https://www.doyle.caltech.edu/api.php?action=feedcontributions&feedformat=atom&user=Lijun John C. Doyle - User contributions [en] 2026-04-25T23:37:37Z User contributions MediaWiki 1.41.5 https://www.doyle.caltech.edu/index.php?title=Main_Page&diff=3200 Main Page 2011-07-04T00:20:56Z <p>Lijun: </p> <hr /> <div>&lt;table border=1 width=100% style=&quot;color:black; &quot; cellpadding=&quot;20&quot; cellspacing=&quot;0&quot;&gt;<br /> &lt;tr&gt;<br /> &lt;td align=center width=20%&gt; [[Image:doyle.jpg]]&lt;/td&gt;<br /> &lt;td width=60% align=center&gt;<br /> &lt;font face=&quot;Comic Sans MS&quot; size=5&gt;&lt;b&gt;John C. Doyle&lt;/b&gt;&lt;br&gt;&lt;br&gt;&lt;/font&gt;<br /> &lt;font face=&quot;Comic Sans MS&quot; size=3&gt;<br /> John G Braun Professor&lt;br&gt;<br /> of Control and Dynamical Systems&lt;br&gt;<br /> Electrical Engineering&lt;br&gt;<br /> and BioEngineering&lt;br&gt;&lt;br&gt;<br /> Division of Engineering and Applied Science&lt;br&gt;<br /> California Institute of Technology&lt;br&gt;<br /> &lt;/font&gt;<br /> &lt;/td&gt;<br /> &lt;td align=center width=20%&gt;<br /> &lt;font face=&quot;Comic Sans MS&quot;&gt;<br /> <br /> [[J. Doyle’s Bio]] <br /> <br /> [[News]]<br /> <br /> [[Calendar]]<br /> <br /> [[#Contact|Contact]]<br /> <br /> [https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]<br /> &lt;/font&gt;&lt;/td&gt;<br /> &lt;/tr&gt;&lt;/table&gt;<br /> {| align=center<br /> |[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]<br /> |}<br /> &lt;hr&gt;<br /> <br /> <br /> <br /> ==News==<br /> *[[Calendar]]<br /> *[[Research|MURI 2008]]<br /> *[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.<br /> <br /> &quot;This man wants to control the internet&quot; by Carl Zimmer, Discover magazine, 10/25/2007.<br /> <br /> ==Papers==<br /> *[[Papers|'''More Papers''']]<br /> <br /> == Research ==<br /> &quot;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.&quot; &lt;http://www.cds.caltech.edu/people/&gt; Aug 16, 2008<br /> <br /> *[[Research|Research projects and grants list]]<br /> &lt;!--<br /> **[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]<br /> **[http://openwetware.org/wiki/Doyle Physiology hosted at Openwetware.org]<br /> **[[Physiology]]<br /> **[[Systems Verification]]<br /> --&gt;<br /> <br /> == Teaching ==<br /> <br /> *[[CDS 213|The Architecture of Robust, Evolvable Networks (Wi10)]]<br /> <br /> == Contact ==<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> <br /> '''Mailing Address'''<br /> <br /> John Doyle &lt;br&gt;<br /> California Institute of Technology&lt;br&gt;<br /> Control and Dynamical Systems, MC 107-81&lt;br&gt;<br /> 1200 E. California Blvd&lt;br&gt;<br /> Pasadena, CA 91125 USA<br /> | width=50% |<br /> <br /> '''Contact information'''<br /> <br /> E-mail: doyle AT cds dot caltech dot edu &lt;br&gt; <br /> Office: 109 Steele,&lt;br&gt;<br /> Phone: 626.395.4808 Fax: 626.395.6170&lt;br&gt;<br /> <br /> '''Admin Assistant''': &lt;!--Gloria Bain, --&gt; Charis Brown&lt;br&gt;<br /> Office: 107 Steele,&lt;br&gt;<br /> Email: charismb AT caltech dot edu&lt;br&gt;<br /> Phone: 626.395.4140 &lt;br&gt;<br /> Labs: 12 STL, 110 GUG (x2319) <br /> |-<br /> |<br /> <br /> ===Other Caltech links===<br /> <br /> *[http://www.caltech.edu California Institute of Technology]<br /> **[http://www.eas.caltech.edu Engineering and Applied Science Division]<br /> ***[http://www.be.caltech.edu/ Bioengineering Department]<br /> ***[http://www.cds.caltech.edu Control and Dynamical Systems Department]<br /> ***[http://www.ee2.caltech.edu/ Electrical Engineering Department]<br /> |}</div> Lijun https://www.doyle.caltech.edu/index.php?title=Main_Page&diff=3199 Main Page 2011-07-04T00:20:28Z <p>Lijun: </p> <hr /> <div>&lt;table border=1 width=100% style=&quot;color:black; &quot; cellpadding=&quot;20&quot; cellspacing=&quot;0&quot;&gt;<br /> &lt;tr&gt;<br /> &lt;td align=center width=20%&gt; [[Image:doyle.jpg]]&lt;/td&gt;<br /> &lt;td width=60% align=center&gt;<br /> &lt;font face=&quot;Comic Sans MS&quot; size=5&gt;&lt;b&gt;John C. Doyle&lt;/b&gt;&lt;br&gt;&lt;br&gt;&lt;/font&gt;<br /> &lt;font face=&quot;Comic Sans MS&quot; size=3&gt;<br /> John G Braun Professor&lt;br&gt;<br /> of Control and Dynamical Systems&lt;br&gt;<br /> Electrical Engineering&lt;br&gt;<br /> and BioEngineering&lt;br&gt;&lt;br&gt;<br /> Division of Engineering and Applied Science&lt;br&gt;<br /> California Institute of Technology&lt;br&gt;<br /> &lt;/font&gt;<br /> &lt;/td&gt;<br /> &lt;td align=center width=20%&gt;<br /> &lt;font face=&quot;Comic Sans MS&quot;&gt;<br /> <br /> [[J. Doyle’s Bio]] <br /> <br /> [[New]]<br /> <br /> [[Calendar]]<br /> <br /> [[#Contact|Contact]]<br /> <br /> [https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]<br /> &lt;/font&gt;&lt;/td&gt;<br /> &lt;/tr&gt;&lt;/table&gt;<br /> {| align=center<br /> |[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]<br /> |}<br /> &lt;hr&gt;<br /> <br /> <br /> <br /> ==News==<br /> *[[Calendar]]<br /> *[[Research|MURI 2008]]<br /> *[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.<br /> <br /> &quot;This man wants to control the internet&quot; by Carl Zimmer, Discover magazine, 10/25/2007.<br /> <br /> ==Papers==<br /> *[[Papers|'''More Papers''']]<br /> <br /> == Research ==<br /> &quot;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.&quot; &lt;http://www.cds.caltech.edu/people/&gt; Aug 16, 2008<br /> <br /> *[[Research|Research projects and grants list]]<br /> &lt;!--<br /> **[http://www.cds.caltech.edu/~dennice/fluids/index.php?title=Main_Page Fluids]<br /> **[http://openwetware.org/wiki/Doyle Physiology hosted at Openwetware.org]<br /> **[[Physiology]]<br /> **[[Systems Verification]]<br /> --&gt;<br /> <br /> == Teaching ==<br /> <br /> *[[CDS 213|The Architecture of Robust, Evolvable Networks (Wi10)]]<br /> <br /> == Contact ==<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> <br /> '''Mailing Address'''<br /> <br /> John Doyle &lt;br&gt;<br /> California Institute of Technology&lt;br&gt;<br /> Control and Dynamical Systems, MC 107-81&lt;br&gt;<br /> 1200 E. California Blvd&lt;br&gt;<br /> Pasadena, CA 91125 USA<br /> | width=50% |<br /> <br /> '''Contact information'''<br /> <br /> E-mail: doyle AT cds dot caltech dot edu &lt;br&gt; <br /> Office: 109 Steele,&lt;br&gt;<br /> Phone: 626.395.4808 Fax: 626.395.6170&lt;br&gt;<br /> <br /> '''Admin Assistant''': &lt;!--Gloria Bain, --&gt; Charis Brown&lt;br&gt;<br /> Office: 107 Steele,&lt;br&gt;<br /> Email: charismb AT caltech dot edu&lt;br&gt;<br /> Phone: 626.395.4140 &lt;br&gt;<br /> Labs: 12 STL, 110 GUG (x2319) <br /> |-<br /> |<br /> <br /> ===Other Caltech links===<br /> <br /> *[http://www.caltech.edu California Institute of Technology]<br /> **[http://www.eas.caltech.edu Engineering and Applied Science Division]<br /> ***[http://www.be.caltech.edu/ Bioengineering Department]<br /> ***[http://www.cds.caltech.edu Control and Dynamical Systems Department]<br /> ***[http://www.ee2.caltech.edu/ Electrical Engineering Department]<br /> |}</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2983 Group Meetings 2009-06-03T00:31:57Z <p>Lijun: </p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - no meeting<br /> <br /> '''May 7th''' - Na Li<br /> <br /> '''May 12th''' - Andy Lamperski<br /> <br /> '''May 21st''' - Antonis Papachristodoulou<br /> <br /> '''May 28th''' - Krister Jacobsson<br /> <br /> '''June 8th''' - Guest Speaker<br /> <br /> '''June 18th''' - Nader Motee (tentative)<br /> <br /> '''June 25th''' - Aristotelis Asimakopoulos (tentative)<br /> <br /> '''July 2th''' - Jerry Cruz (tentative)<br /> <br /> '''July 9th''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2982 Group Meetings 2009-05-22T18:19:55Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - no meeting<br /> <br /> '''May 7th''' - Na Li<br /> <br /> '''May 12th''' - Andy Lamperski<br /> <br /> '''May 21st''' - Antonis Papachristodoulou<br /> <br /> '''May 