Complex networks: Difference between revisions

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Introductory and review papers on complex networks, biological complexity and robustness.
Keywords: '''complex networks''', complexity, robustness, biology, feedback, internet


Copied from "http://www.cds.caltech.edu/~doyle/CmplxNets/"
==Slides==
===Introductory slides 2002-2004===
Introductory and review slides on complex networks, biological complexity and robustness.


*Physics talk (slides) Nov 11, 2004
*Physics talk [http://www.cds.caltech.edu/~doyle/CmplxNets/PhysicsIntro.ppt (slides)] Nov 11, 2004
*Emergent complexity (slides) Nov 22, 2004 Georgia Tech
*Emergent complexity [http://www.cds.caltech.edu/~doyle/CmplxNets/Emergent.ppt (slides)] Nov 22, 2004 Georgia Tech
*Old IPAM slides  
*Old IPAM [http://www.cds.caltech.edu/~doyle/IPAM slides] 2002  
*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==
===Slides from old talks on Complexity and Robustness===
*CDC plenary slides [http://www.cds.caltech.edu/~doyle/CmplxNets/CDC_plenary.ppt (ppt)]


*Biological examples (pdf)
*Introduction to complex networks [http://www.cds.caltech.edu/~doyle/CmplxNets/intro_cmplx_net.ppt (ppt)]
*Feedback examples (pdf)
*Legos and protocols: Notes and Pictures
*Biology and protocols: Slides
*Integral feedback: Proofs and Notes


==Links==
*Allerton plenary [http://www.cds.caltech.edu/~doyle/CmplxNets/allerton.ppt (ppt)]
*[Feedback Control Theory, by Doyle, Francis and Tannenbaum]
*[Internet Protocols, Evolution, and Theory]
*[Systems Biology Workbench (SBW) and Markup Language (SBML)]


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


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


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/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)


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


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/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)


[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)


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/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)


http://www.acm.org/sigs/sigcomm/sigcomm2004/papers.html#A_First_Principles
[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.


Mutation, specialization, and hypersensitivity in highly optimized tolerance, Zhou, Carlson, and Doyle, PNAS (pdf)
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/c/c5/PRLPLR2000.pdf  ''Power Laws, Highly Optimized Tolerance and Generalized Source Coding''],<br>
PNAS 2002 99: 2049-2054; published online before print February 12 2002, 10.1073/pnas.261714399
J. Doyle and J.M. Carlson,<br>
Phys. Rev. Let., 84(24):5656-5659, 2000.  


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


Highly Optimized Tolerance: A Mechanism for Power Laws in Designed Systems, Carlson and Doyle, PRE, (pdf)
*''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


Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Yi, Huang, Simon, and Doyle, PNAS, (Link or PDF)
''Highly optimized tolerance: A mechanism for power laws in designed systems''<br>
JM Carlson, J Doyle<br>
Phys Rev E 60(2), 1999


Feedback regulation of the heat shock response in E. Coli, Kurata, El-Samad, Yi, Khammash, and Doyle, draft, (PS (7M) or Zipped (300k))
===Drafts===


Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization, Pablo Parrilo, PhD Thesis, Control and Dynamical Systems, Caltech, (Gzipped postscript)
==Related topics==
*[[Network architecture and protocols]]
*[[General complexity]]
*[[Complexity and robustness]]
*[[Research|HOT]]


==Slides from old talks on Complexity and Robustness==
==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)]


1.     CDC plenary slides (ppt)
*''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)]


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


3.     Allerton plenary (ppt)
===Books===
[http://www.cds.caltech.edu/~doyle/SFI_robustness/books.htm Covers of some recommended books below]


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


==Additional recommended books==
''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)]


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


Essentials of Robust Control, Zhou, Prentice-Hall
''Cells, Embryos, and Evolution'',<br>
J Gerhart and M Kirschner
Blackwell Sience, 1997 (ISBN 0-86542-574-4)


Cells, Embryos, and Evolution, Gerhart and Kirschner
===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


==Related news and commentary items==
[http://www.nature.com/nature/journal/v405/n6785/full/405412b0.html ''Applied mathematics: The power of design'']<br>
*http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm
Mark Newman <br>
*http://helix.nature.com/nsu/000323/000323-2.html
Nature 405, 6785, pp 412-413 (25 May 2000)
*The power of design, Mark Newman, Nature 405, 412-413 (2000)
 
*http://unisci.com/stories/20001/0314004.htm:
[http://www.pnas.org/cgi/content/full/97/10/5031 ''Cell signaling pathways as control modules: Complexity for simplicity?'']<br>
*http://www.pnas.org/cgi/content/full/97/10/5031
Douglas A. Lauffenburger, <br>
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. [http://unisci.com/stories/20001/0314004.htm]
<!-- Hana unable to find original article for this link-->
 
==Note==
*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]]
 
 
[[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"