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<td align=center><font color='blue' size='+2'>The Architecture of Robust, Evolvable Networks</font></td>
<td align=center><font color='blue' size='+2'>The Architecture of Robust, Evolvable Networks</font></td>
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<tr valign=top><td align=center><font color='blue' size='+1'>Winter 2010</font></td></tr>
 
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<td align=center><font color='blue' size='+1'>Winter 2010</font></td>
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* Instructor: [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=J._Doyle’s_Bio John C. Doyle]
* Instructor: [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=J._Doyle’s_Bio John C. Doyle]
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* [http://listserv.cds.caltech.edu/mailman/listinfo/cds-213 Course mailing list]
* [http://listserv.cds.caltech.edu/mailman/listinfo/cds-213 Course mailing list]
* Lectures: TTh 4-5:30 pm, 105 Annenberg, changes announced by email
* Lectures: TTh 4-5:30 pm, 107 Annenberg, changes emailed to course mailing list
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== Course Schedule ==
== Course Schedule ==
{| border=1 width=100%
{| border=1 width=100%
|-
|-
| Week || Date || Topic || Reading
| Week || Date || Topic || Reading
|-
|-
| align=center rowspan=5 | 1  
| align=center rowspan=3 | 1  
| colspan=3 | '''Introduction to Networked Control Systems (R. Murray)'''
| colspan=3 | '''Introduction to Network Architectures'''
|-
|-
| 5 Jan (T)
| 12 Jan (T)
| [[IST Seminar: The Architecture of Robust, Evolvable Networks]]
| [[IST Seminar: The Architecture of Robust, Evolvable Networks]]
| Network is IPC:[[Media:IPC-arch-rearch08.pdf | Day et al, 2008 (Paper)]];[[Media:IPC-arch.pdf | Matta (Slides)]]; [[Media:DAYIEEECCW2009.pdf | Implications PNA, Day, 2009 (Slides)]];[[Media:Touchccw2009.pdf | Multihop/Multiparty influences on Net. Arch., Touch (Slides)]]
|  
|  
|-
|-
| 7 Jan (Th)
| 14 Jan (Th)
| [[Alice: Introduction|Case study: Alice]]
| [[Internet Architecture]]
| [http://www.cds.caltech.edu/~murray/papers/2005t_cre+06-jfr.html Cremean et al, 2005]
| Network is IPC:[[Media:IPC-arch-rearch08.pdf | Day et al, 2008 (Paper)]];[[Media:IPC-arch.pdf | Matta (Slides)]]; [[Media:DAYIEEECCW2009.pdf | Implications PNA, Day, 2009 (Slides)]];[[Media:Touchccw2009.pdf | Multihop/Multiparty influences on Net. Arch., Touch (Slides)]]
|-
| colspan=3 | '''Networked embedded systems programming (R. Murray)'''
|-
| 12 Jan (T)
| [[NCS: Message Transfer Systems|Message transfer systems: spread]]
| {{ncsbook|embedded|Ch 2}}; [http://portal.acm.org/citation.cfm?id=359563 Lamport, 1978]
|-
|-
| align=center rowspan=3 | 2
| align=center rowspan=3 | 2
| 14 Jan (Th)
| colspan=3 | '''Network Architectures: Operating Systems and Cell Biology '''
| [[NCS: Multi-Threaded Control Systems|Multi-threaded control systems: pthreads]]
| {{ncsbook|embedded|Ch 2}}; [http://www.llnl.gov/computing/tutorials/pthreads Pthreads]
|-
|-
| 19 Jan (T)
| 19 Jan (T)
| [[Alice: Vehicle Control|Alice: adrive, astate, trajFollower]]
| [[Network Architectures: Internet vs. Biology| Internet and Biology Architectures]]
| {{ncsbook|alice|App A}}; [http://gc.caltech.edu/wiki/index.php/Alice  GCwiki]
| [[Media:RINA_Security_11209.pdf | <i>Assessing Security of a Clean Slate Internet Architecture </i>, Boddapati, Day]];[[Media:GlycolysisACCFinal.pdf | <i>Linear Control Analysis of the Autocatalytic Glycolysis System </i>, Chandra, Buzi, Doyle]]
|-
|-
| 21 Jan (Th)
| 21 Jan (Th)
| No class
| [[Robustness and Fragility, Hard limits and Tradeoffs| Robustness and Fragility, Hard Limits and Tradeoffs]]
