John C. Doyle - User contributions [en]

Doyle:Copyrights

2008-09-23T00:58:22Z

Hana: /* Copyright note */

==Copyright note==

* Some items ©2006 IEEE. "Personal use of this material from IEEE Xplore is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE" and also the authors of publication on this website.

* Further more, the material on this website "is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying or using this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder." ©2006 IEEE.

Doyle:Copyrights

2008-09-23T00:58:03Z

Hana:

==Copyright note==

* Some items ©2006 IEEE. "Personal use of this material from IEEE Xplore is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE" and also the authors of publication on this website.

Further more, the material on this website "is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying or using this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder." ©2006 IEEE.

Papers

2008-09-23T00:56:35Z

Hana: /* See also */

'''Papers''' span many years and cover a diverse range of topics, from understanding the internet to financial market analysis, control theory and also covering certain aspects of biology, physics and physiology. '''Papers''' have been sorted by topic and year (see below.) These pages list some of Doyle's papers and related reading in these areas!



==Year==
[[2005-2009]]

[[2000-2004]]

[[1995-1999]]

[[1990-1994]]

[[1985-1989]]

==Topic==
*[[General complexity]]
*[[Networking]]
*[[Network architecture and protocols]]
*[[Wildfire ecology]]
*[[Systems biology]]
*[[Physiology]]

==Older topics==
*[[Complex networks]]
*[[Complexity and robustness]]

==See also==
[[Tips: Research papers, Publishing and Other Trivia]]

[[Research]]

See [[DoyleWiki:Copyrights|Copyright statment]] before downloading or viewing papers.

[[Category:Papers]]
[[Category:Papers by year]]
[[Category:Papers by topic]]

Physiology

2008-09-12T23:12:57Z

Hana:

Intro: ...How does exercise or diabetes influence the body's '''physiology''' , including heart function and metabolism?

Keywords: '''physiology''', heart function, metabolism, respiration, exercise, disease 
reverse engineering, complexity, proteins

==Papers==
*Csete ME and Doyle JC. [http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/7a/Science1664-2002.pdf Reverse engineering of biological complexity]. Science 2002 Mar 1; 295(5560) 1664-9

*Tanaka R, Yi TM, and Doyle J. [http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf Some protein interaction data do not exhibit power law statistics.] FEBS Lett 2005 Sep 26; 579(23) 5140-4.

==Related reading==
*[[Systems biology]]
*[http://openwetware.org/wiki/Doyle:Readings Doyle's Openwetware website]
*[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11872830,16143331 Pubmed]
*[http://www.hubmed.org/display.cgi?uids=11872830,16143331 HubMed]

==Other==
* [http://www.cochrane.org/evidenceaid/project.htm Cochrane Collaboration] (Reviews of research in healthcare)

[[Category:Papers by topic]]
[[Category:Papers]]

Research

2008-09-12T23:10:25Z

Hana: /* Current Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology external link]
**[[Physiology]]
*[[Systems Verification]]

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Complexity and robustness

2008-09-12T23:05:16Z

Hana: /* Slides */

'''Complexity and Robustness''' can be observed in communication networks and in biological systems. Some introductory notes, slides and references are listed below.

==Slides==

1. Overview of robustness (SFI robustness workshop) [http://www.cds.caltech.edu/~doyle/SFI_robustness/robustness.ppt (ppt)]

2. Design degree of freedom [http://www.cds.caltech.edu/~doyle/SFI_robustness/SFI_net1.ppt (ppt)]

3. NAS symposium on self-organizing systems [http://www.cds.caltech.edu/~doyle/SFI_robustness/NAS.ppt (ppt)]

4. SFI networking workshop [http://www.cds.caltech.edu/~doyle/SFI_robustness/SFI_net2.ppt (ppt)]

5. IMA talks by J. C. Doyle [http://www.cds.caltech.edu/~doyle/Networks/IMA1.ppt (ppt)] and by S. H. Low [http://www.cds.caltech.edu/~doyle/Networks/TCPaqm.ppt (ppt)]

6. ITP biology talk [http://www.cds.caltech.edu/~doyle/Networks/ITP_bio.ppt (ppt)]

7. Robustness of Signal Transduction Networks [http://online.itp.ucsb.edu/online/infobio01/doyle/ slides from UCSB] Apr 12, 2001

Note: there is a large overlap in material in the above slides

===Older slides===
*CDC plenary slides [http://www.cds.caltech.edu/~doyle/CmplxNets/CDC_plenary.ppt (ppt)]

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

*Allerton plenary [http://www.cds.caltech.edu/~doyle/CmplxNets/allerton.ppt (ppt)]

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

*Slides from an Old physics seminar slides [http://www.cds.caltech.edu/~doyle/SFI_robustness/UCSD_1.ppt (ppt)]

==Papers==
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/c/c5/PRLPLR2000.pdf ''Power Laws, Highly Optimized Tolerance and Generalized Source Coding''], 
J. Doyle and J.M. Carlson, 
Phys. Rev. Let., 84(24):5656-5659, 2000.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/3f/Cdc01.ps ''Scalable Laws for Stable Network Congestion Control''] 
Fernando Paganini, J. C. Doyle and S. H. Low. 
in Proceedings of IEEE CDC, Orlando, FL, Dec 2001 (475k).

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/Infocom2001.pdf ''Heavy Tails, Generalized Coding, and Optimal Web Layout''] 
Zhu X, Yu J, Doyle J, 
in Proc. IEEE Infocom joint with CCS, Vol. 3: pp1617 - 1626, Apr 2001

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

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

*''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

===Drafts===
''Theoretical Foundations for Ubiquitous, Networked Control, Communications, and Computing'', 
working paper, [http://www.cds.caltech.edu/~doyle/Networks/th_nets.ps (PS)]

''Multiscale networking, robustness, and rigor'', 
informal essay, [http://www.cds.caltech.edu/~doyle/Networks/rigor_robust.htm (html)]

''Notes on feedback'' [http://www.cds.caltech.edu/~doyle/Networks/fdbck_1.ppt (ppt)]

==Related topics==
[[Complex networks]]

[[General complexity]]

[[Research|HOT]]

==Related reading==
===PhD Thesis===
*''Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization'', 
PhD Thesis CDS, Caltech by Pablo Parrilo, 2000 [http://www.cds.caltech.edu/~pablo/thesis.ps.gz (Gzipped postscript)]

===Book===
[http://www.cds.caltech.edu/~doyle/SFI_robustness/books.htm Covers of recommended books below]

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

===Other books===
[http://www.springer.com/math/book/978-0-387-98945-7 ''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)

===Link===
For more introductory papers on HOT, see <http://www.physics.ucsb.edu/~carlson>

===Related news and commentary items===
[http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm ''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

[http://www.nature.com/nature/journal/v405/n6785/full/405412b0.html ''Applied mathematics: The power of design''] 
Mark Newman 
Nature 405, 6785, pp 412-413 (25 May 2000)

[http://www.pnas.org/cgi/content/full/97/10/5031 ''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. [http://unisci.com/stories/20001/0314004.htm]
<! Hana unable to find original article for this link-->

==Note==
This page was copied from 2005 <http://www.cds.caltech.edu/~doyle/SFI_robustness/> and re-formatted with updated citation details. Note there are both internal wiki links, external links to <http://www.cds.caltech.edu/~doyle/SFI_robustness/> and elsewhere. Content from <http://www.cds.caltech.edu/~doyle/Networks/>, was merged onto this page due to large overlap in content.

[[To Do]]

[[Category:Papers by topic]]
[[Category:Papers]]

Complexity and robustness

2008-09-12T23:04:59Z

Hana: /* Slides */

'''Complexity and Robustness''' can be observed in communication networks and in biological systems. Some introductory notes, slides and references are listed below.

==Slides==

1. Overview of robustness (SFI robustness workshop) [http://www.cds.caltech.edu/~doyle/SFI_robustness/robustness.ppt (ppt)]

2. Design degree of freedom [http://www.cds.caltech.edu/~doyle/SFI_robustness/SFI_net1.ppt (ppt)]

3. NAS symposium on self-organizing systems [http://www.cds.caltech.edu/~doyle/SFI_robustness/NAS.ppt (ppt)]

4. SFI networking workshop [http://www.cds.caltech.edu/~doyle/SFI_robustness/SFI_net2.ppt (ppt)]

5. IMA talks by J. C. Doyle [http://www.cds.caltech.edu/~doyle/Networks/IMA1.ppt (ppt)] and by S. H. Low [http://www.cds.caltech.edu/~doyle/Networks/TCPaqm.ppt (ppt)]

6. ITP biology talk [http://www.cds.caltech.edu/~doyle/Networks/ITP_bio.ppt (ppt)]

7. Robustness of Signal Transduction Networks [http://online.itp.ucsb.edu/online/infobio01/doyle/ slides from UCSB] Apr 12, 2001
Note: there is a large overlap in material in the above slides

===Older slides===
*CDC plenary slides [http://www.cds.caltech.edu/~doyle/CmplxNets/CDC_plenary.ppt (ppt)]

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

*Allerton plenary [http://www.cds.caltech.edu/~doyle/CmplxNets/allerton.ppt (ppt)]

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

*Slides from an Old physics seminar slides [http://www.cds.caltech.edu/~doyle/SFI_robustness/UCSD_1.ppt (ppt)]

==Papers==
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/c/c5/PRLPLR2000.pdf ''Power Laws, Highly Optimized Tolerance and Generalized Source Coding''], 
J. Doyle and J.M. Carlson, 
Phys. Rev. Let., 84(24):5656-5659, 2000.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/3f/Cdc01.ps ''Scalable Laws for Stable Network Congestion Control''] 
Fernando Paganini, J. C. Doyle and S. H. Low. 
in Proceedings of IEEE CDC, Orlando, FL, Dec 2001 (475k).

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/Infocom2001.pdf ''Heavy Tails, Generalized Coding, and Optimal Web Layout''] 
Zhu X, Yu J, Doyle J, 
in Proc. IEEE Infocom joint with CCS, Vol. 3: pp1617 - 1626, Apr 2001

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

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

*''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

===Drafts===
''Theoretical Foundations for Ubiquitous, Networked Control, Communications, and Computing'', 
working paper, [http://www.cds.caltech.edu/~doyle/Networks/th_nets.ps (PS)]

''Multiscale networking, robustness, and rigor'', 
informal essay, [http://www.cds.caltech.edu/~doyle/Networks/rigor_robust.htm (html)]

''Notes on feedback'' [http://www.cds.caltech.edu/~doyle/Networks/fdbck_1.ppt (ppt)]

==Related topics==
[[Complex networks]]

[[General complexity]]

[[Research|HOT]]

==Related reading==
===PhD Thesis===
*''Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization'', 
PhD Thesis CDS, Caltech by Pablo Parrilo, 2000 [http://www.cds.caltech.edu/~pablo/thesis.ps.gz (Gzipped postscript)]

===Book===
[http://www.cds.caltech.edu/~doyle/SFI_robustness/books.htm Covers of recommended books below]

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

===Other books===
[http://www.springer.com/math/book/978-0-387-98945-7 ''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)

===Link===
For more introductory papers on HOT, see <http://www.physics.ucsb.edu/~carlson>

===Related news and commentary items===
[http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm ''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

[http://www.nature.com/nature/journal/v405/n6785/full/405412b0.html ''Applied mathematics: The power of design''] 
Mark Newman 
Nature 405, 6785, pp 412-413 (25 May 2000)

[http://www.pnas.org/cgi/content/full/97/10/5031 ''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. [http://unisci.com/stories/20001/0314004.htm]
<! Hana unable to find original article for this link-->

==Note==
This page was copied from 2005 <http://www.cds.caltech.edu/~doyle/SFI_robustness/> and re-formatted with updated citation details. Note there are both internal wiki links, external links to <http://www.cds.caltech.edu/~doyle/SFI_robustness/> and elsewhere. Content from <http://www.cds.caltech.edu/~doyle/Networks/>, was merged onto this page due to large overlap in content.

[[To Do]]

[[Category:Papers by topic]]
[[Category:Papers]]

Physiology

2008-09-12T23:01:22Z

Hana: /* Media articles */ error in reference

Intro: ...How does exercise or diabetes influence the body's '''physiology''' , including heart function and metabolism?

Keywords: '''physiology''', heart function, metabolism, respiration, exercise, disease 
reverse engineering, complexity, proteins

==Papers==
*Csete ME and Doyle JC. [http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/7a/Science1664-2002.pdf Reverse engineering of biological complexity]. Science 2002 Mar 1; 295(5560) 1664-9

*Tanaka R, Yi TM, and Doyle J. [http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf Some protein interaction data do not exhibit power law statistics.] FEBS Lett 2005 Sep 26; 579(23) 5140-4.

==Related reading==
*[[Systems biology]]
*[http://openwetware.org/wiki/Doyle:Readings Doyle's Openwetware website]
*[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11872830,16143331 Pubmed]
*[http://www.hubmed.org/display.cgi?uids=11872830,16143331 HubMed]

==Media articles==

[[Category:Papers by topic]]
[[Category:Papers]]

Physiology

2008-09-12T23:00:43Z

Hana:

Intro: ...How does exercise or diabetes influence the body's '''physiology''' , including heart function and metabolism?

Keywords: '''physiology''', heart function, metabolism, respiration, exercise, disease 
reverse engineering, complexity, proteins

==Papers==
*Csete ME and Doyle JC. [http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/7a/Science1664-2002.pdf Reverse engineering of biological complexity]. Science 2002 Mar 1; 295(5560) 1664-9

*Tanaka R, Yi TM, and Doyle J. [http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf Some protein interaction data do not exhibit power law statistics.] FEBS Lett 2005 Sep 26; 579(23) 5140-4.