28th''' - Krister Jacobsson<br /> <br /> '''June 4th''' - Ufuk Topcu<br /> <br /> '''June 11th''' - Dennice Gayme (tentative)<br /> <br /> '''June 18th''' - Nader Motee (tentative)<br /> <br /> '''June 25th''' - Aristotelis Asimakopoulos (tentative)<br /> <br /> '''July 2th''' - Jerry Cruz (tentative)<br /> <br /> '''July 9th''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2981 Group Meetings 2009-05-22T18:14:06Z <p>Lijun: </p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - no meeting<br /> <br /> '''May 7th''' - Na Li<br /> <br /> '''May 12th''' - Andy Lamperski<br /> <br /> '''May 21st''' - Antonis Papachristodoulou<br /> <br /> '''May 28th''' - Krister Jacobsson<br /> <br /> '''June 4th''' - Ufuk Topcu<br /> <br /> '''June 11th''' - Dennice Gayme (tentative)<br /> <br /> '''June 18th''' - Nader Motee (tentative)<br /> <br /> '''June 25th''' - Aristotelis Asimakopoulos (tentative)<br /> <br /> '''July 2th''' - Jerry Cruz (tentative)<br /> <br /> '''July 2th''' - Nader Motee<br /> <br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2980 Group Meetings 2009-05-05T19:30:43Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - no meeting<br /> <br /> '''May 7th''' - Na Li<br /> <br /> '''May 12th''' - Andy Lamperski<br /> <br /> '''May 21st''' - Antonis Papachristodoulou<br /> <br /> '''May 28th''' - Nader Motee<br /> <br /> '''June 4th''' - Ufuk Topcu<br /> <br /> '''June 11th''' - Dennice Gayme<br /> <br /> '''June 18th''' - Krister Jacobsson<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2979 Group Meetings 2009-04-28T18:43:10Z <p>Lijun: </p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - no meeting<br /> <br /> '''May 7th''' - Na Li<br /> <br /> '''May 12th''' - Andy Lamperski<br /> <br /> '''May 14th''' - Krister Jacobson<br /> <br /> '''May 21st''' - Antonis Papachristodoulou<br /> <br /> '''May 28th''' - Nader Motee<br /> <br /> '''June 4th''' - Ufuk Topcu<br /> <br /> '''June 11th''' - Dennice Gayme<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2978 Group Meetings 2009-04-27T19:25:40Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - no meeting<br /> <br /> '''May 7th''' - Na Li<br /> <br /> '''May 14th''' - Krister Jacobson<br /> <br /> '''May 21st''' - Antonis Papachristodoulou<br /> <br /> '''May 28th''' - Nader Motee<br /> <br /> '''June 4th''' - Ufuk Topcu<br /> <br /> '''June 11th''' - Dennice Gayme<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2977 Group Meetings 2009-04-20T23:46:03Z <p>Lijun: </p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - Na Li<br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' - Antonis Papachristodoulou<br /> <br /> '''May 28th''' - Nader Motee<br /> <br /> '''June 4th''' - Ufuk Topcu<br /> <br /> '''June 11th''' - Dennice Gayme<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2976 Group Meetings 2009-04-13T15:03:39Z <p>Lijun: </p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - Na Li<br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' - Antonis Papachristodoulou<br /> <br /> '''May 28th''' -<br /> <br /> '''June 4th''' - Ufuk Topcu<br /> <br /> '''June 11th''' - Dennice Gayme<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2975 Group Meetings 2009-04-10T19:07:43Z <p>Lijun: </p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - Na Li<br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' -<br /> <br /> '''May 28th''' -<br /> <br /> '''June 4th''' - Ufuk Topcu<br /> <br /> '''June 11th''' - Dennice Gayme<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2974 Group Meetings 2009-04-09T21:59:05Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - no meeting<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - Na Li<br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' -<br /> <br /> '''May 28th''' -<br /> <br /> '''June 4th''' - Dennice Gayme<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2973 Group Meetings 2009-04-07T17:43:45Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - Na Li<br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - <br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' -<br /> <br /> '''May 28th''' -<br /> <br /> '''June 4th''' - Dennice Gayme<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2972 Group Meetings 2009-04-07T17:26:56Z <p>Lijun: </p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - <br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - <br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' -<br /> <br /> '''May 28th''' -<br /> <br /> '''June 4th''' - Dennice Gayme<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2971 Group Meetings 2009-04-07T03:49:11Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - <br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30th''' - <br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' -<br /> <br /> '''May 28th''' -<br /> <br /> '''June 4th''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2970 Group Meetings 2009-04-07T03:36:56Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - <br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30''' - <br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' -<br /> <br /> '''May 28st''' -<br /> <br /> '''June 4th''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2969 Group Meetings 2009-04-07T03:35:31Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''April 9th''' - John Doyle<br /> <br /> '''April 16th''' - <br /> <br /> '''April 22th''' - Vanessa Jonsson (Joint meeting with Richard's group)<br /> <br /> '''April 30''' - <br /> <br /> '''May 7th''' - Krister Jacobsson<br /> <br /> '''May 14th''' - <br /> <br /> '''May 21st''' -<br /> <br /> '''May 28st''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2968 Group Meetings 2009-04-07T03:30:45Z <p>Lijun: /* Schedule: Winter 2009 */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''Jan 29th''' - Nader Motee (SetUp Volunteer: Lijun)<br /> <br /> '''Feb 5th''' - Andrew Lamperski (SetUp Volunteer: _______________)<br /> <br /> '''Feb 9th''' - Ben Rchet (SetUp Volunteer: _______________)<br /> <br /> '''Feb 19th''' - Javad Lavaei (SetUp Volunteer: _______________)<br /> <br /> '''Feb 26th''' - John Doyle (SetUp Volunteer: _______________)<br /> <br /> '''March 4th''' - Andy/Vanessa (SetUp Volunteer: _______________)<br /> <br /> '''March 12th''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> Jan 29th - Nader Motee<br /> <br /> Feb 5th - Andrew Lamperski<br /> <br /> Feb 9th - Ben Rchet<br /> <br /> Feb 19th - Javad Lavaei<br /> <br /> Feb 26th - John Doyle<br /> <br /> March 12th - Genti Buzi<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2967 Group Meetings 2009-04-07T03:28:19Z <p>Lijun: /* Schedule: Winter and Spring 2008 */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''Jan 29th''' - Nader Motee (SetUp Volunteer: Lijun)<br /> <br /> '''Feb 5th''' - Andrew Lamperski (SetUp Volunteer: _______________)<br /> <br /> '''Feb 9th''' - Ben Rchet (SetUp Volunteer: _______________)<br /> <br /> '''Feb 19th''' - Javad Lavaei (SetUp Volunteer: _______________)<br /> <br /> '''Feb 26th''' - John Doyle (SetUp Volunteer: _______________)<br /> <br /> '''March 4th''' - Andy/Vanessa (SetUp Volunteer: _______________)<br /> <br /> '''March 12th''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter 2009===<br /> <br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2966 Group Meetings 2009-02-10T04:17:57Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''Jan 29th''' - Nader Motee (SetUp Volunteer: Lijun)<br /> <br /> '''Feb 5th''' - Andrew Lamperski (SetUp Volunteer: _______________)<br /> <br /> '''Feb 9th''' - Ben Rchet (SetUp Volunteer: _______________)<br /> <br /> '''Feb 19th''' - Javad Lavaei (SetUp Volunteer: _______________)<br /> <br /> '''Feb 26th''' - John Doyle (SetUp Volunteer: _______________)<br /> <br /> '''March 4th''' - Andy/Vanessa (SetUp Volunteer: _______________)<br /> <br /> '''March 12th''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2962 Group