|  
| [[Media:TAC-statmech-revised-final.pdf | <i>On Lossless Approximations, Fluctuation-Dissipation and Limitations of Measurements </i>, Sandberg, Doyle]]
|-
|-
| align=center rowspan=4 | 3
| align=center rowspan=3 | 3
| colspan=3 | '''Real-time trajectory generation and receding horizon control (R. Murray)'''
| colspan=3 | '''Case Studies: Cell Biology, Clothing and Legos '''
|-
|-
| 26 Jan (T)
| 26 Jan (T)
| [[NCS: Real-Time Trajectory Generation|Real-time trajectory generation]]
| [[Glycolysis | Network architecture and control of glycolysis; Clothing; Legos]]
| {{ncsbook|trajgen|Ch 3}}
| [[Media:GlycolysisACCFinal.pdf | <i>Linear Control Analysis of the Autocatalytic Glycolysis System </i>, Chandra, Buzi, Doyle]];[[Media:RedBloodCellsGlycolysis.pdf | <i>Assembly and Regulation of a Glycolytic Enzyme Complex on the Human Erythrocyte Membrane </i>, Campanella et al]]
|-
|-
| 28 Jan (Th)
| 28 Jan (Th)
| [[NCS: Receding Horizon Control|Receding horizon control]] (T. Keviczky)
| [[ Heat Shock| Heat Shock in cells; Clothing; Legos]]
| {{ncsbook|trajgen|Ch 3}}
|[[Media: PNASHeatShock.pdf | <i>Surviving Heat Shock: Control strategies for robustness and performance </i>, El-Samad, et al]];[[Media: Cell.pdf |<i> Robustness of Cellular Functions Review</i>, Stelling, et al]];[[Media: ScienceOnlinePDF.pdf | <i>Reverse Engineering of Biological Complexity</i>, Csete, Doyle]]
|-
| align=center rowspan=3 | 4
| colspan=3 | '''Naming, Addressing and Control in Cell Biology '''
|-
|-
| 2 Feb (T)
| 2 Feb (T)
| [[Alice: Path Planning|Alice: plannerModule]]
| [[Naming, Addressing and Control in Cell Biology | Naming, Addressing and Control in Cell Biology ]]
| {{ncsbook|alice|App A}}; [http://grandchallenge.caltech.edu/wiki/images/b/b3/Thesis.pdf Kogan, 2005]
| [http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/Final_IEE_SB.pdf <i>Highly optimised global organisation of metabolic networks</i>, R. Tanaka, M. Csete and J. Doyle];[http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/ScaleRichMetabolism.pdf <i>Quantitative evaluation of scale-rich metabolic networks, Tanaka, Doyle]
|-
|-
| align=center rowspan=4 | 4
| 4 Feb (Th)
| colspan=3 | '''State estimation (H. Sandberg)'''
| [[ Signal Transduction | Signal Transduction]]
|[http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/YiEtAlPNAS.pdf Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Yi, Huang, Simon and Doyle]; [http://www.amazon.com/Introduction-Systems-Biology-Mathematical-Computational/dp/1584886420  Chapter 7: Robustness of Protein Circuits: The Example of Bacterial Chemotaxis of "An Introduction to Systems Biology", Uri Alon]
|-
|-
| 4 Feb (Th)
| align=center rowspan=3 | 5
| [[NCS: Kalman Filtering|Kalman filtering]]
| colspan=3 | '''Architecture and Modeling in Cell Biology '''
| {{ncsbook|estim|Ch 4}}; [http://www.cs.unc.edu/~welch/media/pdf/kalman_intro.pdf Welch and Bishop]
|-
|-
| 8 Feb (M)
| 9 Feb (T)
| [[NCS: Moving Horizon Estimation|Moving horizon estimation]]  
| [[Modeling Biological Systems | Architecture and Layering in Cell Biology]]
| {{ncsbook|estim|Ch 4}}
|  
|-
|-
| 11 Feb (Th)
| 11 Feb (Th)
| [[Alice: Road Following|Alice: roadFollowing]] (L. Cremean)
| [[ Modeling Biological Systems | Modeling Bio Systems, Speaker: James Faeder]]
| {{ncsbook|alice|App A}}
|[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf Rule-Based Modeling of Biochemical Systems with BioNetGen, Faeder, Blinov and Hlavacek]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models, Colvin et al.]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder];[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.]
