]


3.     Allerton plenary (ppt)
===Other books===
[http://www.springer.com/math/book/978-0-387-98945-7 ''A Course in Robust Control Theory: A Convex Approach'']<br>
Geir E. Dullerud and Fernando G. Paganini<br>
Springer, 2000 (ISBN 0387989455, 9780387989457)


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


==Additional recommended books==
===Links===
*[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)]
[http://www.cds.caltech.edu/erato/ broken link for ERATO ]
===Related news and commentary items===
[http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm ''Highly Optimized Tolerance]''<br>
by Phillip F. Schewe and Ben Stein <br>
in American Institute of Physics (AIP) Physics News Update<br>
Number 474 (Story #1), March 10, 2000


A course in Robust Control Theory: A Convex Approach, Dullerud and Paganini, Springer
[http://www.nature.com/nature/journal/v405/n6785/full/405412b0.html ''Applied mathematics: The power of design'']<br>
Mark Newman <br>
Nature 405, 6785, pp 412-413 (25 May 2000)


Essentials of Robust Control, Zhou, Prentice-Hall
[http://www.pnas.org/cgi/content/full/97/10/5031 ''Cell signaling pathways as control modules: Complexity for simplicity?'']<br>
Douglas A. Lauffenburger, <br>
Proc. Natl. Acad. Sc.  May 9, 2000  vol. 97  no. 10  5031-5033


Cells, Embryos, and Evolution, Gerhart and Kirschner
*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-->


==Related news and commentary items==
==Note==
*http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm
*This page was copied from <http://www.cds.caltech.edu/~doyle/CmplxNets/> and re-formatted with updated citation details.  
*http://helix.nature.com/nsu/000323/000323-2.html
*On this page there are both internal wiki links, external links to <http://www.cds.caltech.edu/~doyle/CmplxNets/> and elsewhere .
*The power of design, Mark Newman, Nature 405, 412-413 (2000)
*[[To Do]]
*http://unisci.com/stories/20001/0314004.htm:
 
*http://www.pnas.org/cgi/content/full/97/10/5031
 
[[Category:Research]]
[[Category:Papers]]
[[Category:Papers by topic]]

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

Retrieved from "https://doyle.caltech.edu/index.php?title=Complex_networks&oldid=2912"