Meetings 2009-01-29T19:08:00Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''Jan 29th''' - Nader Motee (SetUp Volunteer: Lijun)<br /> <br /> '''Feb 5th''' - Andrew Lamperski (SetUp Volunteer: _______________)<br /> <br /> '''Feb 11th''' - Vanessa D. Jönsson (SetUp Volunteer: _______________)<br /> <br /> '''Feb 19th''' - Javad Lavaei (SetUp Volunteer: _______________)<br /> <br /> '''Feb 26th''' - Ben Recht (SetUp Volunteer: _______________)<br /> <br /> '''March 4th''' - Andy/Vanessa (SetUp Volunteer: _______________)<br /> <br /> '''March 12th''' -<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2961 Group Meetings 2009-01-29T19:06:11Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''Jan 29th''' - Nader Motee (SetUp Volunteer: Lijun)<br /> <br /> '''Feb 5th''' - Andrew Lamperski (SetUp Volunteer: _______________)<br /> <br /> '''Feb 11th''' - Vanessa D. Jönsson (SetUp Volunteer: _______________)<br /> <br /> '''Feb 19th''' - Javad Lavaei (SetUp Volunteer: _______________)<br /> <br /> '''Feb 26th''' - Ben Recht (SetUp Volunteer: _______________)<br /> <br /> '''March 4th''' - Andy/Vanessa (SetUp Volunteer: _______________)<br /> <br /> '''March 12th''' - Ben Recht (SetUp Volunteer: _______________)<br /> <br /> == Past Meetings ==<br /> ===Schedule: Winter and Spring 2008===<br /> {| border=&quot;1&quot;<br /> |-<br /> |'''February 8''' Aaron Ames<br /> <br /> '''February 15'''Fiona Chandra<br /> <br /> '''February 22''' VISIT DAY <br /> <br /> NO GROUP MEETING<br /> <br /> '''February 29''' Ben Recht <br /> <br /> |'''March 7''' Genti Buzi<br /> <br /> '''March 14''' Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- <br /> <br /> NO GROUP MEETING<br /> |'''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' Marcos Nahmad Bensusan<br /> <br /> '''April 14''' Special lecture <br /> <br /> by John C. Doyle<br /> <br /> '''April 18''' Sujit Nair<br /> <br /> '''April 25''' Javad Lavaei<br /> <br /> |'''May 2''' NO GROUP MEETING<br /> <br /> '''May 7''' Vanessa Carson<br /> <br /> '''Thu May 22''' Ali Jadbabaie<br /> <br /> '''Fri May 30''' Javad Lavaei-Yanesi<br /> <br /> '''Tues June 3''' Lijun Chen/John Doyle<br /> <br /> '''Wed June 4''' Aristotelis Asimakopoulos<br /> |}<br /> <br /> ==See also==<br /> [[Calendar]]<br /> <br /> [[Tips: Research papers, Publishing and Other Trivia]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2299 Group Meetings 2008-05-27T22:52:02Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>== '''Schedule: Winter and Spring 2008''' ==<br /> <br /> <br /> ''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''Fri May 30''' - Javad Lavaei-Yanesi (SetUp Volunteer: _______________)<br /> <br /> '''Mon June 2''' - Lijun Chen/John Doyle (SetUp Volunteer: _______________)<br /> <br /> '''Wed June 4''' - Aristotelis Asimakopoulos (SetUp Volunteer: _______________)<br /> <br /> === Past Meetings ===<br /> <br /> '''February 8''' - Aaron Ames<br /> <br /> '''February 15''' - Fiona Chandra<br /> <br /> '''February 22''' - VISIT DAY --- NO GROUP MEETING<br /> <br /> '''February 29''' - Ben Recht<br /> <br /> '''March 7''' - Genti Buzi<br /> <br /> '''March 14''' - Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- NO GROUP MEETING<br /> <br /> '''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' - Marcos Nahmad Bensusan<br /> <br /> '''April 14''' - Special lecture by John C. Doyle<br /> <br /> '''April 18''' - Sujit Nair<br /> <br /> '''April 25''' - Javad Lavaei<br /> <br /> '''May 2''' - NO GROUP MEETING<br /> <br /> '''May 7''' - Vanessa Carson [Note that this is a WEDNESDAY not a Friday]<br /> <br /> '''Thu May 22''' - Ali Jadbabaie</div> Lijun https://www.doyle.caltech.edu/index.php?title=Calendar&diff=2298 Calendar 2008-05-27T22:51:41Z <p>Lijun: /* Group Meetings */</p> <hr /> <div>== Group Meetings ==<br /> <br /> '''Fri May 30''' - Javad Lavaei-Yanesi (SetUp Volunteer: _______________)<br /> <br /> '''Mon June 2''' - Lijun Chen/John Doyle (SetUp Volunteer: _______________)<br /> <br /> '''Wed June 4''' - Aristotelis Asimakopoulos (SetUp Volunteer: _______________)<br /> <br /> Past [[Group Meetings]]<br /> <br /> ==Courses==<br /> <br /> [http://www.cds.caltech.edu/academics/courses/ CDS courses] CDS 212 / CDS 213<br /> <br /> ==Workshops==<br /> <br /> *[http://www.systems-biology.org/006/ Systems biology workshops]<br /> <br /> ==CDS calendar==<br /> *[http://www.cds.caltech.edu/ CDS Events &amp; Related Events]<br /> *[http://www.cds.caltech.edu/research/seminars/ CDS seminars]<br /> *[http://www.cds.caltech.edu/research/conferences/ CDS Conferences]<br /> *[http://www.cds.caltech.edu/research/related/ CDS related events]<br /> *[http://www.cds.caltech.edu/academics/courses/ Course schedules]<br /> <br /> *[http://www.cds.caltech.edu/news/mailinglists/ CDS Mailing lists]<br /> <br /> ==Past events==<br /> <br /> ===Past workshops===<br /> *[http://www.cds.caltech.edu/~murray/wiki/Connections_II R Murray's Connections II Workshop 2006]<br /> *[http://www.cds.caltech.edu/research/conferences/index.php?year=2005 Connections II Workshop 2005]<br /> *[http://www.cds.caltech.edu/doyle-fest/ J Doyle's Birthday, Connections Workshop, 2004]<br /> <br /> *[http://www.cds.caltech.edu/~prajna/biowkshop/ Bio Workshop: The Challenge of Complexity] <br /> <br /> *Materials from March 2003 Workshop at UCSB on Robustness Analysis Tools <br /> with Applications to the Biological and Physical Sciences<br /> <br /> <br /> ===Past courses===<br /> <br /> *[http://www.cds.caltech.edu/~doyle/shortcourse.htm Systems Biology Shortcourse Schedule, May 21-24, 2004 Caltech]<br /> <br /> *Lijun Chen's [https://www.cds.caltech.edu/help/cms.php?op=wiki&amp;wiki_op=view&amp;id=187 CDS270]: Optimization, Game and Layering in Communication Networks, Fall 2006, Caltech.</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group_Meetings&diff=2297 Group Meetings 2008-05-27T17:22:58Z <p>Lijun: /* Next Meetings */</p> <hr /> <div>== '''Schedule: Winter and Spring 2008''' ==<br /> <br /> <br /> ''All meetings are held at noon in the CDS library.''<br /> <br /> === Next Meetings ===<br /> <br /> '''Fri May 30''' - Javad Lavaei-Yanesi (SetUp Volunteer: _______________)<br /> <br /> '''Mon June 2''' - Lijun Chen/John Doyle (SetUp Volunteer: _______________)<br /> <br /> '''Fri June 6''' - Aristotelis Asimakopoulos (SetUp Volunteer: _______________)<br /> <br /> === Past Meetings ===<br /> <br /> '''February 8''' - Aaron Ames<br /> <br /> '''February 15''' - Fiona Chandra<br /> <br /> '''February 22''' - VISIT DAY --- NO GROUP MEETING<br /> <br /> '''February 29''' - Ben Recht<br /> <br /> '''March 7''' - Genti Buzi<br /> <br /> '''March 14''' - Dennice Maynard Gayme<br /> <br /> '''March 21''' - SPRING RECESS --- NO GROUP MEETING<br /> <br /> '''March 28''' - SPRING RECESS --- NO GROUP MEETING<br /> <br /> '''April 4''' - Andy Lamperski<br /> <br /> '''April 11''' - Marcos Nahmad Bensusan<br /> <br /> '''April 14''' - Special lecture by John C. Doyle<br /> <br /> '''April 18''' - Sujit Nair<br /> <br /> '''April 25''' - Javad Lavaei<br /> <br /> '''May 2''' - NO GROUP MEETING<br /> <br /> '''May 7''' - Vanessa Carson [Note that this is a WEDNESDAY not a Friday]<br /> <br /> '''Thu May 22''' - Ali Jadbabaie</div> Lijun https://www.doyle.caltech.edu/index.php?title=Calendar&diff=2296 Calendar 2008-05-27T17:21:34Z <p>Lijun: /* Group Meetings */</p> <hr /> <div>== Group Meetings ==<br /> <br /> '''Fri May 30''' - Javad Lavaei-Yanesi (SetUp Volunteer: _______________)<br /> <br /> '''Mon June 2''' - Lijun Chen/John Doyle (SetUp Volunteer: _______________)<br /> <br /> '''Fri June 6''' - Aristotelis Asimakopoulos (SetUp Volunteer: _______________)<br /> <br /> Past [[Group Meetings]]<br /> <br /> ==Courses==<br /> <br /> [http://www.cds.caltech.edu/academics/courses/ CDS courses] CDS 212 / CDS 213<br /> <br /> ==Workshops==<br /> <br /> *[http://www.systems-biology.org/006/ Systems biology workshops]<br /> <br /> ==CDS calendar==<br /> *[http://www.cds.caltech.edu/ CDS Events &amp; Related Events]<br /> *[http://www.cds.caltech.edu/research/seminars/ CDS seminars]<br /> *[http://www.cds.caltech.edu/research/conferences/ CDS Conferences]<br /> *[http://www.cds.caltech.edu/research/related/ CDS related events]<br /> *[http://www.cds.caltech.edu/academics/courses/ Course schedules]<br /> <br /> *[http://www.cds.caltech.edu/news/mailinglists/ CDS Mailing lists]<br /> <br /> ==Past events==<br /> <br /> ===Past workshops===<br /> *[http://www.cds.caltech.edu/~murray/wiki/Connections_II R Murray's Connections II Workshop 2006]<br /> *[http://www.cds.caltech.edu/research/conferences/index.php?year=2005 Connections II Workshop 2005]<br /> *[http://www.cds.caltech.edu/doyle-fest/ J Doyle's Birthday, Connections Workshop, 2004]<br /> <br /> *[http://www.cds.caltech.edu/~prajna/biowkshop/ Bio Workshop: The Challenge of Complexity] <br /> <br /> *Materials from March 2003 Workshop at UCSB on Robustness Analysis Tools <br /> with Applications to the Biological and Physical Sciences<br /> <br /> <br /> ===Past courses===<br /> <br /> *[http://www.cds.caltech.edu/~doyle/shortcourse.htm Systems Biology Shortcourse Schedule, May 21-24, 2004 Caltech]<br /> <br /> *Lijun Chen's [https://www.cds.caltech.edu/help/cms.php?op=wiki&amp;wiki_op=view&amp;id=187 CDS270]: Optimization, Game and Layering in Communication Networks, Fall 2006, Caltech.</div> Lijun https://www.doyle.caltech.edu/index.php?title=Calendar&diff=2295 Calendar 2008-05-27T17:20:48Z <p>Lijun: /* Group Meetings */</p> <hr /> <div>== Group Meetings ==<br /> <br /> '''Fri May 30''' - Javad Lavaei-Yanesi (SetUp Volunteer: _______________)<br /> <br /> '''Mon June 2''' - Lijun/John (SetUp Volunteer: _______________)<br /> <br /> '''Fri June 6''' - Aristotelis Asimakopoulos (SetUp Volunteer: _______________)<br /> <br /> Past [[Group Meetings]]<br /> <br /> ==Courses==<br /> <br /> [http://www.cds.caltech.edu/academics/courses/ CDS courses] CDS 212 / CDS 213<br /> <br /> ==Workshops==<br /> <br /> *[http://www.systems-biology.org/006/ Systems biology workshops]<br /> <br /> ==CDS calendar==<br /> *[http://www.cds.caltech.edu/ CDS Events &amp; Related Events]<br /> *[http://www.cds.caltech.edu/research/seminars/ CDS seminars]<br /> *[http://www.cds.caltech.edu/research/conferences/ CDS Conferences]<br /> *[http://www.cds.caltech.edu/research/related/ CDS related events]<br /> *[http://www.cds.caltech.edu/academics/courses/ Course schedules]<br /> <br /> *[http://www.cds.caltech.edu/news/mailinglists/ CDS Mailing lists]<br /> <br /> ==Past events==<br /> <br /> ===Past workshops===<br /> *[http://www.cds.caltech.edu/~murray/wiki/Connections_II R Murray's Connections II Workshop 2006]<br /> *[http://www.cds.caltech.edu/research/conferences/index.php?year=2005 Connections II Workshop 2005]<br /> *[http://www.cds.caltech.edu/doyle-fest/ J Doyle's Birthday, Connections Workshop, 2004]<br /> <br /> *[http://www.cds.caltech.edu/~prajna/biowkshop/ Bio Workshop: The Challenge of Complexity] <br /> <br /> *Materials from March 2003 Workshop at UCSB on Robustness Analysis Tools <br /> with Applications to the Biological and Physical Sciences<br /> <br /> <br /> ===Past courses===<br /> <br /> *[http://www.cds.caltech.edu/~doyle/shortcourse.htm Systems Biology Shortcourse Schedule, May 21-24, 2004 Caltech]<br /> <br /> *Lijun Chen's [https://www.cds.caltech.edu/help/cms.php?op=wiki&amp;wiki_op=view&amp;id=187 CDS270]: Optimization, Game and Layering in Communication Networks, Fall 2006, Caltech.</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group&diff=1955 Group 2007-10-01T05:27:16Z <p>Lijun: /* Alumni */</p> <hr /> <div>John Doyle's research group is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.<br /> <br /> ==Current Group==<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''Faculty'''<br /> |'''Postdocs<br /> |'''Students'''<br /> |-<br /> |John Doyle<br /> |[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames] <br /> <br /> [http://www.cds.caltech.edu/~chen/ Lijun Chen] <br /> <br /> [http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]<br /> <br /> Ben Recht <br /> <br /> [http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]<br /> <br /> |''Graduate students''<br /> [http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos] <br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi] <br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme] <br /> <br /> [http://www.cds.caltech.edu/~andyl/ Andrew Lamperski] <br /> <br /> [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]<br /> <br /> Na Li<br /> <br /> <br /> <br /> <br /> |-<br /> |'''Admin staff'''<br /> |'''Visitors'''<br /> |''Undergraduate students'' <br /> |-<br /> |[http://www.cds.caltech.edu/people/portal/?id=469 Gloria Bain]<br /> |[http://www.cds.caltech.edu/people/portal/?id=713 Rutika Muchhala (student)]<br /> <br /> [http://www.cds.caltech.edu/~lun/ Lun Li]<br /> |<br /> <br /> |}<br /> <br /> ==Past Group==<br /> ===Alumni===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006'''<br /> <br /> |'''1990-1999'''<br /> |-<br /> |[http://www.cds.caltech.edu/~chen/ Lijun Chen]<br /> <br /> [http://www.cds.caltech.edu/~lun Lun Li]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]<br /> <br /> [http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]<br /> <br /> | <br /> <br /> Nizar Batada<br /> <br /> [http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]<br /> <br /> Irene Gregory<br /> <br /> [http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=40 Yindi Jing]<br /> <br /> Sven Khatri<br /> <br /> [http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]<br /> <br /> [http://www.mit.edu/~parrilo/ Pablo Parrilo]<br /> <br /> [http://www.cds.caltech.edu/~prajna/ Stephen Prajna]<br /> <br /> [http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]<br /> <br /> [http://www.cds.caltech.edu/~jyu/ Jie Yu]<br /> <br /> [http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]<br /> <br /> |Carolyn Beck<br /> <br /> Raff D'Andrea<br /> <br /> Sonja Glavaski<br /> <br /> Irene Gregory<br /> <br /> Yun Huang<br /> <br /> Michael Kantner<br /> <br /> [http://www.ee.ucla.edu/~paganini/ Fernando Paganini]<br /> <br /> [http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]<br /> <br /> Stefano Soatto<br /> <br /> Jorge Tierno <br /> <br /> |}<br /> <br /> ===Past Postdocs===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006<br /> Masahiro Yanagisawa<br /> <br /> [http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]<br /> <br /> [http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]<br /> <br /> |'''1990-1999'''<br /> |-<br /> |?<br /> |[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]<br /> <br /> [http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]<br /> <br /> |?<br /> |}<br /> <br /> ===Past Visitors===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006<br /> |'''1990-1999'''<br /> |-<br /> |Panagiota Stratou<br /> |?<br /> |?<br /> |}<br /> <br /> ==MURF and SURF==<br /> {| border=&quot;1&quot;<br /> |2007 ||2000-2006<br /> |-<br /> |[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||<br /> |-<br /> | ||<br /> |}<br /> <br /> ==Other collaborators==<br /> 2007 Commencement: Prof.'s John Doyle, Richard Murray &amp; Steven Low.<br /> [[Image:3profs07.jpg|200px]]<br /> <br /> <br /> <br /> Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004: [[Image:JCDgraph.jpg]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group&diff=1954 Group 2007-10-01T05:26:33Z <p>Lijun: /* Alumni */</p> <hr /> <div>John Doyle's research group is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.