|-
|-
| align=center rowspan=4 | 5
| align=center rowspan=3 | 6
| colspan=3 | '''Packet-based estimation and control, I (B. Sinopoli)'''
| colspan=3 | '''Complexity and Fragility '''
|-
|-
| 15 Feb (M)
| 16 Feb (T)
| [[NCS: Packet-based Estimation| Packet-based estimation]]
| [[Complexity and Fragility | Complexity and Fragility: Examples with NPP and Mandelbrot sets]]
| {{ncsbook|pack_estim|Ch 5}}
| [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/logFinalCDC2006_X.pdf  Complexity in Automation of SOS Proofs: An Illustrative Example, Gayme et al.];[http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/mandel2.pdf <i>Optimization Based Methods for Determining Basins of Attraction in the Logistic Map and Set Membership in the Mandelbrot Set</i>, Gayme et al. ]; [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/DenniceConnections2006.pdf Studying the Logistic Map and the Mandelbrot Set Using SOS Methods, Gayme, Fazel, Doyle]
|-
|-
| 18 Feb (Th)
| 18 Feb (Th)
| [[NCS: Packet-based Control: the TCP case|Packet-based Control: the TCP case]]  
| [[Complexity and Fragility | Complexity and Fragility (continued)]]
| {{ncsbook|pack_cont|Ch 5}}
| [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/AldersonDoyle-SMCA.pdf Contrasting Views of Complexity and Their Implications For Network-Centric Infrastructures, Alderson, Doyle ]
|-
| 22 Feb (M) 
| [[NCS: Packet-based Control: the UDP case|Packet-based Control: the UDP case]]
| {{ncsbook|pack_cont2|Ch 5}}
|-
|-
| align=center rowspan=4 | 6
| align=center rowspan=3 | 7
| colspan=3 | '''Packet-based estimation and control, II (L. Shi, Y. Mostofi)'''
| colspan=3 | '''Power Laws/ TCP IP '''
|-
| 25 Feb (Th) 
| [[Packet-based Control with Norm Bounded Uncertainties]]
| {{ncsbook|pack_cont_uncertainty|Ch 6}}
|-
|-
| 1 Mar (M)
| 23 Feb (T)
| [[Impact of Communication Noise on Estimation over Wireless Links]]
| [[Power Laws | Power Laws]]
| {{ncsbook|pack_cont_uncertainty|Ch 6}}
| [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=Power_Laws Reading ]
|-
|-
| 4 Mar (Th)
| 25 Feb (Th)
| [[Optimum Receiver Design for Estimation over Wireless Links]]
| [[The Internet | Steven Low guest speaker: TCP IP]]
| {{ncsbook|pack_cont_uncertainty|Ch 6}}
| [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=The_Internet Reading ]
|-
|-
| align=center rowspan=4 | 7
| colspan=3 | '''Distributed estimation and control (V. Gupta)'''
|-
| 8 Mar (M)
| [[Distributed Estimation|Distributed Estimation]]
| {{ncsbook|pack_cont_uncertainty|Ch 7}}
|-
|-
| 11 Mar (Th)
| [[Introduction to Distributed Control|Introduction to Distributed Control]]
| {{ncsbook|pack_cont_uncertainty|Ch 7}}
|-
| 12 May (F)
| [[Estimation and Control in Networked Systems|Estimation and Control in Networked Systems]]
| {{ncsbook|pack_cont_uncertainty|Ch 7}}
|-
| align=center rowspan=4 | 8
| colspan=3 | '''Cooperative control of multi-agent systems (Z. Jin, T. Keviczky)'''
|-
| 15 May (M)
| [[Consensus Problem and Algorithms|Consensus Problem and Algorithms]]
| {{ncsbook|pack_cont_uncertainty|Ch 8}}
|-
| 17 May* (W)
| [[Cooperative and Coordinated Control Scheme for Multi-Agent Systems|Cooperative and Coordinated Control Scheme for Multi-Agent Systems]]
| {{ncsbook|pack_cont_uncertainty|Ch 8}}
|-
| 19 May (F)
| [[Distributed Receding Horizon Control|Distributed Receding Horizon Control]]
| {{ncsbook|pack_cont_uncertainty|Ch 8}}
|-
| align=center rowspan=4 | 9
| colspan=3 | '''Project Presentations (All)'''
{{MWFrow|
  week=9|
  mondate=22 May|montopic=No class|monreading=|
  weddate=24 May|wedtopic=Project presentations|wedreading=|
  fridate=26 May|fritopic=Project presentations|frireading=|
}}
|}
|}