==Related reading==
*[[Systems biology]]
*[http://openwetware.org/wiki/Doyle:Readings Doyle's Openwetware website]
*[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11872830,16143331 Pubmed]
*[http://www.hubmed.org/display.cgi?uids=11872830,16143331 HubMed]

==Media articles==
*[http://www.biotechtransferweek.com/issues/2_17/features/146644-1.html Pfizer to Give Public-Private Consortium $14M to Study Biology of Obesity, Diabetes] 
By Ben Butkus in BiotechTransferWeek, April 30, 2008 
(noted Sept 2008)

[[Category:Papers by topic]]
[[Category:Papers]]

Tips: Research papers, Publishing and Other Trivia

2008-09-12T05:22:58Z

Hana: /* Biology */

Here are some '''quick links''' for '''searching the literature''' and '''guidelines to publishing papers'''. 
Some of these links were used to list and upload papers onto this wiki. Please note copyright still applies and wherever possible uploaded papers have information about URL/paper details attached to the upload.

==Searching literature==
===Searching Doyle's papers on this wiki===
*Click on sidebar [[Papers]], then select papers by year or by topic!
*Or click on sidebar [[Special:Specialpages|"Special pages"]] and then click on [[Special:Categories|Categories]], then select <nowiki>[[Category:Papers]]</nowiki>.
*Or click on sidebar [[Special:Allpages|"All articles"]] and then select '''from the namespace box''' pull down menu '''images''' then click "go".

===Libraries===
*[http://library.caltech.edu/ Caltech Library]
*[http://scholar.google.com/ Google scholar]
*[http://www.sciencedirect.com/ Science Direct]

====Engineering, Networking, Control====
*[http://ieeexplore.ieee.org/Xplore/dynhome.jsp IEEE Explore]
*[http://netlab.caltech.edu/pubs_search.php Netlab papers]
*[http://portal.acm.org/dl.cfm ACM portal digital library]

====Biology====
*[http://www.hubmed.org/ Hubmed]
*[http://www.nlm.nih.gov/medlineplus/ Medline plus]
*[http://openwetware.org/wiki/Main_Page OpenWetWare sharing information]
*[http://www.pnas.org/ Proceedings of National Academy of Sciences of the United States of America] (PNAS)
*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed Pubmed]
*[http://www.systems-biology.org/ Systems biology portal]
*[http://www.cochrane.org/ Cochrane Project (dissemination of reviews of healthcare research)]

====Physics====
[http://prola.aps.org/ PROLA (Physical Review Archive)]

====Economics====

==Publication guidelines==
Some specific guidelines for publishing in some journals, conferences and websites.
====Biology & Physiology====
*[http://www.plosone.org/static/guidelines.action PLoS ONE]
*[http://journals.plos.org/plosbiology/guidelines.php PLoS Biology]
*[http://www.pnas.org/site/misc/iforc.shtml PNAS]
*[http://www.pubmedcentral.nih.gov/pmcdoc/tagging-guidelines/article/style.html PMC XML Tagging Guidelines]

====Engineering====
*[http://www.ieee.org/web/publications/pubtoolsandpolicyinfo/ IEEE Publishing Tools & Policy Information For Authors, Editors & Conference Organizers]
*[http://www.acm.org/pubs/rights.html Rights and Responsibilities in ACM Publishing]

====Economics====

==Interestingly popular reads and URL's==

===Books===
... mentioned by Prof. Doyle recently:

*''Robustness'' 
by Lars Peter Hansen and Thomas J. Sargent 
Princeton University Press, USA 2008. 
ISBN-13: 978-0691-11442-2 
(cites Prof Doyle's stuff and applies it to economics)

*''Simplexity: Why Simple Things Become Complex (And How Complex Things Can Be Made Simple)'' 
By Jeffrey Kluger, Hyperion books, USA 2008. 
ISBN 978-1-4013-0301 

===URL's===
*[http://www.mathworks.com/ Mathsworks] for software including Matlab, Simulink, etc
*[http://www.cs.caltech.edu/~adamw/advising.html Advice] from Asst Prof Adam Wierman, including [http://www.cs.cmu.edu/~jrs/sins.html Three sins of authors in computer science and math] by Jonathan Shewchuk, UC Berkeley

===wiki, blog, social networking===
*[http://openwetware.org/wiki/Doyle OpenWetWare]
*[http://sbml.org/Main_Page SBML]

*[http://www.reddit.com/ reddit] (recommended by Matthew Maurer at CS, Caltech)
*[http://digg.com/ digg] (mentioned by Lachlan Andrew, Netlab)
*[http://gigaom.com/ GigaOm] (recommended by Paul Fang, high school visitor)

User:Hana

2008-09-11T03:27:18Z

Hana: /* 2008 */

==Hana's log hours==
===July -Dec 2007===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|7/8/07 Lun helped! ||2-6.30pm ||4.5||8/2/07||2.30-4.30||2.0||9/5/07 ||4.30-5 ||0.5 ||11/02/07||6.30-7.30||1
|-
|7/9/07 ||10am-1pm ||3||8/4/07||4.30-5||0.5||9/8/07 ||7.30-8 ||0.5
||11/30/07||5-7, 11-12||3
|-
|7/15/07 Lun helped||12-3.30pm||3.5||8/10/07||4-6.30||2.5||9/14/07||7.45-8.15||0.5
||12/1/07||3.30-7||4.5
|-
|7/16/07||12-12.30am||0.5||8/14/07 ||9.30-11.30||2||9/17/07||11.30-12.30||1
||12/3/07||9-10.30||1.5
|-
|7/18/07||4-4.30pm, 6-7pm||1.5||8/17/07||6.30-7.30||1||9/19/07||11.30-12.30||1
|-
|7/27/07||10-10.30||0.5
|-
|7/31/07||12-12.30||0.5
|}
===Jan-Aug 2008===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs

|-
|01/25/08||2-2.30||0.5||7/16/08||10-12.30, 2-6||6.5
|-
|01/28/08||6.30-7.30||0.5||7/17/08||8-8.5pm||0.5
|-
|2/22/08||6.30-7.30||1.0||7/21/08 ||8-8.5pm||0.5
|}

{| border="1"
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|8/15/08||12.30-1||0.5
|-
|8/1/08||10-10.5||0.5
|-
|8/7/08||8-8.5pm ||0.5
|-
|8/16/08||2.30-4.30pm, 6.30-7.30pm ||3
|-
| || ||
|-
|8/17/08|| ||1||8/18/08|| ||1.5
|-
|8/22/08 || ||1||8/23/08|| || 2.5
|-
|8/26/08|| ||1 ||8/27/08|| ||0.5
|-
|8/28/08|| ||2||8/29/08|| ||2
|}
Based on [[Special:contributions/Hana]]

==Items completed==
===2007===
Betta has arranged Purchasing Order for Hana's Netlab website consulting. Betta is giving Gloria & research group copy of Netlab Purchasing Order. Prof. Doyle's group to arrange separate Purchasing order for Hana's website consulting. Hana waiting on Prof. Doyle's group to approve set up of wiki & to pass on website maintainance to the group.

*Copied links to papers from Netlab pages & Lun's page, Systems-Biol page, J DOyle's old page onto wiki,
*set up to do list / main page/stucture/help page/sidebar/research/papers pages & bio copied.
*Added IEEE explore publications to pages.
*changed monoskins to remove edit tabs, for viewers/users not logged in.
*created accounts for GB, LL, MF, LC, HK, to stop using Doyle's account in Sept 2007. Used Special pages:Login, User list, User rights management
*Added links to Discover magazine and uploaded photo, added link to Prof Murray's Panama updates.
*Copied and uploaded over papers, filed by topic and by year, as per Prof's instructions.
*Given Gloria Netlab Purchase order and Wiki log hours.
*Copied over Panama adventures by Prof to Wiki. To get Prof Murray's version.
*Uploaded article from Discover magazine on John Doyle. Uploaded other images for wiki.

===2008===
*Cited 80-90 papers and uploaded pdf versions to wiki. Copied athetics page. Topics and some papers from Prof Doyle copied over. More old website pages copied over.
* Added awards and patents 2000-2008.
*Edited [[Help:Contents]] for future Doyle users.
*Copied over joint projects and links from Prof Murray's wiki and Netlab website.
*Sent Invoice 3 to Gloria Bain. Updated [[Group]] with Lijun.
*Showed wiki and passed on URL to visitor
*Pages had text copied from Doyle's old website then reformatted and citations/links added [[Complex networks]] and [[Complexity and robustness]].
*Tidied added keywords and copied papers to relvant pages under [[ Category: Papers by topic ]]
*Tidied added suggestions/links to [[To Do Q]] and [[Tips: Research papers, Publishing and Other Trivia]], hopefully to
improve wiki, add features ... and help students with quick links...
*Added another 3-5 papers from various URL's.
*Added suggestions to [[To Do Q]] for others to improve wiki.
*Added links to websites, portals, events, Caltech calendar!
*Created more user accounts, contacted more [[Group|people]] to take over wiki.
*Full list of items done on wiki at [[Special:Contributions/Hana]]
*Re-submitted updated invoice to new Admin - Charis Brown on Sept 6

==To Do==
Pass on wiki stuff to Doyle's [[Group]] to continue updates.

Main Page

2008-09-11T03:25:51Z

Hana: /* News */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==News==
*[[Calendar]]
*[[Research|MURI 2008]]
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

==Papers==
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems." <http://www.cds.caltech.edu/people/> Aug 16, 2008

*[[Research|Research projects and grants list]]


== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''':  Charis Brown 
Office: 107 Steele, 
Email: charismb AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

News

2008-09-11T03:25:11Z

Hana: /* Current news! */

==Current news!==
* Prof Doyle is co-PI on [[Research|MURI 2008]] with other collaborators
* [http://www.ipam.ucla.edu/programs/mra2008/ ''Internet Multi-Resolution Analysis: Foundations, Applications and Practice Activities''] activities hosted at ''[http://www.ipam.ucla.edu/ IPAM UCLA]'', September 8 - December 12, 2008. 
J Doyle is an invited speaker and also on the organizing committee. 

==Past News==

===2007===
*John Doyle's website is renovated /drafted late 2007 to mid-2008.

*[http://discovermagazine.com/2007/ Discover Magazine] interviews Prof. Doyle about his academic and competitive sports interests.

[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet" This man wants to control the internet"] by Carl Zimmer, Discover Magazine, 10/25/2007.

[[Image:DoyleDiscover1.jpg|200px]] 
Photo by Trujillo/Paumier from Discover Magazine.

*[[Recent_Adventures_in_Robustness_and_Fragility:_Travels_to_Panama_and_back]] in Aug-Sept 2007
** Prof. Murray's version of [http://www.cds.caltech.edu/~murray/wiki/John_Doyle%27s_Panamanian_Adventure John Doyle's Panamian Adventure]

Some CDS graduates at Caltech Commencement 2007: Prof. John Doyle, ?, Lun Li, Prof. Richard Murray, Lijun Chen, Prof. Steven Low [[Image:GB Grads 07.jpg|200px]]

===2005===
DGA Private Screening
September 7, 2005 @ 8PM
[[Image:Movie2005.jpg|right|100px]]
At an auction for the California Women’s Law Center(CWLC) John Doyle bid and won a private screening for a movie "Everything is Illuminated" staring Elijah Wood was shown at the Directors Guild of America on September 7th at 8pm. The movie All friends of CDS were invited to attend. A preview of the movie can be found here.

===2004===
John Doyle's 50th celebrations at [http://www.cds.caltech.edu/doyle-fest/overview.html Connections Workshop], Caltech. [[Image:JCDgraph.jpg]]

Main Page

2008-09-11T03:22:55Z

Hana: /* Papers */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==News==
*[[Calendar]]
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.
==Papers==
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems." <http://www.cds.caltech.edu/people/> Aug 16, 2008

*[[Research|Research projects and grants list]]


== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''':  Charis Brown 
Office: 107 Steele, 
Email: charismb AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Research

2008-09-11T03:21:50Z

Hana: /* Grants for Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology]
*[[Systems Verification]]

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Research

2008-09-11T03:21:29Z

Hana: /* References */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology]
*[[Systems Verification]]

===Grants for Projects===
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Research

2008-09-11T03:20:50Z

Hana:

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology]
*[[Systems Verification]]

===Grants for Projects===
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==References==

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Main Page

2008-09-11T03:12:25Z

Hana: /* Research */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==Papers==
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.
*favourite papers
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems." <http://www.cds.caltech.edu/people/> Aug 16, 2008

*[[Research|Research projects and grants list]]


== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''':  Charis Brown 
Office: 107 Steele, 
Email: charismb AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Main Page

2008-09-10T03:53:52Z

Hana: /* Contact */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==Papers==
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.
*favourite papers
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's [[research]] interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems." [http://www.cds.caltech.edu/people/ from http://www.cds.caltech.edu/people/ Aug 16, 2008]

*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology hosted at Openwetware.org]
**[[Physiology]]
*[[Systems Verification]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''':  Charis Brown 
Office: 107 Steele, 
Email: charismb AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Main Page

2008-09-10T03:53:33Z

Hana: /* Contact */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==Papers==
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.
*favourite papers
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's [[research]] interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems." [http://www.cds.caltech.edu/people/ from http://www.cds.caltech.edu/people/ Aug 16, 2008]

*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology hosted at Openwetware.org]
**[[Physiology]]
*[[Systems Verification]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''':  Charis Brown 
Office: 107 Steele, 
Email: charismb AT caltech dot edu>
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Group

2008-09-10T03:41:52Z

Hana: /* Admin */

John Doyle's research '''group''' is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.