<br /> <br /> ==Current Group==<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''Faculty'''<br /> |'''Postdocs<br /> |'''Students'''<br /> |-<br /> |John Doyle<br /> |[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames] <br /> <br /> [http://www.cds.caltech.edu/~chen/ Lijun Chen] <br /> <br /> [http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]<br /> <br /> Ben Recht <br /> <br /> [http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]<br /> <br /> |''Graduate students''<br /> [http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos] <br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi] <br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme] <br /> <br /> [http://www.cds.caltech.edu/~andyl/ Andrew Lamperski] <br /> <br /> [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]<br /> <br /> Na Li<br /> <br /> <br /> <br /> <br /> |-<br /> |'''Admin staff'''<br /> |'''Visitors'''<br /> |''Undergraduate students'' <br /> |-<br /> |[http://www.cds.caltech.edu/people/portal/?id=469 Gloria Bain]<br /> |[http://www.cds.caltech.edu/people/portal/?id=713 Rutika Muchhala (student)]<br /> <br /> [http://www.cds.caltech.edu/~lun/ Lun Li]<br /> |<br /> <br /> |}<br /> <br /> ==Past Group==<br /> ===Alumni===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006'''<br /> <br /> |'''1990-1999'''<br /> |-<br /> |[http://www.cds.caltech.edu/~chen/ Lijun Chen]<br /> <br /> [http://www.cds.caltech.edu/~lun Lun Li]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]<br /> <br /> [http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]<br /> <br /> | Nizar Batada<br /> <br /> [http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]<br /> <br /> Irene Gregory<br /> <br /> [http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=40 Yindi Jing]<br /> <br /> Sven Khatri<br /> <br /> [http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]<br /> <br /> [http://www.mit.edu/~parrilo/ Pablo Parrilo]<br /> <br /> [http://www.cds.caltech.edu/~prajna/ Stephen Prajna]<br /> <br /> [http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]<br /> <br /> [http://www.cds.caltech.edu/~jyu/ Jie Yu]<br /> <br /> [http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]<br /> <br /> |Carolyn Beck<br /> <br /> Raff D'Andrea<br /> <br /> Sonja Glavaski<br /> <br /> Irene Gregory<br /> <br /> Yun Huang<br /> <br /> Michael Kantner<br /> <br /> [http://www.ee.ucla.edu/~paganini/ Fernando Paganini]<br /> <br /> [http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]<br /> <br /> Stefano Soatto<br /> <br /> <br /> Jorge Tierno <br /> <br /> |}<br /> <br /> ===Past Postdocs===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006<br /> Masahiro Yanagisawa<br /> <br /> [http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]<br /> <br /> [http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]<br /> <br /> |'''1990-1999'''<br /> |-<br /> |?<br /> |[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]<br /> <br /> [http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]<br /> <br /> |?<br /> |}<br /> <br /> ===Past Visitors===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006<br /> |'''1990-1999'''<br /> |-<br /> |Panagiota Stratou<br /> |?<br /> |?<br /> |}<br /> <br /> ==MURF and SURF==<br /> {| border=&quot;1&quot;<br /> |2007 ||2000-2006<br /> |-<br /> |[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||<br /> |-<br /> | ||<br /> |}<br /> <br /> ==Other collaborators==<br /> 2007 Commencement: Prof.'s John Doyle, Richard Murray &amp; Steven Low.<br /> [[Image:3profs07.jpg|200px]]<br /> <br /> <br /> <br /> Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004: [[Image:JCDgraph.jpg]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1953 Network architecture and protocols 2007-10-01T05:16:50Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> ......<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of technological and biological networks.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> <br /> [http://netlab.caltech.edu/publications/RobustInternetII-Doyle-2002.pdf ''Robustness and the Internet: Theoretical foundations'']<br /> <br /> John C. Doyle, Jean Carlson, Steven H. Low, Fernando Paganini, Glenn Vinnicombe, Walter Willinger, Jason Hickey, Pablo Parrilo and Lieven Vandenberghe<br /> <br /> in Robust design: a repertoire from biology, ecology, and engineering E. Jen (eds.), Oxford University Press, 2003.<br /> <br /> [http://netlab.caltech.edu/publications/Layering-IEEEProc-060402.pdf ''Layering as optimization decomposition: A Mathematical Theory of Network Architectures'']<br /> <br /> Mung Chiang, Steven H. Low, A. Robert Calderbank and John C. Doyle<br /> <br /> in Proceedings of the IEEE, vol.95 pp.255-312. Jan 2007.<br /> <br /> ===Research papers===<br /> <br /> [http://netlab.caltech.edu/publications/SHLowduality2003.ps ''A Duality Model of TCP and Queue Management Algorithms'']<br /> <br /> S. H. Low<br /> <br /> IEEE/ACM Transactions on Networking, 11(4):525-536, Aug 2003.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks'']<br /> <br /> J. Wang, L. Li, S. H. Low and J. C. Doyle<br /> <br /> IEEE/ACM Transactions on Networking, 13(3):582-568, Jun 2005.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/1/1b/Tcpmac-infocom05.pdf ''Joint congestion control and media access control design for wireless ad hoc networks'']<br /> <br /> Lijun Chen, Steven H. Low and John C. Doyle<br /> <br /> in Proceedings of IEEE Infocom, vol.3 pp.2212-2222. Miami, FL, 13-17 Mar 2005.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/a/ae/Wireless-Chen-infocom06.pdf ''Cross-layer congestion control, routing and scheduling design in ad hoc wireless networks'']<br /> <br /> L. Chen, S. H. Low, M. Chiang and J. C. Doyle<br /> <br /> in IEEE Infocom, pp.1-13. Barcelona, Spain, Apr 2006.<br /> <br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1952 Network architecture and protocols 2007-10-01T05:11:45Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of technological and biological networks.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> <br /> [http://netlab.caltech.edu/publications/RobustInternetII-Doyle-2002.pdf ''Robustness and the Internet: Theoretical foundations'']<br /> <br /> John C. Doyle, Jean Carlson, Steven H. Low, Fernando Paganini, Glenn Vinnicombe, Walter Willinger, Jason Hickey, Pablo Parrilo and Lieven Vandenberghe<br /> <br /> in Robust design: a repertoire from biology, ecology, and engineering E. Jen (eds.), Oxford University Press, 2003.<br /> <br /> [http://netlab.caltech.edu/publications/Layering-IEEEProc-060402.pdf ''Layering as optimization decomposition: A Mathematical Theory of Network Architectures'']<br /> <br /> Mung Chiang, Steven H. Low, A. Robert Calderbank and John C. Doyle<br /> <br /> in Proceedings of the IEEE, vol.95 pp.255-312. Jan 2007.<br /> <br /> ===Research papers===<br /> <br /> [http://netlab.caltech.edu/publications/SHLowduality2003.ps ''A Duality Model of TCP and Queue Management Algorithms'']<br /> <br /> S. H. Low<br /> <br /> IEEE/ACM Transactions on Networking, 11(4):525-536, Aug 2003.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks'']<br /> <br /> J. Wang, L. Li, S. H. Low and J. C. Doyle<br /> <br /> IEEE/ACM Transactions on Networking, 13(3):582-568, Jun 2005.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/1/1b/Tcpmac-infocom05.pdf ''Joint congestion control and media access control design for wireless ad hoc networks'']<br /> <br /> Lijun Chen, Steven H. Low and John C. Doyle<br /> <br /> in Proceedings of IEEE Infocom, vol.3 pp.2212-2222. Miami, FL, 13-17 Mar 2005.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/a/ae/Wireless-Chen-infocom06.pdf ''Cross-layer congestion control, routing and scheduling design in ad hoc wireless networks'']<br /> <br /> L. Chen, S. H. Low, M. Chiang and J. C. Doyle<br /> <br /> in IEEE Infocom, pp.1-13. Barcelona, Spain, Apr 2006.