== Course Description ==
== Course Projects ==
 
Increases in fast and inexpensive computing and communications have enabled a new generation information-rich control systems that rely on multi-threaded networked execution, distributed optimization, adaptation and learning, and contingency management in increasingly sophisticated ways.  This course will describe a framework for building such systems and lay out some of the challenges to control theory that must be addressed to enable systematic design and analysis.  Two examples will be used to illustrate the results and to serve as testbeds for course projects: [[Alice]], an autonomous vehicle that competed in the 2005 DARPA Grand
Challenge and [[RoboFlag]], a robotic version of capture the flag.  Key features of these systems include highly sensory-driven, information rich feedback systems, higher levels of decision making for goal and contingency management, and multi-threaded, networked control architectures.
 
== Course Administration ==
 
This course is a special topics course in which advanced students will prepare and present much of the lecture material.  There is no required homework and no midterm or final exam.  Course grades will be based on a course project.
 
== Course Project ==
 
All students in the course will demonstrate their knowledge of the material by analyzing or implementing a networked control system algorithm.  Two testbeds are available for use by the class:
 
* <p> '''[[Alice]]''' - Alice is an autonomous vehicle that was built by [http://team.caltech.edu Caltech undergraduates] to compete in the 2005 DARPA Grand Challenge.  It is fully equipped with multiple terrain sensing cameras and LADARS, two GPS units and an inertial measurement unit (IMU) for measuring position and orientation, and 10 CPUs of computing horsepower inteconnected by a 1 Gb/s ethernet network.  A module software architecture allows new functionality to be implemented and tested with relative ease.  Requires knowledge of C/C++ programming under linux.</p>
 
* <p> '''[[RoboFlag]]''' - RoboFlag is a robotic version of capture the flag in which teams of 6-8 robots with 1-2 humans compete against a like team.  A high fidelity simulator is available that allow full simulation of the dynamics, sensing and communications subsystems, providing realistic operation.  Features include limited bitrate communication channels, limited sensor range for detecting opposing robots, and a graphical user interface for human-in-the-loop operation.  Required knowlege of C/C++ program under Windows.</p>
 
'''Project ideas''' (will be expanded during the term)
* Benchmark the performance of different messaging protocols (eg, broadcast, UDP, TCP) for communicating the state and terrain data on Alice
* Implement and analyze the effect of "shock absobers" (control buffers, state estimators) on RoboFlag
* Implement state estimation and/or multi-description coding on Alice to handle lost packets of terrain data


<span id=archive />
There will be a course project to be discussed.