==Current Group==

===Faculty===
John Doyle

===Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]
|[http://www.cs.caltech.edu/~krister/ Krister Jacobsson]
|[http://www.ist.caltech.edu/~brecht/ Ben Recht]
|}

===Graduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos]
|[http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi]
|[http://www.cds.caltech.edu/people/portal/?id=758 Vanessa Carson]
|-
|[http://www.cds.caltech.edu/people/portal/?id=760 Fiona Chandra]
|[http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme]
|[http://www.cds.caltech.edu/~andyl/ Andrew Lamperski]
|-
|[http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]
|[http://www.cds.caltech.edu/people/portal/?id=753 Na Li]
|[http://www.cds.caltech.edu/people/portal/?id=522 Marcos Nahmad Bensusan]
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=797 Somayeh Sojoudi]
|Jerry Cruz||
|}
===Undergraduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=772 George Hines]||[http://www.cds.caltech.edu/people/portal/?id=803 Nicholas Fette]
|}
===Admin===
Charis Brown

===Visitors===
[http://www.cds.caltech.edu/~lun/ Lun Li, also alumni]
====Students====
{| class="wikitable" border="1"
|-
|''SURF 2008''||''Other''
|-
|Jackson Wang Ji Young Lee||Paul Fang, student from Temple City High School
|}

==Past Group==
===Alumni===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''||'''2000-2006'''||'''1990-1999'''
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]

[http://www.cds.caltech.edu/~lun Lun Li]

[http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]

[http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]

[http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]
|
[http://faculty.nps.edu/dlalders/ David Alderson]

Nizar Batada

[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]

Irene Gregory

[http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]

[http://webfiles.uci.edu/yjing/www/ Yindi Jing]

Sven Khatri

[http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]

[http://www.mit.edu/~parrilo/ Pablo Parrilo]

[http://www.cds.caltech.edu/~prajna/ Stephen Prajna]

[http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]

[http://www.cds.caltech.edu/~jyu/ Jie Yu]

[http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]

|Carolyn Beck

Raff D'Andrea

Sonja Glavaski

Irene Gregory

Yun Huang

Michael Kantner

[http://www.ee.ucla.edu/~paganini/ Fernando Paganini]

[http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]

Stefano Soatto

Jorge Tierno
|}

===Past Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|'''2007-2008'''||'''2000-2006'''||'''1990-1999'''
|-
|
[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames]

[http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]

[http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]
|
Masahiro Yanagisawa

[http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]

[http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]
|
[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]

[http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]
|}
===Past Admin===

?-2008 Gloria Bain

===Past Visitors===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''
|'''2000-2006
|'''1990-1999'''
|-
|Panagiota Stratou
|?
|?
|}

==MURF and SURF Students==
{| class="wikitable" border="0" width="80%"
|'''2008'''||'''2007''' ||'''2000-2006'''
|-
|Jackson Wang Ji Young Lee ||[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||
|-
| ||
|}

==Other collaborators==
{| class="wikitable" border="0" width="80%"
|-
|[[Image:3profs07.jpg|200px]]||[[Image:John-and-marie.jpg]]
|-
|2007 Commencement: Prof.'s John Doyle, Richard Murray & Steven Low. ||John Doyle and Marie Csete
|}

[[Image:JCDgraph.jpg]]

Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004:

*[http://userwww.service.emory.edu/~mcsete/ Marie Csete, Lab] at [http://www.emory.edu/change_mode.cfm?mode=text Emory University], Atlanta.
**[http://www.emory.edu/PROVOST/greatscholars/MarieCsete.htm About Marie Csete's work.]

==See also==
*[[Group Meetings]]
*[[Calendar]]
*<http://www.cds.caltech.edu/people/portal/?un=doyle>

Main Page

2008-09-10T03:41:16Z

Hana: /* Contact */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==Papers==
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.
*favourite papers
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's [[research]] interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems." [http://www.cds.caltech.edu/people/ from http://www.cds.caltech.edu/people/ Aug 16, 2008]

*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology hosted at Openwetware.org]
**[[Physiology]]
*[[Systems Verification]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''':  Charis Brown 
Office: 107 Steele, 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Main Page

2008-09-10T03:40:03Z

Hana: /* Research */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==Papers==
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.
*favourite papers
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's [[research]] interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems." [http://www.cds.caltech.edu/people/ from http://www.cds.caltech.edu/people/ Aug 16, 2008]

*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology hosted at Openwetware.org]
**[[Physiology]]
*[[Systems Verification]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''':  
626.395.4140
 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Complexity and robustness

2008-09-06T21:33:50Z

Hana:

'''Complexity and Robustness''' can be observed in communication networks and in biological systems. Some introductory notes, slides and references are listed below.

==Slides==

1. Overview of robustness (SFI robustness workshop) [http://www.cds.caltech.edu/~doyle/SFI_robustness/robustness.ppt (ppt)]

2. Design degree of freedom [http://www.cds.caltech.edu/~doyle/SFI_robustness/SFI_net1.ppt (ppt)]

3. NAS symposium on self-organizing systems [http://www.cds.caltech.edu/~doyle/SFI_robustness/NAS.ppt (ppt)]

4. SFI networking workshop [http://www.cds.caltech.edu/~doyle/SFI_robustness/SFI_net2.ppt (ppt)]

5. IMA talks by J. C. Doyle [http://www.cds.caltech.edu/~doyle/Networks/IMA1.ppt (ppt)] and by S. H. Low [http://www.cds.caltech.edu/~doyle/Networks/TCPaqm.ppt (ppt)]

6. ITP biology talk [http://www.cds.caltech.edu/~doyle/Networks/ITP_bio.ppt (ppt)]

Note: there is a large overlap in material in the above slides

===Older slides===
*CDC plenary slides [http://www.cds.caltech.edu/~doyle/CmplxNets/CDC_plenary.ppt (ppt)]

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

*Allerton plenary [http://www.cds.caltech.edu/~doyle/CmplxNets/allerton.ppt (ppt)]

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

*Slides from an Old physics seminar slides [http://www.cds.caltech.edu/~doyle/SFI_robustness/UCSD_1.ppt (ppt)]

==Papers==
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/c/c5/PRLPLR2000.pdf ''Power Laws, Highly Optimized Tolerance and Generalized Source Coding''], 
J. Doyle and J.M. Carlson, 
Phys. Rev. Let., 84(24):5656-5659, 2000.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/3f/Cdc01.ps ''Scalable Laws for Stable Network Congestion Control''] 
Fernando Paganini, J. C. Doyle and S. H. Low. 
in Proceedings of IEEE CDC, Orlando, FL, Dec 2001 (475k).

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/Infocom2001.pdf ''Heavy Tails, Generalized Coding, and Optimal Web Layout''] 
Zhu X, Yu J, Doyle J, 
in Proc. IEEE Infocom joint with CCS, Vol. 3: pp1617 - 1626, Apr 2001

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

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

*''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

===Drafts===
''Theoretical Foundations for Ubiquitous, Networked Control, Communications, and Computing'', 
working paper, [http://www.cds.caltech.edu/~doyle/Networks/th_nets.ps (PS)]

''Multiscale networking, robustness, and rigor'', 
informal essay, [http://www.cds.caltech.edu/~doyle/Networks/rigor_robust.htm (html)]

''Notes on feedback'' [http://www.cds.caltech.edu/~doyle/Networks/fdbck_1.ppt (ppt)]

==Related topics==
[[Complex networks]]

[[General complexity]]

[[Research|HOT]]

==Related reading==
===PhD Thesis===
*''Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization'', 
PhD Thesis CDS, Caltech by Pablo Parrilo, 2000 [http://www.cds.caltech.edu/~pablo/thesis.ps.gz (Gzipped postscript)]

===Book===
[http://www.cds.caltech.edu/~doyle/SFI_robustness/books.htm Covers of recommended books below]

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

===Other books===
[http://www.springer.com/math/book/978-0-387-98945-7 ''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)

===Link===
For more introductory papers on HOT, see <http://www.physics.ucsb.edu/~carlson>

===Related news and commentary items===
[http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm ''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

[http://www.nature.com/nature/journal/v405/n6785/full/405412b0.html ''Applied mathematics: The power of design''] 
Mark Newman 
Nature 405, 6785, pp 412-413 (25 May 2000)

[http://www.pnas.org/cgi/content/full/97/10/5031 ''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. [http://unisci.com/stories/20001/0314004.htm]
<! Hana unable to find original article for this link-->

==Note==
This page was copied from 2005 <http://www.cds.caltech.edu/~doyle/SFI_robustness/> and re-formatted with updated citation details. Note there are both internal wiki links, external links to <http://www.cds.caltech.edu/~doyle/SFI_robustness/> and elsewhere. Content from <http://www.cds.caltech.edu/~doyle/Networks/>, was merged onto this page due to large overlap in content.

[[To Do]]

[[Category:Papers by topic]]
[[Category:Papers]]

Physiology

2008-09-06T21:32:03Z

Hana:

Systems biology

2008-09-06T21:30:47Z

Hana:

Intro: ...'''systems biology'''...

....the development of machine-readable language to discuss biological systems '''SBML''' has resulted from a collaborative effort between many other diverse research groups...this has opended up...

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism...
===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''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)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''Robustness as a measure of plausibility in models of biochemical networks''], 
Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H, 
Journal Of Theoretical Biology 216 (1): 19-30 May 7, 2002.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project''], 
M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano 
IEE Systems Biology. 1:41-53, 2004

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology'' (Abstract)] 
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H. 
in Proc. Pac Symp Biocomput. 450-61, 2002.

===2001===
*''The Systems Biology Markup Language'' 
Finney AM, Hucka M, Sauro HM, Doyle J, Kitano H, Bolouri H, 
Molecular Biology of the Cell 12: 708 Suppl. S NOV 2001.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''Model validation and robust stability analysis of the bacterial heat shock response using SOSTOOLS.''] 
H. El-Samad, S. Prajna, A. Papachristodoulou, M. Khammash and J. C. Doyle 
in Proc. IEEE CDC, vol. 4:3766 - 3771; Maui, Hawaii, 9-12 Dec. 2003.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''Oxygen-mediated regulation of skeletal muscle satellite cell proliferation and adipogenesis in culture'' 
Csete M, Walikonis J, Slawny N, Wei Y, Korsnes S , Doyle JC, Wold B, 
Journal of Cellular Physiology, Volume 189, Issue 2, Nov. 2001. 189-196

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

Wildfire ecology

2008-09-06T21:28:25Z

Hana:

Intro: '''wildfire ecology'''

Keywords: '''wildfire ecology'''

Copied one paper from <http://www.cds.caltech.edu/~doyle/RecentPapers/>

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

Q: Does paper on "Heat-shock proteins" belong here?

==Related reading==
[[Category:Papers by topic]]
[[Category:Papers]]

Wildfire ecology

2008-09-06T21:28:00Z

Hana:

Intro:

Keywords: '''wildfire ecology'''

Copied one paper from <http://www.cds.caltech.edu/~doyle/RecentPapers/>

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

Q: Does paper on "Heat-shock proteins" belong here?

==Related reading==
[[Category:Papers by topic]]
[[Category:Papers]]

General complexity

2008-09-06T21:27:18Z

Hana:

Intro: ... is interested in the understanding '''complexity''' of ...

... aspects of complexity in nature and computer networks are compared...

Keywords: '''Complexity''', systems, biology, internet...

Copied one paper from <http://www.cds.caltech.edu/~doyle/RecentPapers/>

==General Complexity in nature==
Keywords: complexity, HOT (highly optimized tolerance), biology systems,

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f3/IEEETACSideInfo07.pdf ''Fundamental Limitations of Disturbance Attenuation in the Presence of Side Information''] 
Martins, N. C.; Dahleh, M. A.; Doyle, J. C.; 
IEEE Trans Auto Control, 52(1):56 - 66, Jan 2007 (389K)
===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/CDC2005.pdf ''Fundamental Limitations of Disturbance Attenuation in the Presence of Side Information''] 
Martins, N.C.; Dahleh, M.A.; Doyle, J.C.; 
IEEE CDC - ECC pp2523 - 2529, Seville, Spain, 12-15 Dec 2005.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/7a/Science1664-2002.pdf ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

==Complexity in Networks==
Keywords:

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6e/CSMC2007.pdf ''Can complexity science support the engineering of critical network infrastructures?''] 
Alderson, D.L. and Doyle, J.C.; 
IEEE International Conference on Systems, Man and Cybernetics, pp 44 - 51 , 7-10 Oct. 2007

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/af/CDC2006.pdf ''Complexity in Automation of SOS Proofs: An Illustrative Example''] 
Gayme, D.; Fazel, M.; Doyle, J.C. 
in Proc. IEEE CDC, pp5851 - 5856, San Diego, CA, 13-15 Dec 2006.
===2005===
''[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/4e/Part1_vers4.pdf Robustness and the Internet: Design and evolution]'', 
W. Willinger, J Doyle, 
in Robust Design: A Repertoire of Biological, Ecological, and Engineering Case Studies 
(Santa Fe Institute Studies on the Sciences of Complexity), 
Erica Jen, Editor 2005

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/02/Wsc04.pdf ''More 'Normal' Than Normal: Scaling Distributions and Complex Systems''], 
W. Willinger, D. Alderson, J. C. Doyle and L. Li, 
WSC (Winter Simulation Conference), Washington D. C., 2004.

* ''Managing complexity and uncertainty'' [http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a0/SICE2004.pdf (chair person for plenary lecture)] 
Doyle, J.C. 
SICE 2004 Annual Conference vol. 3; ppxlvii - l; 4-6 Aug. 2004.

==Related reading==
*[[Complex_networks]]
===External links===

[[Category:Papers by topic]]
[[Category:Papers]]

Papers

2008-09-06T21:24:15Z

Hana:

'''Papers''' span many years and cover a diverse range of topics, from understanding the internet to financial market analysis, control theory and also covering certain aspects of biology, physics and physiology. '''Papers''' have been sorted by topic and year (see below.) These pages list some of Doyle's papers and related reading in these areas!



==Year==
[[2005-2009]]

[[2000-2004]]

[[1995-1999]]

[[1990-1994]]

[[1985-1989]]

==Topic==
*[[General complexity]]
*[[Networking]]
*[[Network architecture and protocols]]
*[[Wildfire ecology]]
*[[Systems biology]]
*[[Physiology]]

==Older topics==
*[[Complex networks]]
*[[Complexity and robustness]]

==See also==
[[Tips: Research papers, Publishing and Other Trivia]]

[[Research]]

[[Category:Papers]]
[[Category:Papers by year]]
[[Category:Papers by topic]]

Networking

2008-09-06T21:22:37Z

Hana: add intro line

Intro: ...'''networking''' at Doyle's [[group]] covers...

Keywords: '''network(s)''',

'''internet''', architecture, infrastructure, graphs, game theory, congestion control, coding, ...

and biological, biochemical, metabolic...

