Network architecture and protocols - Revision history

Hana: /* Note */

2008-08-23T01:02:24Z

Note

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	*This page was drafted by Lijun Chen and Hana 2007-2008. Needs editing and updating papers.		*This page was drafted by Lijun Chen and Hana 2007-2008. Needs editing and updating papers.
	[[Category:Papers by topic]]		[[Category:Papers by topic]]
			[[Category:Papers]]

Hana: /* Note */

2008-08-22T23:46:08Z

Note

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	===Note===		===Note===
	*This page was drafted by Lijun Chen~~, Lun Li,~~ and Hana 2007-2008. Needs editing and updating.		*This page was drafted by Lijun Chen and Hana 2007-2008. Needs editing and updating papers.
	[[Category:Papers by topic]]		[[Category:Papers by topic]]

Hana at 23:45, 22 August 2008

2008-08-22T23:45:26Z

← Older revision		Revision as of 23:45, 22 August 2008
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	The key to understanding ~~complex~~ '''network'''s is understanding their '''architecture'''. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or principles 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.		The key to understanding '''complex network'''s is understanding their '''architecture'''. Architecture is the most universal, high-level, and persistent elemments of structure and organization (or principles 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.

	==Internet==		==Internet==

Hana: /* Related reading */

2008-08-22T23:45:09Z

Hana: /* Related reading */

2008-08-22T23:43:52Z

Hana: /* Research papers */

2008-08-22T23:43:29Z

Research papers

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	===Research papers===		===Research papers===
	~~[http://netlab.caltech.edu/publications/SHLowduality2003.ps ''A Duality Model of TCP and Queue Management Algorithms'']<br>~~
	~~S. H. Low<br>~~
	~~IEEE/ACM Transactions on Networking, 11(4):525-536, Aug 2003.~~

	[http://www.cds.caltech.edu/~doyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks'']<br>		[http://www.cds.caltech.edu/~doyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks'']<br>
	J. Wang, L. Li, S. H. Low and J. C. Doyle<br>		J. Wang, L. Li, S. H. Low and J. C. Doyle<br>

Hana: /* Coherent theory */

2008-08-22T23:40:05Z

Coherent theory

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	==Coherent theory==		==Coherent theory==
	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.		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.

	(adopted from John's writing & to be continued, Lijun)		(adopted from John's writing & to be continued, Lijun)


	==Internet Papers==		==Internet Papers==

Hana: /* Reverse engineering */

2008-08-22T23:39:48Z

Reverse engineering

← Older revision		Revision as of 23:39, 22 August 2008
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	There are now major developments 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.		There are now major developments 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.
	==Reverse engineering==		==Reverse engineering==
	In reverse 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 trade-offs 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.		In '''reverse 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 trade-offs 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.

	==Coherent theory==		==Coherent theory==

Hana at 23:39, 22 August 2008

2008-08-22T23:39:20Z

Hana: /* Related reading */

2008-08-18T22:59:39Z

← Older revision		Revision as of 23:45, 22 August 2008
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	[[General complexity]]		[[General complexity]]

			[[Complex networks]]

	===External links===		===External links===

← Older revision		Revision as of 22:59, 18 August 2008
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	==Related reading==		==Related reading==
	[[~~Networks~~]]		[[Networking]]

	[[~~Complexity~~]]		[[General complexity]]

	===External links===		===External links===

← Older revision		Revision as of 23:43, 22 August 2008
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	[[General complexity]]		[[General complexity]]


	===External links===		===External links===
			[http://netlab.caltech.edu/publications/SHLowduality2003.ps ''A Duality Model of TCP and Queue Management Algorithms'']<br>
			S. H. Low<br>
			IEEE/ACM Transactions on Networking, 11(4):525-536, Aug 2003.

	===Note===		===Note===
	*This page was drafted by Lijun Chen, Lun Li, and Hana 2007-2008. Needs editing and updating.		*This page was drafted by Lijun Chen, Lun Li, and Hana 2007-2008. Needs editing and updating.
	[[Category:Papers by topic]]		[[Category:Papers by topic]]

← Older revision		Revision as of 23:39, 22 August 2008
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	==Internet==		==Internet==
	~~Take the 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		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
	thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper		thin, hidden “waist” of universally shared feedback control (TCP/IP) between the visible upper
	(application software) and lower (hardware) layers. The term “hourglass” has been used because		(application software) and lower (hardware) layers. The term “hourglass” has been used because
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	==Microbiology==		==Microbiology==
	Similarly, in the ~~microbial biosphere~~, genes that “talk” central transcription and translation		Similarly, in the '''microbiology''', genes that “talk” central transcription and translation
	protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of		protocols can move by horizontal gene transfer (HGT), also accelerating evolution in a kind of
	“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.”		“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.”
	==Bowties==		==Bowties==
	In most networked systems, protocols within a layer can be visualized as ~~“bowties~~,” which have		In most networked systems, protocols within a layer can be visualized as '''“bowties”''' , which have
	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		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
	blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,		blocks in advance manufacturing. In these and the biologic examples, the currencies, carriers,
	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.		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.

	==Layers of networks in internet and biology==		==Layers of networks in internet and biology==
	There are now major ~~developements~~ 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.		There are now major developments 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.
	==Reverse engineering==		==Reverse engineering==
	In reverse 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 trade-offs 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.		In reverse 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 trade-offs 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.