<br /> <br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1951 Network architecture and protocols 2007-10-01T05:09:27Z <p>Lijun: /* Papers */</p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> <br /> [http://netlab.caltech.edu/publications/RobustInternetII-Doyle-2002.pdf ''Robustness and the Internet: Theoretical foundations'']<br /> <br /> John C. Doyle, Jean Carlson, Steven H. Low, Fernando Paganini, Glenn Vinnicombe, Walter Willinger, Jason Hickey, Pablo Parrilo and Lieven Vandenberghe<br /> <br /> in Robust design: a repertoire from biology, ecology, and engineering E. Jen (eds.), Oxford University Press, 2003.<br /> <br /> [http://netlab.caltech.edu/publications/Layering-IEEEProc-060402.pdf ''Layering as optimization decomposition: A Mathematical Theory of Network Architectures'']<br /> <br /> Mung Chiang, Steven H. Low, A. Robert Calderbank and John C. Doyle<br /> <br /> in Proceedings of the IEEE, vol.95 pp.255-312. Jan 2007.<br /> <br /> ===Research papers===<br /> <br /> [http://netlab.caltech.edu/publications/SHLowduality2003.ps ''A Duality Model of TCP and Queue Management Algorithms'']<br /> <br /> S. H. Low<br /> <br /> IEEE/ACM Transactions on Networking, 11(4):525-536, Aug 2003.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks'']<br /> <br /> J. Wang, L. Li, S. H. Low and J. C. Doyle<br /> <br /> IEEE/ACM Transactions on Networking, 13(3):582-568, Jun 2005.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/1/1b/Tcpmac-infocom05.pdf ''Joint congestion control and media access control design for wireless ad hoc networks'']<br /> <br /> Lijun Chen, Steven H. Low and John C. Doyle<br /> <br /> in Proceedings of IEEE Infocom, vol.3 pp.2212-2222. Miami, FL, 13-17 Mar 2005.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/a/ae/Wireless-Chen-infocom06.pdf ''Cross-layer congestion control, routing and scheduling design in ad hoc wireless networks'']<br /> <br /> L. Chen, S. H. Low, M. Chiang and J. C. Doyle<br /> <br /> in IEEE Infocom, pp.1-13. Barcelona, Spain, Apr 2006.<br /> <br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1950 Network architecture and protocols 2007-10-01T05:08:17Z <p>Lijun: /* Papers */</p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> <br /> [http://netlab.caltech.edu/publications/RobustInternetII-Doyle-2002.pdf ''Robustness and the Internet: Theoretical foundations'']<br /> <br /> John C. Doyle, Jean Carlson, Steven H. Low, Fernando Paganini, Glenn Vinnicombe, Walter Willinger, Jason Hickey, Pablo Parrilo and Lieven Vandenberghe<br /> <br /> in Robust design: a repertoire from biology, ecology, and engineering E. Jen (eds.), Oxford University Press, 2003.<br /> <br /> [http://netlab.caltech.edu/publications/Layering-IEEEProc-060402.pdf ''Layering as optimization decomposition: A Mathematical Theory of Network Architectures'']<br /> <br /> Mung Chiang, Steven H. Low, A. Robert Calderbank and John C. Doyle<br /> <br /> in Proceedings of the IEEE, vol.95 pp.255-312. Jan 2007.<br /> <br /> ===Research papers===<br /> <br /> [http://netlab.caltech.edu/publications/SHLowduality2003.ps ''A Duality Model of TCP and Queue Management Algorithms'']<br /> <br /> S. H. Low<br /> <br /> IEEE/ACM Transactions on Networking, 11(4):525-536, Aug 2003.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks'']<br /> <br /> J. Wang, L. Li, S. H. Low and J. C. Doyle<br /> <br /> IEEE/ACM Transactions on Networking, 13(3):582-568, Jun 2005.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/1/1b/Tcpmac-infocom05.pdf ''Joint congestion control and media access control design for wireless ad hoc networks'']<br /> <br /> Lijun Chen, Steven H. Low and John C. Doyle<br /> <br /> in Proceedings of IEEE Infocom, vol.3 pp.2212-2222. Miami, FL, 13-17 Mar 2005.<br /> <br /> [http://www.cds.caltech.edu/~doyle2/wiki/images/a/ae/Wireless-Chen-infocom06.pdf ''Cross-layer congestion control, routing and scheduling design in ad hoc wireless networks'']<br /> <br /> L. Chen, S. H. Low, M. Chiang and J. C. Doyle<br /> <br /> in IEEE Infocom, pp.1-13. Barcelona, Spain, Apr 2006.<br /> <br /> ===?===<br /> <br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1949 Network architecture and protocols 2007-10-01T05:02:27Z <p>Lijun: /* Papers */</p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> <br /> [http://netlab.caltech.edu/publications/RobustInternetII-Doyle-2002.pdf ''Robustness and the Internet: Theoretical foundations'']<br /> <br /> John C. Doyle, Jean Carlson, Steven H. Low, Fernando Paganini, Glenn Vinnicombe, Walter Willinger, Jason Hickey, Pablo Parrilo and Lieven Vandenberghe<br /> <br /> in Robust design: a repertoire from biology, ecology, and engineering E. Jen (eds.), Oxford University Press, 2003.<br /> <br /> [http://netlab.caltech.edu/publications/Layering-IEEEProc-060402.pdf ''Layering as optimization decomposition: A Mathematical Theory of Network Architectures'']<br /> <br /> Mung Chiang, Steven H. Low, A. Robert Calderbank and John C. Doyle<br /> <br /> in Proceedings of the IEEE, vol.95 pp.255-312. Jan 2007.<br /> <br /> ===Research papers===<br /> <br /> [http://netlab.caltech.edu/publications/SHLduality2003.ps ''A Duality Model of TCP and Queue Management Algorithms'']<br /> <br /> S. H. Low<br /> <br /> IEEE/ACM Transactions on Networking, 11(4):525-536, Aug 2003<br /> <br /> ===?===<br /> <br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1948 Network architecture and protocols 2007-10-01T04:59:00Z <p>Lijun: /* Overview papers */</p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> <br /> [http://netlab.caltech.edu/publications/RobustInternetII-Doyle-2002.pdf ''Robustness and the Internet: Theoretical foundations'']<br /> <br /> John C. Doyle, Jean Carlson, Steven H. Low, Fernando Paganini, Glenn Vinnicombe, Walter Willinger, Jason Hickey, Pablo Parrilo and Lieven Vandenberghe<br /> <br /> in Robust design: a repertoire from biology, ecology, and engineering E. Jen (eds.), Oxford University Press, 2003.<br /> <br /> [http://netlab.caltech.edu/publications/Layering-IEEEProc-060402.pdf ''Layering as optimization decomposition: A Mathematical Theory of Network Architectures'']<br /> <br /> Mung Chiang, Steven H. Low, A. Robert Calderbank and John C. Doyle<br /> <br /> in Proceedings of the IEEE, vol.95 pp.255-312. Jan 2007.<br /> <br /> ===Research papers===<br /> ===?===<br /> <br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1947 Network architecture and protocols 2007-10-01T04:56:43Z <p>Lijun: /* Papers */</p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> <br /> ''Robustness and the Internet: Theoretical foundations''<br /> <br /> John C. Doyle, Jean Carlson, Steven H. Low, Fernando Paganini, Glenn Vinnicombe, Walter Willinger, Jason Hickey, Pablo Parrilo and Lieven Vandenberghe<br /> <br /> in Robust design: a repertoire from biology, ecology, and engineering E. Jen (eds.), Oxford University Press, 2003.<br /> <br /> ''Layering as optimization decomposition: A Mathematical Theory of Network Architectures''<br /> <br /> Mung Chiang, Steven H. Low, A. Robert Calderbank and John C. Doyle<br /> <br /> in Proceedings of the IEEE, vol.95 pp.255-312. Jan 2007.<br /> <br /> ===Research papers===<br /> ===?===<br /> <br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1946 Network architecture and protocols 2007-10-01T04:49:13Z <p>Lijun: /* Papers */</p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Research papers===<br /> ===?