Some papers from <http://www.cds.caltech.edu/~doyle/RecentPapers/>

==Networks==
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f5/PRE06.pdf ''Diversity of graphs with highly variable connectivity''] 
David Alderson and Lun Li 
Phys. Rev. E 75, 046102, 2007. (3.9MB)

==Internet networks==
Keywords: '''internet''', '''networks''', architecture, coding, infrastructure, graphs, game theory, congestion control,...

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/36/IEEEProc_NetsLayer.pdf'' Layering as optimization decomposition: A Mathematical Theory of Network Architectures''] (invited), 
Mung Chiang, Steven H. Low, A. Robert Calderbank, John C. Doyle 
in Proc. IEEE 95(1) Jan 2007. (3.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/96/Netcod-info07.pdf ''Optimization Based Rate Control for Multi-cast with Network Coding''] 
Lijun Chen, Tracey Ho, Steven H. Low, Mung Chiang and John C. Doyle. 
in Proc. IEEE Infocom, Anchorage, Alaska, May 2007. (191K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6b/Oscor_mass.pdf Opportunistic Source Coding for Data Gathering in Wireless Sensor Networks]
Tao Cui, Lijun Chen, Tracey Ho, Steven H. Low and Lachlan H. Andrew 
in Proc. IEEE MASS (Mobile Ad-hoc and Sensor Systems), Pisa, Italy, Oct 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/71/Rag07.pdf ''Game-Theoretic Model for Medium Access Control''] 
Lijun Chen, Tao Cui, Steven H. Low and John C. Doyle 
in Proc. WICON, Austin,Texas, Oct 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/96/Netcod-info07.pdf ''Optimization Based Rate Control for Multi-cast with Network Coding''] 
Lijun Chen, Tracey Ho, Steven H. Low, Mung Chiang and John C. Doyle. 
in Proc. IEEE Infocom, Anchorage, Alaska, May 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6e/CSMC2007.pdf ''Can complexity science support the engineering of critical network infrastructures?''] 
Alderson, D.L. and Doyle, J.C.; 
IEEE International Conference on Systems, Man and Cybernetics, pp 44 - 51 , 7-10 Oct. 2007

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/38/Ragmac07.pdf Contention Control: A Game-Theoretic Approach] (invited) 
Lijun Chen, Steven H. Low and John C. Doyle 
in Proc. IEEE CDC pp3428 - 3434, New Orleans, LA, 12-14 Dec 2007.

[http://www.springerlink.com/content/qp4x0125v16p2g83/?p=cd9b949b2ef14cef910ce160b6ead5c2&pi=6 ''Dual scheduling algorithm in a generalized switch: asymptotic optimality and throughput optimality''], 
L. Chen and S. H. Low and J. C. Doyle, 
in [http://www.springer.com/west/home?SGWID=4-102-22-92732347-0&changeHeader=true ''High-Performance Packet Switching Architectures''], Itamar Elhanany and Mounir Hamdi (Eds), Springer, 2007.

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1d/InternetMath06.pdf ''Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications''] 
L. Li, D. Alderson, J. C. Doyle and W. Willinger, 
Internet Mathematics, 2(4): 431-523, Mar 2006 (1.8MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/ae/Wireless-Chen-infocom06.pdf ''Cross-layer congestion control, routing and scheduling design in ad hoc wireless network''], 
L. Chen and S. H. Low and M. Chiang and J. C. Doyle, 
in Proc. IEEE Infocom, pp1-13; Barcelona, Spain, Apr 2006. (431K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/fe/Hotnets06.pdf ''Discovering Dependencies for Network Management''], 
Victor Bahl, Paul Barham, Richard Black, Ranveer Chandra, Moises Goldszmidt, Rebecca Isaacs, Srikanth Kandula, Lun Li, John MacCormick, David A. Maltz, Richard Mortier, Mike Wawrzoniak, and Ming Zhang, 
In Proc. ACM/SIGCOMM HotNets, Irvine, CA, Sept 2006.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/5/58/Informs-tc04-chap6.pdf ''The Optimization-based Approach to Modeling Internet Topology''] 
D. Alderson, W. Willinger, L. Li, and J. Doyle, 
[http://www.springer.com/west/home/engineering/electronics?SGWID=4-191-22-81597755-detailsPage=ppmmedia|aboutThisBook Telecommunications Planning: Innovations in Pricing, Network Design and Management.] S. Raghavan and G. Anandlingham, eds. Springer. 2006.

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/Ton_topology.pdf ''Understanding Internet Topology: Principles, Models, and Validation,''] 
D. Alderson, L. Li, W. Willinger, J. C. Doyle, 
IEEE/ACM Transaction on Networking, 13(6), Dec. 2005. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/16/PNAS_Internet05.pdf ''The ‘‘robust yet fragile’’ nature of the Internet''] 
John C. Doyle, David L. Alderson, Lun Li, Steven Low, Matthew Roughan, Stanislav Shalunov, Reiko Tanaka, and Walter Willinger 
Proc. Natl. Acad. Sci. USA, 102(41):14497-14502, Oct 11 2005. (635K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/64/Fast-network05.pdf ''FAST TCP: From Theory to Experiments''], 
C. Jin, D. X. Wei, S. H. Low, G. Buhrmaster, J. Bunn, D. H. Choe, R. L. A. Cottrell, J. C. Doyle, W. Feng, O. Martin, H. Newman, F. Paganini, S. Ravot and S. Singh, 
IEEE Network, 19(1):4-11, Jan/Feb 2005.(638k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks''] 
J. Wang, L. Li, S. H. Low and J. C. Doyle. 
IEEE/ACM Transactions on Networking, 13(3):582-568, Jun 2005 (409k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/e/e5/Paganini-fast-jour-2005.pdf ''Congestion control for high performance, stability and fairness in general networks''] 
F. Paganini, Z. Wang, J. C. Doyle and S. H. Low. 
IEEE/ACM Transactions on Networking, 13(1):43-56, Feb 2005 (444k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1b/Tcpmac-infocom05.pdf ''Joint congestion control and media access control design for wireless ad hoc networks''] 
Lijun Chen, Steven H. Low and John C. Doyle. 
in Proc. IEEE Infocom, Miami, FL, Mar 2005 (193k).

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/d/dd/Sigmetrics05.pdf ''Optimization model of internet protocols''] 
Steven H. Low, John Doyle, Lun Li, Ao Tang and Jiantao Wang 
in Proceedings of SIGMETRICS, pp277 - 277, Banff, Alberta, Canada, June 6-10, 2005.

''[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/4e/Part1_vers4.pdf Robustness and the Internet: Design and evolution]'', 
W. Willinger, J Doyle, 
in Robust Design: A Repertoire of Biological, Ecological, and Engineering Case Studies 
(Santa Fe Institute Studies on the Sciences of Complexity), 
Erica Jen, Editor

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f6/Li-SFGraph-IM-0508-2005.pdf ''Towards a theory of scale-free graphs: definitions, properties, and implications''] 
L. Li, D. Alderson, J. C. Doyle and W. Willinger 
Internet Mathematics, 2005 (909k).

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/2/28/Ccr-papachr04.pdf ''Methodological Frameworks for Large-scale Network Analysis and Design''] 
Antonis Papachristodoulou, Lun Li and John C. Doyle, 
CCR (Computer Communication Review), 34(3), Jul 2004 (828Kk)

==Biological networks==
Keywords: '''network''', biological, biochemical, metabolic...

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)
===2003===
*''The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models'', 
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, 
Bioinformatics 19 (4): 524-531, Mar 1 2003.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''Robustness as a measure of plausibility in models of biochemical networks''], 
Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H, 
Journal Of Theoretical Biology 216 (1): 19-30 May 7, 2002 .

==Related reading==
[[Network architecture and protocols]]
[[Category:Papers]]

[[Category:Papers by topic]]

J. Doyle’s Bio

2008-09-06T21:21:13Z

Hana: /* Projects */

'''John Doyle''' is the John G Braun Professor of [http://www.cds.caltech.edu Control & Dynamical Systems], [http://www.ee2.caltech.edu/ Electrical Engineering], and [http://www.be.caltech.edu/ BioEngineering] at [http://www.caltech.edu Caltech].

==Recent Adventures==
[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine interviews] Prof. Doyle.

in "This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

===Aug-Sept 2007 ===
[[Recent Adventures in Robustness and Fragility: Travels to Panama and back]]

[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Murray]'s version of [[John Doyle's Panamanian Adventure]]

==Academic summary==

===University===
*BS, MS EE [http://web.mit.edu/ MIT], 1977.
*Ph.D. Math, [http://www.berkeley.edu/ UC Berkeley], 1984.
*Assoc Prof with tenure at [http://www.caltech.edu Caltech], 1986.
*Prof at Caltech, 1991 - present.

===Awards===
====Projects and Grants====
Grants for various projects have been listed on the following pages:

*[[Research#Current_Projects|Research awards for projects]]
*[[Research#Past_Projects|Research awards for past projects]]

====Individual awards====
*[http://www.ieee.org/portal/pages/about/awards/pr/cntrlpr.html IEEE Control Systems Field Award recipient] for "For fundamental contributions to the analysis and control of uncertain systems" in 2004
*[http://www.ieee-centennial.org/ IEEE Centennial] Outstanding Young Engineer Award 
(as the top young researcher under 40 from the IEEE Controls Systems Society, 1984).
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html IEEE Hickernell Award], 1976
*[http://a2c2.org/index.php?option=com_content&task=view&id=32&Itemid=46 American Automatic Control Council (AACC) Eckman Award], 1983
*[http://math.berkeley.edu/aboutus_gifts_funds.html Bernard Friedman Award] (from UC Berkeley)1984
*[http://www.onr.navy.mil/ ONR] Presidential Young Investigator 1986
*[http://www.nsf.gov/index.jsp NSF] Presidential Young Investigator 1986

===Prize papers===
*[http://www.ieee.org/web/publications/journmag/index.html IEEE Transactions] [http://www.ieeecss.org/main.php?levelsecid=171&secid=171&expandsecid=24 George S. Axelby Outstanding Paper Awards] 1990 (two papers)
*[http://www.ieee.org/portal/pages/about/awards/pr/bakepr.html IEEE Baker prize] paper, 1991 
was also ranked in the top 10 ``most important'' papers world-wide in pure and applied mathematics from 1981-1993 in a bibliometric analysis and survey conducted by CTWS-Leiden. It was the most recently published paper to be so ranked.
This prize is awarded once each year to the outstanding paper reporting new research results among all of the IEEE's over 50 technical journals,
*[http://www.a2c2.org/awards/schuck/index.php AACC Hugo Schuck Award], 1994

===Patents===
*[http://www.patentstorm.us/patents/6414827.html US Patent 6414827 - Closed-loop scaling for discrete-time servo controller in a disc drive] Issued July 2, 2002

*[http://www.patentstorm.us/patents/5978752/claims.html US Patent 5978752 - Model validation algorithm for characterizing parameters and uncertainty in a disc drive] Issued Nov 2, 1999

===Academic Bio 1990's===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]

==Industry summary==
*Served as a consultant to Honeywell Technology Center since 1976

==Research interests==
His research interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development.

Research applications interests are motivated by the interplay between control, dynamical systems, and design and analysis of large, complex systems.

==Athletics==
John Doyle is an athlete in his spare time.

===Some athletic achievements from 1990's:===
*World champion, [http://www.ihpva.org/ IHPVA] speed championships time trial.
*US Record, indoor rowing (former world record).
*2 Gold medals, [http://hosting2.sportingpulse.com/www.imga-masters.com/ World Masters Games].
*Member, Duathlon Team USA.
*Age group wins:
**Duathlon in Exile (world championship qualifier),
**Fall Showdown Duathlon,
**Big Bear Duathlon,
**Powerman Chicago Sprint,
**Steamboat Triathlon,
**USCF District 6 cycling time trial...

*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]
*See [[J. Doyle's Bio Athletics]] for details and photos!

==Portraits==
{| class="wikitable"
|-
|[[Image:John-and-marie.jpg]] ||[[Image:bike2.jpg]]||http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet/doyle2.jpg
|-
|John and Marie||Cycling||From " This Man Wants To Control the Internet 
This man wants to control the Internet. And you should let him. 
by Carl Zimmer, Photographs by Trujillo/Paumier 
published online October 25, 2007
|}

==See also==
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html 2004 IEEE bio and photo of J Doyle]
*[http://www.cds.caltech.edu/people/ J Doyle's bio at CDS, Caltech]
===older webpages===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]
*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]

J. Doyle’s Bio

2008-09-06T21:20:41Z

Hana: /* Projects */

'''John Doyle''' is the John G Braun Professor of [http://www.cds.caltech.edu Control & Dynamical Systems], [http://www.ee2.caltech.edu/ Electrical Engineering], and [http://www.be.caltech.edu/ BioEngineering] at [http://www.caltech.edu Caltech].

==Recent Adventures==
[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine interviews] Prof. Doyle.

in "This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

===Aug-Sept 2007 ===
[[Recent Adventures in Robustness and Fragility: Travels to Panama and back]]

[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Murray]'s version of [[John Doyle's Panamanian Adventure]]

==Academic summary==

===University===
*BS, MS EE [http://web.mit.edu/ MIT], 1977.
*Ph.D. Math, [http://www.berkeley.edu/ UC Berkeley], 1984.
*Assoc Prof with tenure at [http://www.caltech.edu Caltech], 1986.
*Prof at Caltech, 1991 - present.