[[Category:Courses]] [[Category:2005-06 Courses]]
* [[Molecular Cell Biology Project | Molecular Cell Biology Project]]

Latest revision as of 17:36, 3 April 2010

The Architecture of Robust, Evolvable Networks
Winter 2010
  • Course mailing list
  • Lectures: TTh 4-5:30 pm, 107 Annenberg, changes emailed to course mailing list

Course Schedule

Week Date Topic Reading
1 Introduction to Network Architectures
12 Jan (T) IST Seminar: The Architecture of Robust, Evolvable Networks
14 Jan (Th) Internet Architecture Network is IPC: Day et al, 2008 (Paper); Matta (Slides); Implications PNA, Day, 2009 (Slides); Multihop/Multiparty influences on Net. Arch., Touch (Slides)
2 Network Architectures: Operating Systems and Cell Biology
19 Jan (T) Internet and Biology Architectures Assessing Security of a Clean Slate Internet Architecture , Boddapati, Day; Linear Control Analysis of the Autocatalytic Glycolysis System , Chandra, Buzi, Doyle
21 Jan (Th) Robustness and Fragility, Hard Limits and Tradeoffs On Lossless Approximations, Fluctuation-Dissipation and Limitations of Measurements , Sandberg, Doyle
3 Case Studies: Cell Biology, Clothing and Legos
26 Jan (T) Network architecture and control of glycolysis; Clothing; Legos Linear Control Analysis of the Autocatalytic Glycolysis System , Chandra, Buzi, Doyle; Assembly and Regulation of a Glycolytic Enzyme Complex on the Human Erythrocyte Membrane , Campanella et al
28 Jan (Th) Heat Shock in cells; Clothing; Legos Surviving Heat Shock: Control strategies for robustness and performance , El-Samad, et al; Robustness of Cellular Functions Review, Stelling, et al; Reverse Engineering of Biological Complexity, Csete, Doyle
4 Naming, Addressing and Control in Cell Biology
2 Feb (T) Naming, Addressing and Control in Cell Biology Highly optimised global organisation of metabolic networks, R. Tanaka, M. Csete and J. Doyle;Quantitative evaluation of scale-rich metabolic networks, Tanaka, Doyle
4 Feb (Th) Signal Transduction Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Yi, Huang, Simon and Doyle; Chapter 7: Robustness of Protein Circuits: The Example of Bacterial Chemotaxis of "An Introduction to Systems Biology", Uri Alon
5 Architecture and Modeling in Cell Biology
9 Feb (T) Architecture and Layering in Cell Biology
11 Feb (Th) Modeling Bio Systems, Speaker: James Faeder Rule-Based Modeling of Biochemical Systems with BioNetGen, Faeder, Blinov and Hlavacek; Simulation of large-scale rule-based models, Colvin et al.; The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder;Rules for Modeling Signal-Transduction Systems, Hlavacek et al.; Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.
6 Complexity and Fragility
16 Feb (T) Complexity and Fragility: Examples with NPP and Mandelbrot sets Complexity in Automation of SOS Proofs: An Illustrative Example, Gayme et al.;Optimization Based Methods for Determining Basins of Attraction in the Logistic Map and Set Membership in the Mandelbrot Set, Gayme et al. ; Studying the Logistic Map and the Mandelbrot Set Using SOS Methods, Gayme, Fazel, Doyle
18 Feb (Th) Complexity and Fragility (continued) Contrasting Views of Complexity and Their Implications For Network-Centric Infrastructures, Alderson, Doyle
7 Power Laws/ TCP IP
23 Feb (T) Power Laws Reading
25 Feb (Th) Steven Low guest speaker: TCP IP Reading

Course Projects

There will be a course project to be discussed.

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