===<br /> <br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1945 Network architecture and protocols 2007-10-01T04:48:11Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> (adopted from John's writing &amp; to be continued, Lijun)<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1944 Network architecture and protocols 2007-10-01T04:44:17Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. Then, network layering can be understood as a decomposition of this large optimization problem into ‘decentralized’ subproblems, and various protocol layers are regarded as carrying out asynchronous, distributed computation to implicitly solve this global optimization problem. Different layers iterate on different subsets of the decision variables using local information to achieve individual optimality. Taken together, these local algorithms attempt to achieve a global objective. Such a theory facilitates both understanding and design of network architectures, and as such could potentially be relevant to problems in both systems and synthetic biology. In reserve engineering a given network, identifying an underlying optimization problem being solved will expose the interconnection between protocol layers and can be used to study rigorously performance tradeoffs in protocol layering as different ways to distribute a centralized computation. In the context of design or ‘forward engineering’, this framework formalizes the common practice of breaking down the desired system into simpler modules, and allows us to systematically carry out the layering process and explicitly trade off design objectives.<br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1943 Network architecture and protocols 2007-10-01T04:40:13Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now major developement and progress in both technology and biology towards a unified and coherent theory of architecture. Especially, a rich optimization theory has recently been developed to reverse and forward engineer the architecture of the Internet and related technologies. This framework views the network as solving an appropriately defined optimization problem, ranging from the classical network flow problems often formulated as linear programs, to the recent and more general Network Utility Maximization (NUM) problem. It has led to both<br /> understanding how existing networks operate (e.g., reverse-engineering TCP congestion control),<br /> and designing new network protocols.<br /> <br /> <br /> We aim to combine and extend these ideas to provide a coherent theory of the layering, protocols, bowties, and hourglasses that make up the architecture of biology.<br /> <br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1942 Network architecture and protocols 2007-10-01T04:26:51Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> Similarly, in the microbial biosphere, genes that “talk” central transcription and translation<br /> protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of<br /> “bacterial internet.” But also like the technological Internet, the functionality of the resulting new proteins that result is enhanced by when they have additional shared protocols, such as group transfers and carriers in metabolism, and conserved residue pairs in signal transduction. Thus selection acting at the protocol level could evolve and preserve shared architecture, essentially “evolving evolvability.”<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now enough examples from technology and biology that suggest the required mathemtical foundations and the needed research issues along the way to a unified and coherent theory of architecture. Especially, in recent decades there has been a phenomenal increase in the wides-spread deployment and development of &quot;communications technology&quot;, (eg., computers, the internet and the world wide web). This includes '''communication networks''', where various '''protocols''' have been adopted and used to help with ......this upscale growth???<br /> The '''architecture''' of these communications networks ...<br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1941 Network architecture and protocols 2007-10-01T04:24:27Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness. The architecture of TCP/IP (Transmission Control and Internet Protocols), or the hourglass protocol stack as it’s known, has a<br /> thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper<br /> (application software) and lower (hardware) layers. The term “hourglass” has been used because<br /> there is a vast diversity of applications and hardware that sit above and below the thin waist of universally shared control mechanisms (TCP/IP). Roughly, IP controls the routes for packet flows and thus, available bandwidth. Applications split files into packets, and the TCP controls their rates and guarantees delivery. This allows “plug-and-play” between modules that obey shared protocols; any set of applications that “talks” TCP can run transparently and robustly on any set of hardware that “talks” IP.<br /> <br /> In most networked systems, protocols within a layer can be visualized as “bowties,” which have<br /> large fan-ins and -outs of energy, materials, and information via a thin ‘knot’ of universal protocols specifying carriers, building blocks, or interfaces. Other engineered examples of bowties include networks which connect energy sources to diverse consumers via carriers and standard socket-plug interfaces, and raw materials to assemblies via standardized building<br /> blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,<br /> intermediates, precursors, plugs, packets, conserved residues, and interfaces in the bowtie “knot” are highly constrained by protocols. Yet their shared universality allows diverse and robust edges toadapt and evolve, as long as they have appropriate (and typically hidden) layers of feedback control such as TCP/IP.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now enough examples from technology and biology that suggest the required mathemtical foundations and the needed research issues along the way to a unified and coherent theory of architecture. Especially, in recent decades there has been a phenomenal increase in the wides-spread deployment and development of &quot;communications technology&quot;, (eg., computers, the internet and the world wide web). This includes '''communication networks''', where various '''protocols''' have been adopted and used to help with ......this upscale growth???<br /> The '''architecture''' of these communications networks ...<br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1940 Network architecture and protocols 2007-10-01T04:09:52Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> Take, Internet, as an example. <br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now enough examples from technology and biology that suggest the required mathemtical foundations and the needed research issues along the way to a unified and coherent theory of architecture. Especially, in recent decades there has been a phenomenal increase in the wides-spread deployment and development of &quot;communications technology&quot;, (eg., computers, the internet and the world wide web). This includes '''communication networks''', where various '''protocols''' have been adopted and used to help with ......this upscale growth???<br /> The '''architecture''' of these communications networks ...<br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1939 Network architecture and protocols 2007-10-01T04:00:12Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> While there does not yet exist a coherent theory of architecture, a condition we aim to change,<br /> there are now enough examples from technology and biology that suggest the required mathemtical foundations and the needed research issues along the way to a unified and coherent theory of architecture. In recent decades there has been a phenomenal increase in the wides-spread deployment and development of &quot;communications technology&quot;, (eg., computers, the internet and the world wide web). This includes '''communication networks''', where various '''protocols''' have been adopted and used to help with ......this upscale growth???<br /> The '''architecture''' of these communications networks ...<br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1938 Network architecture and protocols 2007-10-01T03:39:04Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized. Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> In recent decades there has been a phenomenal increase in the wides-spread deployment and development of &quot;communications technology&quot;, (eg., computers, the internet and the world wide web). This includes '''communication networks''', where various '''protocols''' have been adopted and used to help with ......this upscale growth???