===Awards===
====Projects====
Grants for various projects have been listed on the following pages:

*[[Research#Current_Projects|Research awards for projects]]
*[[Research#Past_Projects|Research awards for past projects]]

====Individual awards====
*[http://www.ieee.org/portal/pages/about/awards/pr/cntrlpr.html IEEE Control Systems Field Award recipient] for "For fundamental contributions to the analysis and control of uncertain systems" in 2004
*[http://www.ieee-centennial.org/ IEEE Centennial] Outstanding Young Engineer Award 
(as the top young researcher under 40 from the IEEE Controls Systems Society, 1984).
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html IEEE Hickernell Award], 1976
*[http://a2c2.org/index.php?option=com_content&task=view&id=32&Itemid=46 American Automatic Control Council (AACC) Eckman Award], 1983
*[http://math.berkeley.edu/aboutus_gifts_funds.html Bernard Friedman Award] (from UC Berkeley)1984
*[http://www.onr.navy.mil/ ONR] Presidential Young Investigator 1986
*[http://www.nsf.gov/index.jsp NSF] Presidential Young Investigator 1986

===Prize papers===
*[http://www.ieee.org/web/publications/journmag/index.html IEEE Transactions] [http://www.ieeecss.org/main.php?levelsecid=171&secid=171&expandsecid=24 George S. Axelby Outstanding Paper Awards] 1990 (two papers)
*[http://www.ieee.org/portal/pages/about/awards/pr/bakepr.html IEEE Baker prize] paper, 1991 
was also ranked in the top 10 ``most important'' papers world-wide in pure and applied mathematics from 1981-1993 in a bibliometric analysis and survey conducted by CTWS-Leiden. It was the most recently published paper to be so ranked.
This prize is awarded once each year to the outstanding paper reporting new research results among all of the IEEE's over 50 technical journals,
*[http://www.a2c2.org/awards/schuck/index.php AACC Hugo Schuck Award], 1994

===Patents===
*[http://www.patentstorm.us/patents/6414827.html US Patent 6414827 - Closed-loop scaling for discrete-time servo controller in a disc drive] Issued July 2, 2002

*[http://www.patentstorm.us/patents/5978752/claims.html US Patent 5978752 - Model validation algorithm for characterizing parameters and uncertainty in a disc drive] Issued Nov 2, 1999

===Academic Bio 1990's===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]

==Industry summary==
*Served as a consultant to Honeywell Technology Center since 1976

==Research interests==
His research interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development.

Research applications interests are motivated by the interplay between control, dynamical systems, and design and analysis of large, complex systems.

==Athletics==
John Doyle is an athlete in his spare time.

===Some athletic achievements from 1990's:===
*World champion, [http://www.ihpva.org/ IHPVA] speed championships time trial.
*US Record, indoor rowing (former world record).
*2 Gold medals, [http://hosting2.sportingpulse.com/www.imga-masters.com/ World Masters Games].
*Member, Duathlon Team USA.
*Age group wins:
**Duathlon in Exile (world championship qualifier),
**Fall Showdown Duathlon,
**Big Bear Duathlon,
**Powerman Chicago Sprint,
**Steamboat Triathlon,
**USCF District 6 cycling time trial...

*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]
*See [[J. Doyle's Bio Athletics]] for details and photos!

==Portraits==
{| class="wikitable"
|-
|[[Image:John-and-marie.jpg]] ||[[Image:bike2.jpg]]||http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet/doyle2.jpg
|-
|John and Marie||Cycling||From " This Man Wants To Control the Internet 
This man wants to control the Internet. And you should let him. 
by Carl Zimmer, Photographs by Trujillo/Paumier 
published online October 25, 2007
|}

==See also==
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html 2004 IEEE bio and photo of J Doyle]
*[http://www.cds.caltech.edu/people/ J Doyle's bio at CDS, Caltech]
===older webpages===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]
*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]

Research

2008-09-06T21:15:34Z

Hana: /* Grants for Projects */

Quotes:

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics". [http://www.cds.caltech.edu/people/]

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology" [http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html]

==Current Projects==
*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology]
*[[Systems Verification]]

===Grants for Projects===
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:

**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==References==
1. <http://www.cds.caltech.edu/people/> Aug 17, 2008

2. <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 17, 2008
==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Research

2008-09-06T21:14:34Z

Hana: /* Grants for Projects */

Quotes:

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics". [http://www.cds.caltech.edu/people/]

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology" [http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html]

==Current Projects==
*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology]
*[[Systems Verification]]

===Grants for Projects===
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with Prof. Steven Low:

**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==References==
1. <http://www.cds.caltech.edu/people/> Aug 17, 2008

2. <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 17, 2008
==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Research

2008-09-06T21:11:26Z

Hana: /* Current Projects */

Quotes:

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics". [http://www.cds.caltech.edu/people/]

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology" [http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html]

==Current Projects==
*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology]
*[[Systems Verification]]

===Grants for Projects===
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with Prof. Steven Low:

**NSF RI WAN in Lab Doyle, Newman, Psaltis, Yip 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing Doyle 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering Bunn, Doyle, Newman 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control Doyle 2001-04
**ARO DURIP Hybrid WAN in Lab Doyle, Newman, Psaltis, Yip 2004-05
**ARO Network Research Analytical Theory of Protocols Doyle 2002-05
**ARO Network Science Networked control systems Doyle, Murray, Parrilo (MIT) 2005-2006

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==References==
1. <http://www.cds.caltech.edu/people/> Aug 17, 2008

2. <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 17, 2008
==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

User:Krister

2008-09-06T20:56:47Z

Hana:

also at Netlab and CDS.
asked to check content...Physiology control ...networking etc content

User:Hana

2008-09-06T19:44:09Z

Hana: /* 2008 */

==Hana's log hours==
===July -Dec 2007===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|7/8/07 Lun helped! ||2-6.30pm ||4.5||8/2/07||2.30-4.30||2.0||9/5/07 ||4.30-5 ||0.5 ||11/02/07||6.30-7.30||1
|-
|7/9/07 ||10am-1pm ||3||8/4/07||4.30-5||0.5||9/8/07 ||7.30-8 ||0.5
||11/30/07||5-7, 11-12||3
|-
|7/15/07 Lun helped||12-3.30pm||3.5||8/10/07||4-6.30||2.5||9/14/07||7.45-8.15||0.5
||12/1/07||3.30-7||4.5
|-
|7/16/07||12-12.30am||0.5||8/14/07 ||9.30-11.30||2||9/17/07||11.30-12.30||1
||12/3/07||9-10.30||1.5
|-
|7/18/07||4-4.30pm, 6-7pm||1.5||8/17/07||6.30-7.30||1||9/19/07||11.30-12.30||1
|-
|7/27/07||10-10.30||0.5
|-
|7/31/07||12-12.30||0.5
|}
===Jan-Aug 2008===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs

|-
|01/25/08||2-2.30||0.5||7/16/08||10-12.30, 2-6||6.5
|-
|01/28/08||6.30-7.30||0.5||7/17/08||8-8.5pm||0.5
|-
|2/22/08||6.30-7.30||1.0||7/21/08 ||8-8.5pm||0.5
|}

{| border="1"
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|8/15/08||12.30-1||0.5
|-
|8/1/08||10-10.5||0.5
|-
|8/7/08||8-8.5pm ||0.5
|-
|8/16/08||2.30-4.30pm, 6.30-7.30pm ||3
|-
| || ||
|-
|8/17/08|| ||1||8/18/08|| ||1.5
|-
|8/22/08 || ||1||8/23/08|| || 2.5
|-
|8/26/08|| ||1 ||8/27/08|| ||0.5
|-
|8/28/08|| ||2||8/29/08|| ||2
|}
Based on [[Special:contributions/Hana]]

==Items completed==
===2007===
Betta has arranged Purchasing Order for Hana's Netlab website consulting. Betta is giving Gloria & research group copy of Netlab Purchasing Order. Prof. Doyle's group to arrange separate Purchasing order for Hana's website consulting. Hana waiting on Prof. Doyle's group to approve set up of wiki & to pass on website maintainance to the group.

*Copied links to papers from Netlab pages & Lun's page, Systems-Biol page, J DOyle's old page onto wiki,
*set up to do list / main page/stucture/help page/sidebar/research/papers pages & bio copied.
*Added IEEE explore publications to pages.
*changed monoskins to remove edit tabs, for viewers/users not logged in.
*created accounts for GB, LL, MF, LC, HK, to stop using Doyle's account in Sept 2007. Used Special pages:Login, User list, User rights management
*Added links to Discover magazine and uploaded photo, added link to Prof Murray's Panama updates.
*Copied and uploaded over papers, filed by topic and by year, as per Prof's instructions.
*Given Gloria Netlab Purchase order and Wiki log hours.
*Copied over Panama adventures by Prof to Wiki. To get Prof Murray's version.
*Uploaded article from Discover magazine on John Doyle. Uploaded other images for wiki.

===2008===
*Cited 80-90 papers and uploaded pdf versions to wiki. Copied athetics page. Topics and some papers from Prof Doyle copied over. More old website pages copied over.
* Added awards and patents 2000-2008.
*Edited [[Help:Contents]] for future Doyle users.
*Copied over joint projects and links to Prof Murray's wiki.
*Sent Invoice 3 to Gloria Bain. Updated [[Group]] with Lijun.
*Showed wiki and passed on URL to visitor
*Pages had text copied from Doyle's old website then reformatted and citations/links added [[Complex networks]] and [[Complexity and robustness]].
*Tidied added keywords and copied papers to relvant pages under [[ Category: Papers by topic ]]
*Tidied added suggestions/links to [[To Do Q]] and [[Tips: Research papers, Publishing and Other Trivia]], hopefully to
improve wiki, add features ... and help students with quick links...
*Added another 3-5 papers from various URL's.
*Added suggestions to [[To Do Q]] for others to improve wiki.
*Added links to websites, portals, events, Caltech calendar!
*Full list of items done on wiki at [[Special:Contributions/Hana]]
*Re-submitted updated invoice to new Admin - Charis Brown on Sept 6

==To Do==
Pass on wiki stuff to Doyle's [[Group]] to continue updates.

User:Hana

2008-09-06T19:43:59Z

Hana: /* 2008 */

==Hana's log hours==
===July -Dec 2007===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|7/8/07 Lun helped! ||2-6.30pm ||4.5||8/2/07||2.30-4.30||2.0||9/5/07 ||4.30-5 ||0.5 ||11/02/07||6.30-7.30||1
|-
|7/9/07 ||10am-1pm ||3||8/4/07||4.30-5||0.5||9/8/07 ||7.30-8 ||0.5
||11/30/07||5-7, 11-12||3
|-
|7/15/07 Lun helped||12-3.30pm||3.5||8/10/07||4-6.30||2.5||9/14/07||7.45-8.15||0.5
||12/1/07||3.30-7||4.5
|-
|7/16/07||12-12.30am||0.5||8/14/07 ||9.30-11.30||2||9/17/07||11.30-12.30||1
||12/3/07||9-10.30||1.5
|-
|7/18/07||4-4.30pm, 6-7pm||1.5||8/17/07||6.30-7.30||1||9/19/07||11.30-12.30||1
|-
|7/27/07||10-10.30||0.5
|-
|7/31/07||12-12.30||0.5
|}
===Jan-Aug 2008===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs

|-
|01/25/08||2-2.30||0.5||7/16/08||10-12.30, 2-6||6.5
|-
|01/28/08||6.30-7.30||0.5||7/17/08||8-8.5pm||0.5
|-
|2/22/08||6.30-7.30||1.0||7/21/08 ||8-8.5pm||0.5
|}

{| border="1"
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|8/15/08||12.30-1||0.5
|-
|8/1/08||10-10.5||0.5
|-
|8/7/08||8-8.5pm ||0.5
|-
|8/16/08||2.30-4.30pm, 6.30-7.30pm ||3
|-
| || ||
|-
|8/17/08|| ||1||8/18/08|| ||1.5
|-
|8/22/08 || ||1||8/23/08|| || 2.5
|-
|8/26/08|| ||1 ||8/27/08|| ||0.5
|-
|8/28/08|| ||2||8/29/08|| ||2
|}
Based on [[Special:contributions/Hana]]

==Items completed==
===2007===
Betta has arranged Purchasing Order for Hana's Netlab website consulting. Betta is giving Gloria & research group copy of Netlab Purchasing Order. Prof. Doyle's group to arrange separate Purchasing order for Hana's website consulting. Hana waiting on Prof. Doyle's group to approve set up of wiki & to pass on website maintainance to the group.

*Copied links to papers from Netlab pages & Lun's page, Systems-Biol page, J DOyle's old page onto wiki,
*set up to do list / main page/stucture/help page/sidebar/research/papers pages & bio copied.
*Added IEEE explore publications to pages.
*changed monoskins to remove edit tabs, for viewers/users not logged in.
*created accounts for GB, LL, MF, LC, HK, to stop using Doyle's account in Sept 2007. Used Special pages:Login, User list, User rights management
*Added links to Discover magazine and uploaded photo, added link to Prof Murray's Panama updates.
*Copied and uploaded over papers, filed by topic and by year, as per Prof's instructions.
*Given Gloria Netlab Purchase order and Wiki log hours.
*Copied over Panama adventures by Prof to Wiki. To get Prof Murray's version.
*Uploaded article from Discover magazine on John Doyle. Uploaded other images for wiki.

===2008===
*Cited 80-90 papers and uploaded pdf versions to wiki. Copied athetics page. Topics and some papers from Prof Doyle copied over. More old website pages copied over.
* Added awards and patents 2000-2008.
*Edited [[Help:Contents]] for future Doyle users.
*Copied over joint projects and links to Prof Murray's wiki.
*Sent Invoice 3 to Gloria Bain. Updated [[Group]] with Lijun.
*Showed wiki and passed on URL to visitor
*Pages had text copied from Doyle's old website then reformatted and citations/links added [[Complex networks]] and [[Complexity and robustness]].
*Tidied added keywords and copied papers to relvant pages under [[ Category: Papers by topic ]]
*Tidied added suggestions/links to [[To Do Q]] and [[Tips: Research papers, Publishing and Other Trivia]], hopefully to
improve wiki, add features ... and help students with quick links...
*Added another 3-5 papers from various URL's.
*Added suggestions to [[To Do Q]] for others to improve wiki.
*Added links to websites, portals, events, Caltech calendar!
*Full list of items done on wiki at [[Special:Contributions/Hana]]
*Re-submitted updated invoice to new Admin - Charis Brown

==To Do==
Pass on wiki stuff to Doyle's [[Group]] to continue updates.

User:Hana

2008-09-06T19:43:31Z

Hana: /* Jan-Aug 2008 */

==Hana's log hours==
===July -Dec 2007===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|7/8/07 Lun helped! ||2-6.30pm ||4.5||8/2/07||2.30-4.30||2.0||9/5/07 ||4.30-5 ||0.5 ||11/02/07||6.30-7.30||1
|-
|7/9/07 ||10am-1pm ||3||8/4/07||4.30-5||0.5||9/8/07 ||7.30-8 ||0.5
||11/30/07||5-7, 11-12||3
|-
|7/15/07 Lun helped||12-3.30pm||3.5||8/10/07||4-6.30||2.5||9/14/07||7.45-8.15||0.5
||12/1/07||3.30-7||4.5
|-
|7/16/07||12-12.30am||0.5||8/14/07 ||9.30-11.30||2||9/17/07||11.30-12.30||1
||12/3/07||9-10.30||1.5
|-
|7/18/07||4-4.30pm, 6-7pm||1.5||8/17/07||6.30-7.30||1||9/19/07||11.30-12.30||1
|-
|7/27/07||10-10.30||0.5
|-
|7/31/07||12-12.30||0.5
|}
===Jan-Aug 2008===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs

|-
|01/25/08||2-2.30||0.5||7/16/08||10-12.30, 2-6||6.5
|-
|01/28/08||6.30-7.30||0.5||7/17/08||8-8.5pm||0.5
|-
|2/22/08||6.30-7.30||1.0||7/21/08 ||8-8.5pm||0.5
|}

{| border="1"
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|8/15/08||12.30-1||0.5
|-
|8/1/08||10-10.5||0.5
|-
|8/7/08||8-8.5pm ||0.5
|-
|8/16/08||2.30-4.30pm, 6.30-7.30pm ||3
|-
| || ||
|-
|8/17/08|| ||1||8/18/08|| ||1.5
|-
|8/22/08 || ||1||8/23/08|| || 2.5
|-
|8/26/08|| ||1 ||8/27/08|| ||0.5
|-
|8/28/08|| ||2||8/29/08|| ||2
|}
Based on [[Special:contributions/Hana]]

==Items completed==
===2007===
Betta has arranged Purchasing Order for Hana's Netlab website consulting. Betta is giving Gloria & research group copy of Netlab Purchasing Order. Prof. Doyle's group to arrange separate Purchasing order for Hana's website consulting. Hana waiting on Prof. Doyle's group to approve set up of wiki & to pass on website maintainance to the group.

*Copied links to papers from Netlab pages & Lun's page, Systems-Biol page, J DOyle's old page onto wiki,
*set up to do list / main page/stucture/help page/sidebar/research/papers pages & bio copied.
*Added IEEE explore publications to pages.
*changed monoskins to remove edit tabs, for viewers/users not logged in.
*created accounts for GB, LL, MF, LC, HK, to stop using Doyle's account in Sept 2007. Used Special pages:Login, User list, User rights management
*Added links to Discover magazine and uploaded photo, added link to Prof Murray's Panama updates.
*Copied and uploaded over papers, filed by topic and by year, as per Prof's instructions.
*Given Gloria Netlab Purchase order and Wiki log hours.
*Copied over Panama adventures by Prof to Wiki. To get Prof Murray's version.
*Uploaded article from Discover magazine on John Doyle. Uploaded other images for wiki.

===2008===
*Cited 80-90 papers and uploaded pdf versions to wiki. Copied athetics page. Topics and some papers from Prof Doyle copied over. More old website pages copied over.
* Added awards and patents 2000-2008.
*Edited [[Help:Contents]] for future Doyle users.
*Copied over joint projects and links to Prof Murray's wiki.
*Sent Invoice 3 to Gloria Bain. Updated [[Group]] with Lijun.
*Showed wiki and passed on URL to visitor
*Pages had text copied from Doyle's old website then reformatted and citations/links added [[Complex networks]] and [[Complexity and robustness]].
*Tidied added keywords and copied papers to relvant pages under [[ Category: Papers by topic ]]
*Tidied added suggestions/links to [[To Do Q]] and [[Tips: Research papers, Publishing and Other Trivia]], hopefully to
improve wiki, add features ... and help students with quick links...
*Added another 3-5 papers from various URL's.
*Added suggestions to [[To Do Q]] for others to improve wiki.
*Added links to websites, portals, events, Caltech calendar!
*Full list of items done on wiki at [[Special:Contributions/Hana]]

==To Do==
Pass on wiki stuff to Doyle's [[Group]] to continue updates.

User:Hana

2008-09-06T19:43:10Z

Hana: /* Jan-Aug 2008 */ added hours only for Aug

==Hana's log hours==
===July -Dec 2007===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|7/8/07 Lun helped! ||2-6.30pm ||4.5||8/2/07||2.30-4.30||2.0||9/5/07 ||4.30-5 ||0.5 ||11/02/07||6.30-7.30||1
|-
|7/9/07 ||10am-1pm ||3||8/4/07||4.30-5||0.5||9/8/07 ||7.30-8 ||0.5
||11/30/07||5-7, 11-12||3
|-
|7/15/07 Lun helped||12-3.30pm||3.5||8/10/07||4-6.30||2.5||9/14/07||7.45-8.15||0.5
||12/1/07||3.30-7||4.5
|-
|7/16/07||12-12.30am||0.5||8/14/07 ||9.30-11.30||2||9/17/07||11.30-12.30||1
||12/3/07||9-10.30||1.5
|-
|7/18/07||4-4.30pm, 6-7pm||1.5||8/17/07||6.30-7.30||1||9/19/07||11.30-12.30||1
|-
|7/27/07||10-10.30||0.5
|-
|7/31/07||12-12.30||0.5
|}
===Jan-Aug 2008===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs

|-
|01/25/08||2-2.30||0.5||7/16/08||10-12.30, 2-6||6.5
|-
|01/28/08||6.30-7.30||0.5||7/17/08||8-8.5pm||0.5
|-
|2/22/08||6.30-7.30||1.0||7/21/08 ||8-8.5pm||0.5
|}

{| border="1"
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|8/15/08||12.30-1||0.5
|-
|8/1/08||10-10.5||0.5
|-
|8/7/08||8-8.5pm ||0.5
|-
|8/16/08||2.30-4.30pm, 6.30-7.30pm ||3
|-
| || ||
|-
|8/17/08|| ||1||8/18/08|| ||1.5
|-
|8/22/08 || ||1||8/23/08|| || 2.5
|-
|8/26/08|| ||1 ||8/27/08|| ||0.5
|-
|8/28/08|| ||2||8/29/08|| ||2
|}
Based on Special:contributions/Hana

==Items completed==
===2007===
Betta has arranged Purchasing Order for Hana's Netlab website consulting. Betta is giving Gloria & research group copy of Netlab Purchasing Order. Prof. Doyle's group to arrange separate Purchasing order for Hana's website consulting. Hana waiting on Prof. Doyle's group to approve set up of wiki & to pass on website maintainance to the group.

*Copied links to papers from Netlab pages & Lun's page, Systems-Biol page, J DOyle's old page onto wiki,
*set up to do list / main page/stucture/help page/sidebar/research/papers pages & bio copied.
*Added IEEE explore publications to pages.
*changed monoskins to remove edit tabs, for viewers/users not logged in.
*created accounts for GB, LL, MF, LC, HK, to stop using Doyle's account in Sept 2007. Used Special pages:Login, User list, User rights management
*Added links to Discover magazine and uploaded photo, added link to Prof Murray's Panama updates.
*Copied and uploaded over papers, filed by topic and by year, as per Prof's instructions.
*Given Gloria Netlab Purchase order and Wiki log hours.
*Copied over Panama adventures by Prof to Wiki. To get Prof Murray's version.
*Uploaded article from Discover magazine on John Doyle. Uploaded other images for wiki.

===2008===
*Cited 80-90 papers and uploaded pdf versions to wiki. Copied athetics page. Topics and some papers from Prof Doyle copied over. More old website pages copied over.
* Added awards and patents 2000-2008.
*Edited [[Help:Contents]] for future Doyle users.
*Copied over joint projects and links to Prof Murray's wiki.
*Sent Invoice 3 to Gloria Bain. Updated [[Group]] with Lijun.
*Showed wiki and passed on URL to visitor
*Pages had text copied from Doyle's old website then reformatted and citations/links added [[Complex networks]] and [[Complexity and robustness]].
*Tidied added keywords and copied papers to relvant pages under [[ Category: Papers by topic ]]
*Tidied added suggestions/links to [[To Do Q]] and [[Tips: Research papers, Publishing and Other Trivia]], hopefully to
improve wiki, add features ... and help students with quick links...
*Added another 3-5 papers from various URL's.
*Added suggestions to [[To Do Q]] for others to improve wiki.
*Added links to websites, portals, events, Caltech calendar!
*Full list of items done on wiki at [[Special:Contributions/Hana]]

==To Do==
Pass on wiki stuff to Doyle's [[Group]] to continue updates.

User:Hana

2008-09-06T19:33:02Z

Hana: /* Jan-Aug 2008 */

==Hana's log hours==
===July -Dec 2007===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
!Date
!Time
!Hrs
|-
|7/8/07 Lun helped! ||2-6.30pm ||4.5||8/2/07||2.30-4.30||2.0||9/5/07 ||4.30-5 ||0.5 ||11/02/07||6.30-7.30||1
|-
|7/9/07 ||10am-1pm ||3||8/4/07||4.30-5||0.5||9/8/07 ||7.30-8 ||0.5
||11/30/07||5-7, 11-12||3
|-
|7/15/07 Lun helped||12-3.30pm||3.5||8/10/07||4-6.30||2.5||9/14/07||7.45-8.15||0.5
||12/1/07||3.30-7||4.5
|-
|7/16/07||12-12.30am||0.5||8/14/07 ||9.30-11.30||2||9/17/07||11.30-12.30||1
||12/3/07||9-10.30||1.5
|-
|7/18/07||4-4.30pm, 6-7pm||1.5||8/17/07||6.30-7.30||1||9/19/07||11.30-12.30||1
|-
|7/27/07||10-10.30||0.5
|-
|7/31/07||12-12.30||0.5
|}
===Jan-Aug 2008===
{| border=1
!Date
!Time
!Hrs
!Date
!Time
!Hrs

|-
|01/25/08||2-2.30||0.5||7/16/08||10-12.30, 2-6||6.5
|-
|01/28/08||6.30-7.30||0.5||7/17/08||8-8.5pm||0.5
|-
|2/22/08||6.30-7.30||1.0||7/21/08 ||8-8.5pm||0.5
|}

{| border="1"
!Date
!Time
!Hrs
|-
|8/15/08||12.30-1||0.5||8/18/08|| ||
|-
|8/1/08||10-10.5||0.5||8/22/08 || ||1
|-
|8/7/08||8-8.5pm ||0.5||8/23/08|| || 2.5
|-
|8/16/08||2.30-4.30pm, 6.30-7.30pm ||3||8/26/08|| ||1
|-
| || || ||8/27/08|| ||0.5
|-
| || || ||8/28/08|| ||2
|-
| || || ||8/29/08|| ||2
|}

==Items completed==
===2007===
Betta has arranged Purchasing Order for Hana's Netlab website consulting. Betta is giving Gloria & research group copy of Netlab Purchasing Order. Prof. Doyle's group to arrange separate Purchasing order for Hana's website consulting. Hana waiting on Prof. Doyle's group to approve set up of wiki & to pass on website maintainance to the group.

*Copied links to papers from Netlab pages & Lun's page, Systems-Biol page, J DOyle's old page onto wiki,
*set up to do list / main page/stucture/help page/sidebar/research/papers pages & bio copied.
*Added IEEE explore publications to pages.
*changed monoskins to remove edit tabs, for viewers/users not logged in.
*created accounts for GB, LL, MF, LC, HK, to stop using Doyle's account in Sept 2007. Used Special pages:Login, User list, User rights management
*Added links to Discover magazine and uploaded photo, added link to Prof Murray's Panama updates.
*Copied and uploaded over papers, filed by topic and by year, as per Prof's instructions.
*Given Gloria Netlab Purchase order and Wiki log hours.
*Copied over Panama adventures by Prof to Wiki. To get Prof Murray's version.
*Uploaded article from Discover magazine on John Doyle. Uploaded other images for wiki.

===2008===
*Cited 80-90 papers and uploaded pdf versions to wiki. Copied athetics page. Topics and some papers from Prof Doyle copied over. More old website pages copied over.
* Added awards and patents 2000-2008.
*Edited [[Help:Contents]] for future Doyle users.
*Copied over joint projects and links to Prof Murray's wiki.
*Sent Invoice 3 to Gloria Bain. Updated [[Group]] with Lijun.
*Showed wiki and passed on URL to visitor
*Pages had text copied from Doyle's old website then reformatted and citations/links added [[Complex networks]] and [[Complexity and robustness]].
*Tidied added keywords and copied papers to relvant pages under [[ Category: Papers by topic ]]
*Tidied added suggestions/links to [[To Do Q]] and [[Tips: Research papers, Publishing and Other Trivia]], hopefully to
improve wiki, add features ... and help students with quick links...
*Added another 3-5 papers from various URL's.
*Added suggestions to [[To Do Q]] for others to improve wiki.
*Added links to websites, portals, events, Caltech calendar!
*Full list of items done on wiki at [[Special:Contributions/Hana]]

==To Do==
Pass on wiki stuff to Doyle's [[Group]] to continue updates.

Calendar

2008-09-06T02:13:40Z

Hana: /* Workshops */

== Group Meetings ==
* See '''[[Group Meetings]]'''
* More Meetings for Doyle's Research groups are listed at:
**[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
**[http://openwetware.org/wiki/Doyle Physiology]
**[[Systems Verification]]

==Workshops==
* [http://www.ipam.ucla.edu/programs/mra2008/ ''Internet Multi-Resolution Analysis: Foundations, Applications and Practice Activities''] activities hosted at ''[http://www.ipam.ucla.edu/ IPAM UCLA]'', September 8 - December 12, 2008. 
J Doyle is an invited speaker and also on the organizing committee.
[https://www.ipam.ucla.edu/elements/choose.aspx?pc=mratut Applications] closing soon.