<br /> The '''architecture''' of these communications networks ...<br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1937 Network architecture and protocols 2007-10-01T03:38:17Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized.<br /> Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.<br /> <br /> In recent decades there has been a phenomenal increase in the wides-spread deployment and development of &quot;communications technology&quot;, (eg., computers, the internet and the world wide web). This includes '''communication networks''', where various '''protocols''' have been adopted and used to help with ......this upscale growth???<br /> The '''architecture''' of these communications networks ...<br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Group&diff=1936 Group 2007-10-01T03:27:10Z <p>Lijun: /* Current Group */</p> <hr /> <div>John Doyle's research group is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.<br /> <br /> ==Current Group==<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''Faculty'''<br /> |'''Postdocs<br /> |'''Students'''<br /> |-<br /> |John Doyle<br /> |[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames] <br /> <br /> [http://www.cds.caltech.edu/~chen/ Lijun Chen] <br /> <br /> [http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]<br /> <br /> Ben Recht <br /> <br /> [http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]<br /> <br /> |''Graduate students''<br /> [http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos] <br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi] <br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme] <br /> <br /> [http://www.cds.caltech.edu/~andyl/ Andrew Lamperski] <br /> <br /> [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]<br /> <br /> Na Li<br /> <br /> <br /> <br /> <br /> |-<br /> |'''Admin staff'''<br /> |'''Visitors'''<br /> |''Undergraduate students'' <br /> |-<br /> |[http://www.cds.caltech.edu/people/portal/?id=469 Gloria Bain]<br /> |[http://www.cds.caltech.edu/people/portal/?id=713 Rutika Muchhala (student)]<br /> <br /> [http://www.cds.caltech.edu/~lun/ Lun Li]<br /> |<br /> <br /> |}<br /> <br /> ==Past Group==<br /> ===Alumni===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006'''<br /> <br /> |'''1990-1999'''<br /> |-<br /> |[http://www.cds.caltech.edu/~chen/ Lijun Chen]<br /> <br /> [http://www.cds.caltech.edu/~lun Lun Li]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]<br /> <br /> [http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]<br /> <br /> |[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]<br /> <br /> [http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]<br /> <br /> [http://www.cds.caltech.edu/people/portal/?id=40 Yindi Jing]<br /> <br /> [http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]<br /> <br /> [http://www.mit.edu/~parrilo/ Pablo Parrilo]<br /> <br /> [http://www.cds.caltech.edu/~prajna/ Stephen Prajna]<br /> <br /> [http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]<br /> <br /> [http://www.cds.caltech.edu/~jyu/ Jie Yu]<br /> <br /> [http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]<br /> <br /> |Carolyn Beck<br /> <br /> Raff D'Andrea<br /> <br /> Sonja Glavaski<br /> <br /> Irene Gregory<br /> <br /> Yun Huang<br /> <br /> Michael Kantner<br /> <br /> Sven Khatri<br /> <br /> [http://www.ee.ucla.edu/~paganini/ Fernando Paganini]<br /> <br /> [http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]<br /> <br /> Jorge Tierno <br /> <br /> |}<br /> <br /> ===Past Postdocs===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006<br /> Masahiro Yanagisawa<br /> <br /> [http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]<br /> <br /> [http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]<br /> <br /> |'''1990-1999'''<br /> |-<br /> |?<br /> |[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]<br /> <br /> [http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]<br /> <br /> |?<br /> |}<br /> <br /> ===Past Visitors===<br /> {| width=100% border=0 cellpadding=0 cellspacing=0 <br /> |-<br /> |'''2007'''<br /> |'''2000-2006<br /> |'''1990-1999'''<br /> |-<br /> |Panagiota Stratou<br /> |?<br /> |?<br /> |}<br /> <br /> ==MURF and SURF==<br /> {| border=&quot;1&quot;<br /> |2007 ||2000-2006<br /> |-<br /> |[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||<br /> |-<br /> | ||<br /> |}<br /> <br /> ==Other collaborators==<br /> 2007 Commencement: Prof.'s John Doyle, Richard Murray &amp; Steven Low.<br /> [[Image:3profs07.jpg|200px]]<br /> <br /> <br /> <br /> Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004: [[Image:JCDgraph.jpg]]</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1931 Network architecture and protocols 2007-09-20T00:32:57Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organizzation (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized.<br /> <br /> Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment.... (to be continued, Lijun)<br /> <br /> In recent decades there has been a phenomenal increase in the wides-spread deployment and development of &quot;communications technology&quot;, (eg., computers, the internet and the world wide web). This includes '''communication networks''', where various '''protocols''' have been adopted and used to help with ......this upscale growth???<br /> The '''architecture''' of these communications networks ...<br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Network_architecture_and_protocols&diff=1930 Network architecture and protocols 2007-09-20T00:31:02Z <p>Lijun: </p> <hr /> <div>The key to understand complex networks is understanding their architecture. Architecture is the most universal, high-level, and persistent elemments of structure and organizzation (or princciples of structuring and organizing a complex system). Protocols define how diverse modules interact, and architecture defines how sets of protocols are organized.<br /> <br /> Architecture usually involves specification of protocols (rules of interaction) more than modules (which obey protocols). In engineering, system architecture must facilitate system level functionality as well as robustness and evolvability to uncertainty and change in components, function, and environment....<br /> <br /> In recent decades there has been a phenomenal increase in the wides-spread deployment and development of &quot;communications technology&quot;, (eg., computers, the internet and the world wide web). This includes '''communication networks''', where various '''protocols''' have been adopted and used to help with ......this upscale growth???<br /> The '''architecture''' of these communications networks ...<br /> <br /> ==Papers==<br /> <br /> ===Overview papers===<br /> ===Review papers===<br /> ===?===<br /> ==See also==</div> Lijun https://www.doyle.caltech.edu/index.php?title=Papers&diff=1929 Papers 2007-09-20T00:11:40Z <p>Lijun: /* Topic */</p> <hr /> <div>Needs intro...<br /> Publications have been sorted:<br /> - by year, type of publication<br /> - by topic<br /> <br /> ==Topic==<br /> (Comment: Click on the RED words below, to begin a new page of the same name.)<br /> *[[Complex networks]]<br /> **[[Robust yet fragile &amp; biological networks]]<br /> **[[HOT]]<br /> **[[Internet topology]]<br /> **[[Network architecture and protocols]]<br /> *[[Systems biology]]<br /> **[[Robust yet fragile &amp; biological networks]]<br /> **[[Complexity and robustness]]<br /> *[[Exercise physiology]]<br /> <br /> ==Year==<br /> [[2005-2009]]<br /> <br /> [[2000-2004]]<br /> <br /> [[1995-1999]]<br /> <br /> [[1990-1994]]<br /> <br /> [[1985-1989]]<br /> <br /> <br /> <br /> Format: ''Title'', Author, Journal, Month, Year.<br /> Copy files from hyperlinks onto Wiki<br /> <br /> [[Category:Papers]]</div> Lijun