*[http://www.systems-biology.org/006/ Systems biology workshops] [http://www.systems-biology.org/006/010.html 2008]

==CDS Courses==
[http://www.cds.caltech.edu/academics/courses/ CDS courses]

==CDS calendar==
*[http://www.cds.caltech.edu/ CDS Events & Related Events]
*[http://www.cds.caltech.edu/research/seminars/ CDS seminars]
*[http://www.cds.caltech.edu/research/conferences/ CDS Conferences]
*[http://www.cds.caltech.edu/research/related/ CDS related events]
*[http://www.cds.caltech.edu/academics/courses/ Course schedules]
* [http://www.cds.caltech.edu/~murray/wiki/CDS_SURF Prof. Murray's list of available "CDS SURF"] topics.
SURF = Summer undergraduate research fellowship at Caltech.
===CDS mailing lists===
*[http://www.cds.caltech.edu/news/mailinglists/ CDS Mailing lists]

==Caltech calendar==
*[http://today.caltech.edu/calendar/index?type=terms Academic events]
*[http://today.caltech.edu/calendar/ All calendar events]
===Seminars===
*[http://www.cimms.caltech.edu/ CIMMS] (Center for integrative multi-scale modeling and simulation) [http://www.cimms.caltech.edu/seminars/seminar_scripts/index.cgi seminars] and [http://www.cimms.caltech.edu/workshops.html workshops]
*IST (Information Science Technology) [http://today.caltech.edu/eas/listing.adp?template=ist-all&sponsor_id=325&sponsor_id=328&sponsor_id=1201&sponsor_id=764&sponsor_id=1001&sponsor_id=1181&sponsor_id=362&sponsor_id=401&sponsor_id=340&sponsor_id=330&sponsor_id=501&sponsor_id=143&sponsor_id=109&sponsor_id=1081&sponsor_id=1423&sponsor_id=1543&sponsor_id=1623&range=this_month seminars]
* SISL (Social Information Science Lab) [http://www.sisl.caltech.edu/calendar/index.html seminars]
*Netlab [http://netlab.caltech.edu/seminars.php seminars]

==More conferences==
*[http://www.ieee.org/portal/site IEEE portal] : [http://www.ieeecss.org/main.php?secid=23&expandsecid=23 IEEE CSS conferences including CDC] (CSS = Control Systems society), [http://control.disp.uniroma2.it/CDC08/ CDC 2008], [http://people.bu.edu/johnb/ChinaCDC.html CDC 2009], [http://www.comsoc.org/confs/infocom/index.html Infocom]
*[http://portal.acm.org/dl.cfm ACM portal]:[http://www.sigmetrics.org/ Sigmetrics]
*[http://www.a2c2.org/ American Automatic Control Council (AACC)]: [http://www.a2c2.org/conferences/acc2008/ 2008]
*[http://www.princeton.edu/cav2008/ Computer Aided Verification CAV 2008]
*[http://sbml.org/Events SBML forum meetings and calender]

==Past events==

===Past workshops===
*[http://www.cds.caltech.edu/~murray/wiki/Connections_II R Murray's Connections II Workshop 2006]
*[http://www.cds.caltech.edu/research/conferences/index.php?year=2005 Connections II Workshop 2005]
*[http://www.cds.caltech.edu/doyle-fest/ J Doyle's Birthday, Connections Workshop, 2004]

*[http://www.cds.caltech.edu/~prajna/biowkshop/ Bio Workshop: The Challenge of Complexity]

*Materials from March 2003 Workshop at UCSB on Robustness Analysis Tools
with Applications to the Biological and Physical Sciences

===Past group meetings===
[[Group Meetings]] 2008

===Past courses===
A few of Prof Doyle's past CDS courses.

{| class ="wikitable"
|-
| CDS 212 ||Introduction to Modern Control|| Fall 2006
|-
| CDS 213 || Robust control ||Winter 2008
|-
| CDS 270-2 || Advanced Topics in Systems and Control: Formal Methods for Networked Embedded Systems || Spring 2007
|}

*Lijun Chen's [https://www.cds.caltech.edu/help/cms.php?op=wiki&wiki_op=view&id=187 CDS270]: Optimization, Game and Layering in Communication Networks, Fall 2006, Caltech.

*[http://www.cds.caltech.edu/~doyle/shortcourse.htm Systems Biology Shortcourse Schedule, May 21-24, 2004 Caltech]

==See also==
[[To Do]]

[[Tips: Research papers, Publishing and Other Trivia ]]

Complex networks

2008-09-06T02:13:00Z

Hana: /* Note */

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 [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

===Slides from old talks on Complexity and Robustness===
*CDC plenary slides [http://www.cds.caltech.edu/~doyle/CmplxNets/CDC_plenary.ppt (ppt)]

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

*Allerton plenary [http://www.cds.caltech.edu/~doyle/CmplxNets/allerton.ppt (ppt)]

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

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

===Papers 2000-2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''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)

[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] 
Lun Li, David Alderson, W. Willinger and John C. Doyle 
in Proceedings of ACM SIGCOMM, Portland, OR, Aug 2004 (1.5MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/c/c5/PRLPLR2000.pdf ''Power Laws, Highly Optimized Tolerance and Generalized Source Coding''], 
J. Doyle and J.M. Carlson, 
Phys. Rev. Let., 84(24):5656-5659, 2000.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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==
*[[Network architecture and protocols]]
*[[General complexity]]
*[[Complexity and robustness]]
*[[Research|HOT]]

==Related reading==
===PhD theses===
*''Robust Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence'', 
PhD thesis at Caltech by Kumar Bobba, 2004 [http://www.cds.caltech.edu/~doyle/CmplxNets/Bobba.pdf (pdf)]

*''Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization'', 
PhD Thesis CDS, Caltech by Pablo Parrilo, 2000 [http://www.cds.caltech.edu/~pablo/thesis.ps.gz (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]

===Books===
[http://www.cds.caltech.edu/~doyle/SFI_robustness/books.htm 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'' , 
[http://www.control.utoronto.ca/people/profs/francis/dft.pdf (free version in pdf 1.2MB)] 
[http://www.cds.caltech.edu/~macmardg/cds110b/dft.html (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:
[http://portalparts.acm.org/580000/574259/cover/1078912.gif ACM portal, Prentice Hall Professional Technical Reference, USA 1991 (ISBN:0023300116)]

===Other books===
[http://www.springer.com/math/book/978-0-387-98945-7 ''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===
*[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]'' 
by Phillip F. Schewe and Ben Stein 
in American Institute of Physics (AIP) Physics News Update 
Number 474 (Story #1), March 10, 2000

[http://www.nature.com/nature/journal/v405/n6785/full/405412b0.html ''Applied mathematics: The power of design''] 
Mark Newman 
Nature 405, 6785, pp 412-413 (25 May 2000)

[http://www.pnas.org/cgi/content/full/97/10/5031 ''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. [http://unisci.com/stories/20001/0314004.htm]


==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]]

Help:Contents

2008-09-06T02:08:47Z

Hana:

This page is designed as '''help''' for Prof. Doyle's group to manage, use and edit this wiki.

==About Wiki==
<big>'''[[Special:version|MediaWiki]] has been successfully installed.'''</big>

[http://www.mediawiki.org/wiki/MediaWiki About media Wiki]

In July 2007, this wiki was initially installed by Lun Li.

The wiki pages were initally set up by Prof J Doyle, Lun Li, Lijun Chen, Hana and Lachlan Andrew, with assistance from CDS

This wiki is to document Prof. J. C. Doyle & his groups's research activities.

2007-2008 Wiki admin:
*Hana and Lachlan Andrew from [http://netlab.caltech.edu/people.php Netlab],
*[http://www.cds.caltech.edu/~lun/ Lun Li] and Lijun Chen from [[Group|CDS]] and [http://netlab.caltech.edu/ Netlab], at [http://www.caltech.edu Caltech]
*Prof Doyle

==Using Wiki==
<big>'''MediaWiki has been successfully installed.'''</big>

*Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
* [http://www.mediawiki.org/wiki/Help:Contents MediaWiki Help list]
* The menus on the left are controlled by [[Mediawiki:Sidebar]]

==Editing Wiki==
* Editing this wiki has been restricted to those logged in with an existing [http://www.mediawiki.org/wiki/Help:Navigation#User_links "User account"], where the [http://www.mediawiki.org/wiki/Help:Navigation#Page_Tabs "edit tabs"] at the top of the page should appear after log-in.
** You can edit a page or section on a page by clicking on "edit" tabs.
**After typing your updates to the editing box on any page, use the "show preview" button to preview your editing/links!
*Useful URL's for wiki markup/editing tips:
**<http://www.mediawiki.org/wiki/>:
**<http://meta.wikimedia.org/wiki/>
**[http://www.mediawiki.org/wiki/Help MediaWiki Help list]
**[http://www.mediawiki.org/wiki/Help:Editing_pages Editing pages MediaWiki Help Editing pages]

==Wiki support==
*[[Main Page#Contact|Contact]] webmasters: Prof. John Doyle, [[Group|CDS group]], [http://www.cds.caltech.edu/contact/ Sysadmin at CDS]

or [http://netlab.caltech.edu/contact.php Hana & Lachlan at Netlab, CS]

or [http://www.cds.caltech.edu/contact/ contact CDS]

==Sysops topics==
*The source files for this wiki folder name: '''___''' are mounted onto '''file server:___''' and edited/hosted via '''web server:___''' at CDS, Caltech.
* This wiki URL is <http://www.cds.caltech.edu/~doyle2/wiki/>
* The common CSS definitions can be edited at MediaWiki:Common.css
* [[To Do]] page lists tasks and suggestions for maintaining and updating the wiki.
* Sidebar can be edited at [[MediaWiki:Sidebar]]. For instructions, see <http://www.mediawiki.org/wiki/Manual:Navigation_bar>.
* To change an Infobox template, create a page in the '''Template:''' namespace.
*Paste contents from small page onto a larger page by typing <nowiki> {{:small page name}} </nowiki> onto larger page
*Starting a new page labelled <nowiki>[[Private: ___]]</nowiki> denotes private page requiring restricted password
*More useful links for Sysops topics already listed in sections above.

===Linux commands===
*To view instructions on changing file permissions on Unix, type '''man chmod''' on the Linux command line. Then admin can choose which files are w= writable, R=readable etc by admin or group. If in doubt ask Lun or CDS sysadmin!
*ssh to website, then type in '''cd ..''' enter then '''ln -s hanas_site/filename.php''' creates symbolic link to Hana's Netlab website stored at CS, Caltech.
*For linux users, a short summary of usage can be obtained by typing
<command> --help
into the linux command line.

===Special pages===
*[[Special:Specialpages]] lists links to pages important to managing this wiki, for example,
**[[Special:Userlogin|to log-in/create account]]
**[[Special:Version|to check information about this mediawiki/MySQL/PHP behind this website]]
**[[Special:Recentchanges|to view/control recent changes]]

===Error messages===
* 404 Not Found is an error message when non-existent URL is typed into the browser, ie webpage not found
* 403 Access forbidden, ie when user is not allowed access to some pages

===Create account / Restricting User Level===
Accounts for this wiki have been given mostly to [[Group|Prof. Doyle's group]] and some [http://netlab.caltech.edu/people.php Netlab members].

Editing has been limited to users logged in existing user account and user levels have been restricted in some accounts.

See also section above '''Linux commands''', on ''changing file permissions''!

[[Special:Specialpages]] has pages important to managing user accounts, for example
*[[Special:Userlogin|to log-in/create account]]
**On this wiki, login as a ''Sysops'' user => [[Special:Specialpages|''Special pages'']] => [[Special:Userlogin|"Login/Create Account"]] => ''Create Account'', fill in the fields.
*[[Special:Blockip|block user]]

Useful instructions from <http://meta.wikimedia.org/wiki/> and <http://www.mediawiki.org/wiki/>:
*[http://meta.wikimedia.org/wiki/MediaWiki_FAQ#User_administration Administering user rights]
*[http://www.mediawiki.org/wiki/Manual:FAQ#How_do_I_administrate.2Fmanage_user_rights.3F Managing/administering/restricting user rights]
*[http://www.mediawiki.org/wiki/Manual:FAQ#How_do_I_reset_a_password.3F Reset password]
*[http://www.mediawiki.org/wiki/Manual:FAQ#How_do_I_remove_the_article.2Fedit_etc_tabs_for_users_who_are_not_logged_in.3F Removing tabs to users not logged in]

==Upload file==
===Upload limit===
*[http://www.mediawiki.org/wiki/Manual:Configuring_file_uploads#Set_maximum_size_for_file_uploads Know Media Wiki upload limit 2MB]

===More upload tips===
*Upload file onto this wiki by click on "Upload file" option in Toolbox on the [[MediaWiki:Sidebar]]
* Once the file has been uploaded, remember to acknowledge the '''source''' or '''bibliography''' details on the upload page, and ensure it does not violate copyright and related issues!
*pdf, ppt, jpg are formats can now be uploaded to this wiki, after implementing relevant code in LocalSettings.php

==Images==
===Thumbnails===
To install software to create thumbnails on this mwiki,

* follow instructions on [http://meta.wikimedia.org/wiki/MediaWiki_FAQ#How_do_I_install_Imagemagick_for_Thumbnails_on_Windows_-_MAR_2006_.3F MediaWiki:Help for creating thumbnails]
* edit code in file below, as instructed
...\mwiki\localsettings.php
* ensure the ImageMagick version that you choose to download is compatible with [[Special:Version|this wiki version]] listed above
* create folder "ImageMagick" on CDS server IP: ??? C:\program files
* onto this ImageMagick folder, download [http://www.imagemagick.org/download/www/binary-releases.html ImageMagick]

===Add Images===
...\mwiki\localsettings.php
was edited to enable '''file uploading''' from the Toolbox on the Sidebar.
*Upload image as instructed in section '''more upload tips''' above.
* [http://www.mediawiki.org/wiki/Help:Images MediaWiki:Help Adding images]

===Find images in wiki===
To lists all the image files (jpg, pdf, etc) on this wiki, click on [[Special:Specialpages|Special pages]] on sidebar, then select [[Special:Allpages|All pages]], then on this page select '''image''' in the '''Namespace''' box (pull down menu), and lastly select '''Go'''.

==Navigation==
===Creating a redirect===
Re-directs are useful for searching for specific page by various keywords or other alternative names.

To create a redirect, you must start a new page with the name you want to direct from. Do this by typing the desired name into the search box, or straight into the URL (methods described on Help:Starting a new page)

For the text of the new page, enter the following:

#REDIRECT <nowiki>[[pagename]]</nowiki>

where pagename is the name of the page you want to redirect users to.


You can use the 'preview' button, to check that you have entered the correct page name (Generally you will be redirecting to an existing page name, so the link should be blue, not red)

* Redirect page to another page: On "Old wiki page" type in #REDIRECT <nowiki>[[New page link ]]</nowiki>

===Categories===
*<nowiki>[[Category:___]]</nowiki> files page under new or old category, very useful for grouping pages by category!
===Side bar===
[[Special:Categories]], [[Special:All articles]], '''Wiki help''' was added to side bar to list all pages by category and by article - quicker for user to find specific pages.

==Other features that could be added to wiki==
===Case Sensitivity===
To make page titles and usernames case-sensitive, added ''$wgCapitalLinks = false;'' to Local settings.php

===Social networking bookmarks===
http://www.mediawiki.org/wiki/Extension:ShareThis for downloads and adding social networking bookmarks like <http://digg.com/> and <http://www.reddit.com/>

==John Doyle's other homepages==
*<http://www.cds.caltech.edu/~doyle/>
*<http://www.cds.caltech.edu/~doyle/home.htm>

Group

2008-09-06T02:08:04Z

Hana: /* Admin */

John Doyle's research '''group''' is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.

==Current Group==

===Faculty===
John Doyle

===Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]
|[http://netlab.caltech.edu/people.php Krister Jacobbson]
|[http://www.ist.caltech.edu/~brecht/ Ben Recht]
|}
===Graduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos]
|[http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi]
|[http://www.cds.caltech.edu/people/portal/?id=758 Vanessa Carson]
|-
|[http://www.cds.caltech.edu/people/portal/?id=760 Fiona Chandra]
|[http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme]
|[http://www.cds.caltech.edu/~andyl/ Andrew Lamperski]
|-
|[http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]
|[http://www.cds.caltech.edu/people/portal/?id=753 Na Li]
|[http://www.cds.caltech.edu/people/portal/?id=522 Marcos Nahmad Bensusan]
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=797 Somayeh Sojoudi]
|Jerry Cruz||
|}
===Undergraduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=772 George Hines]||[http://www.cds.caltech.edu/people/portal/?id=803 Nicholas Fette]
|}
===Admin===


===Visitors===
[http://www.cds.caltech.edu/~lun/ Lun Li, also alumni]
====Students====
{| class="wikitable" border="1"
|-
|''SURF 2008''||''Other''
|-
|Jackson Wang Ji Young Lee||Paul Fang, student from Temple City High School
|}

==Past Group==
===Alumni===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''||'''2000-2006'''||'''1990-1999'''
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]

[http://www.cds.caltech.edu/~lun Lun Li]

[http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]

[http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]

[http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]
|
[http://faculty.nps.edu/dlalders/ David Alderson]

Nizar Batada

[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]

Irene Gregory

[http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]

[http://webfiles.uci.edu/yjing/www/ Yindi Jing]

Sven Khatri

[http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]

[http://www.mit.edu/~parrilo/ Pablo Parrilo]

[http://www.cds.caltech.edu/~prajna/ Stephen Prajna]

[http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]

[http://www.cds.caltech.edu/~jyu/ Jie Yu]

[http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]

|Carolyn Beck

Raff D'Andrea

Sonja Glavaski

Irene Gregory

Yun Huang

Michael Kantner

[http://www.ee.ucla.edu/~paganini/ Fernando Paganini]

[http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]

Stefano Soatto

Jorge Tierno
|}

===Past Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|'''2007-2008'''||'''2000-2006'''||'''1990-1999'''
|-
|
[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames]

[http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]

[http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]
|
Masahiro Yanagisawa

[http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]

[http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]
|
[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]

[http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]
|}
===Past Admin===

?-2008 Gloria Bain

===Past Visitors===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''
|'''2000-2006
|'''1990-1999'''
|-
|Panagiota Stratou
|?
|?
|}

==MURF and SURF Students==
{| class="wikitable" border="0" width="80%"
|'''2008'''||'''2007''' ||'''2000-2006'''
|-
|Jackson Wang Ji Young Lee ||[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||
|-
| ||
|}

==Other collaborators==
{| class="wikitable" border="0" width="80%"
|-
|[[Image:3profs07.jpg|200px]]||[[Image:John-and-marie.jpg]]
|-
|2007 Commencement: Prof.'s John Doyle, Richard Murray & Steven Low. ||John Doyle and Marie Csete
|}

[[Image:JCDgraph.jpg]]

Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004:

*[http://userwww.service.emory.edu/~mcsete/ Marie Csete, Lab] at [http://www.emory.edu/change_mode.cfm?mode=text Emory University], Atlanta.
**[http://www.emory.edu/PROVOST/greatscholars/MarieCsete.htm About Marie Csete's work.]

==See also==
*[[Group Meetings]]
*[[Calendar]]
*<http://www.cds.caltech.edu/people/portal/?un=doyle>

Main Page

2008-09-06T02:07:34Z

Hana:

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==Papers==
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.
*favourite papers
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's [[research]] interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems."[http://www.cds.caltech.edu/people/ from http://www.cds.caltech.edu/people/ Aug 16, 2008]

*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology hosted at Openwetware.org]
**[[Physiology]]
*[[Systems Verification]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''':  
626.395.4140
 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Tips: Research papers, Publishing and Other Trivia

2008-08-30T00:13:17Z

Hana: /* Searching literature */

Here are some '''quick links''' for '''searching the literature''' and '''guidelines to publishing papers'''. 
Some of these links were used to list and upload papers onto this wiki. Please note copyright still applies and wherever possible uploaded papers have information about URL/paper details attached to the upload.

==Searching literature==
===Searching Doyle's papers on this wiki===
*Click on sidebar [[Papers]], then select papers by year or by topic!
*Or click on sidebar [[Special:Specialpages|"Special pages"]] and then click on [[Special:Categories|Categories]], then select <nowiki>[[Category:Papers]]</nowiki>.
*Or click on sidebar [[Special:Allpages|"All articles"]] and then select '''from the namespace box''' pull down menu '''images''' then click "go".

===Libraries===
*[http://library.caltech.edu/ Caltech Library]
*[http://scholar.google.com/ Google scholar]
*[http://www.sciencedirect.com/ Science Direct]

====Engineering, Networking, Control====
*[http://ieeexplore.ieee.org/Xplore/dynhome.jsp IEEE Explore]
*[http://netlab.caltech.edu/pubs_search.php Netlab papers]
*[http://portal.acm.org/dl.cfm ACM portal digital library]

====Biology====
*[http://www.hubmed.org/ Hubmed]
*[http://www.nlm.nih.gov/medlineplus/ Medline plus]
*[http://openwetware.org/wiki/Main_Page OpenWetWare sharing information]
*[http://www.pnas.org/ Proceedings of National Academy of Sciences of the United States of America] (PNAS)
*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed Pubmed]
*[http://www.systems-biology.org/ Systems biology portal]

====Physics====
[http://prola.aps.org/ PROLA (Physical Review Archive)]

====Economics====

==Publication guidelines==
Some specific guidelines for publishing in some journals, conferences and websites.
====Biology & Physiology====
*[http://www.plosone.org/static/guidelines.action PLoS ONE]
*[http://journals.plos.org/plosbiology/guidelines.php PLoS Biology]
*[http://www.pnas.org/site/misc/iforc.shtml PNAS]
*[http://www.pubmedcentral.nih.gov/pmcdoc/tagging-guidelines/article/style.html PMC XML Tagging Guidelines]

====Engineering====
*[http://www.ieee.org/web/publications/pubtoolsandpolicyinfo/ IEEE Publishing Tools & Policy Information For Authors, Editors & Conference Organizers]
*[http://www.acm.org/pubs/rights.html Rights and Responsibilities in ACM Publishing]

====Economics====

==Interestingly popular reads and URL's==

===Books===
... mentioned by Prof. Doyle recently:

*''Robustness'' 
by Lars Peter Hansen and Thomas J. Sargent 
Princeton University Press, USA 2008. 
ISBN-13: 978-0691-11442-2 
(cites Prof Doyle's stuff and applies it to economics)

*''Simplexity: Why Simple Things Become Complex (And How Complex Things Can Be Made Simple)'' 
By Jeffrey Kluger, Hyperion books, USA 2008. 
ISBN 978-1-4013-0301 

===URL's===
*[http://www.mathworks.com/ Mathsworks] for software including Matlab, Simulink, etc
*[http://www.cs.caltech.edu/~adamw/advising.html Advice] from Asst Prof Adam Wierman, including [http://www.cs.cmu.edu/~jrs/sins.html Three sins of authors in computer science and math] by Jonathan Shewchuk, UC Berkeley

===wiki, blog, social networking===
*[http://openwetware.org/wiki/Doyle OpenWetWare]
*[http://sbml.org/Main_Page SBML]

*[http://www.reddit.com/ reddit] (recommended by Matthew Maurer at CS, Caltech)
*[http://digg.com/ digg] (mentioned by Lachlan Andrew, Netlab)
*[http://gigaom.com/ GigaOm] (recommended by Paul Fang, high school visitor)

Tips: Research papers, Publishing and Other Trivia

2008-08-30T00:06:09Z

Hana: /* Books */

Here are some '''quick links''' for '''searching the literature''' and '''guidelines to publishing papers'''. 
Some of these links were used to list and upload papers onto this wiki. Please note copyright still applies and wherever possible uploaded papers have information about URL/paper details attached to the upload.

==Searching literature==
===Searching Doyle's papers on this wiki===
*Click on sidebar [[Papers]], then select papers by year or by topic!
*Or click on sidebar [[Special:Specialpages|"Special pages"]] and then click on [[Special:Categories|Categories]], then select <nowiki>[[Category:Papers]]</nowiki>.
*Or click on sidebar [[Special:Allpages|"All articles"]] and then select '''from the namespace box''' pull down menu '''images''' then click "go".
===Libraries===
*[http://library.caltech.edu/ Caltech Library]
*[http://scholar.google.com/ Google scholar]
*[http://www.sciencedirect.com/ Science Direct]
====Engineering, Networking, Control====
*[http://ieeexplore.ieee.org/Xplore/dynhome.jsp IEEE Explore]
*[http://netlab.caltech.edu/pubs_search.php Netlab papers]
*[http://portal.acm.org/dl.cfm ACM portal digital library]

====Biology====
*[http://www.hubmed.org/ Hubmed]
*[http://www.nlm.nih.gov/medlineplus/ Medline plus]
*[http://openwetware.org/wiki/Main_Page OpenWetWare sharing information]
*[http://www.pnas.org/ Proceedings of National Academy of Sciences of the United States of America] (PNAS)
*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed Pubmed]
*[http://www.systems-biology.org/ Systems biology portal]

===Physics===
[http://prola.aps.org/ PROLA (Physical Review Archive)]

====Economics====

==Publication guidelines==
Some specific guidelines for publishing in some journals, conferences and websites.
====Biology & Physiology====
*[http://www.plosone.org/static/guidelines.action PLoS ONE]
*[http://journals.plos.org/plosbiology/guidelines.php PLoS Biology]
*[http://www.pnas.org/site/misc/iforc.shtml PNAS]
*[http://www.pubmedcentral.nih.gov/pmcdoc/tagging-guidelines/article/style.html PMC XML Tagging Guidelines]

====Engineering====
*[http://www.ieee.org/web/publications/pubtoolsandpolicyinfo/ IEEE Publishing Tools & Policy Information For Authors, Editors & Conference Organizers]
*[http://www.acm.org/pubs/rights.html Rights and Responsibilities in ACM Publishing]

====Economics====

==Interestingly popular reads and URL's==

===Books===
... mentioned by Prof. Doyle recently:

*''Robustness'' 
by Lars Peter Hansen and Thomas J. Sargent 
Princeton University Press, USA 2008. 
ISBN-13: 978-0691-11442-2 
(cites Prof Doyle's stuff and applies it to economics)

*''Simplexity: Why Simple Things Become Complex (And How Complex Things Can Be Made Simple)'' 
By Jeffrey Kluger, Hyperion books, USA 2008. 
ISBN 978-1-4013-0301 

===URL's===
*[http://www.mathworks.com/ Mathsworks] for software including Matlab, Simulink, etc
*[http://www.cs.caltech.edu/~adamw/advising.html Advice] from Asst Prof Adam Wierman, including [http://www.cs.cmu.edu/~jrs/sins.html Three sins of authors in computer science and math] by Jonathan Shewchuk, UC Berkeley

===wiki, blog, social networking===
*[http://openwetware.org/wiki/Doyle OpenWetWare]
*[http://sbml.org/Main_Page SBML]

*[http://www.reddit.com/ reddit] (recommended by Matthew Maurer at CS, Caltech)
*[http://digg.com/ digg] (mentioned by Lachlan Andrew, Netlab)
*[http://gigaom.com/ GigaOm] (recommended by Paul Fang, high school visitor)

Research

2008-08-29T04:49:08Z

Hana: /* Collaborative groups */

Quotes:

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics". [http://www.cds.caltech.edu/people/]

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology" [http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html]

==Current Projects==
*[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]
*[http://openwetware.org/wiki/Doyle Physiology]
*[[Systems Verification]]
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray] (links to his wiki)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==References==
1. <http://www.cds.caltech.edu/people/> Aug 17, 2008

2. <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 17, 2008
==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]