Synthetic Biology:Abstraction hierarchy - Revision history

Reshma P. Shetty at 22:33, 22 December 2005

2005-12-22T22:33:22Z

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Reshma P. Shetty: BioBricks abstraction hierarchy moved to Synthetic Biology:Abstraction hierarchy

2005-12-22T21:09:05Z

BioBricks abstraction hierarchy moved to Synthetic Biology:Abstraction hierarchy

←Older revision

Revision as of 21:09, 22 December 2005

Barry Canton: /* Attempt 5 */

2005-09-27T18:23:40Z

Attempt 5

←Older revision		Revision as of 18:23, 27 September 2005
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	Agreed on the specific function clause. With regard to the generality issue, I feel that information processing is maybe the most general description of a device. The catalysis reaction and a metabolic pathway can certainly be described as information processing even if that is not the explicit purpose. Just as a digital circuit is doing information processing even if the explicit function is to display the time. Furthermore, we draw the boundaries between devices deliberately in such a way that they are composable via a common signal carrier. For example, "catalysis events per unit time" may or may not be capable of being a common signal carrier and so may have to live within a device.-[[User:Bcanton\|BC]]		Agreed on the specific function clause. With regard to the generality issue, I feel that information processing is maybe the most general description of a device. The catalysis reaction and a metabolic pathway can certainly be described as information processing even if that is not the explicit purpose. Just as a digital circuit is doing information processing even if the explicit function is to display the time. Furthermore, we draw the boundaries between devices deliberately in such a way that they are composable via a common signal carrier. For example, "catalysis events per unit time" may or may not be capable of being a common signal carrier and so may have to live within a device.-[[User:Bcanton\|BC]]
		+
		+	====Attempt 6====
		+	*'''Part''' = a sequence of DNA with a specific function that can be physically combined with other parts via an assembly standard.
		+	*'''Device''' = a set of parts that can be functionally combined with other devices via a common, standard signal(i.e. PoPS, RiPS, PhPS).
		+	*'''System''' = a set of devices that cannot be functionally combined with other devices via a common, standard signal.
		+	Changes:
		+	#Specific function back.

	==Network layer model==		==Network layer model==

Barry Canton: /* Attempt 5 */

2005-09-27T18:22:40Z

Attempt 5

←Older revision		Revision as of 18:22, 27 September 2005
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	I agree. Devices and systems should not need to reside on a single piece of DNA. Oftentimes they can't ... for instance, a two input NAND gate. Another thing that we may want to take into account in phrasing these definitions is that not all devices will be used in information processing. In some cases, a device might consist of an enzyme that catalyzes a metabolic reaction. So the signal is perhaps catalysis events per unit time? Do we want our definitions to be sufficiently generalizable to apply to these other branches of devices? Quite possibly yes. --[[User:Rshetty\|Reshma]]		I agree. Devices and systems should not need to reside on a single piece of DNA. Oftentimes they can't ... for instance, a two input NAND gate. Another thing that we may want to take into account in phrasing these definitions is that not all devices will be used in information processing. In some cases, a device might consist of an enzyme that catalyzes a metabolic reaction. So the signal is perhaps catalysis events per unit time? Do we want our definitions to be sufficiently generalizable to apply to these other branches of devices? Quite possibly yes. --[[User:Rshetty\|Reshma]]
		+
		+	Agreed on the specific function clause. With regard to the generality issue, I feel that information processing is maybe the most general description of a device. The catalysis reaction and a metabolic pathway can certainly be described as information processing even if that is not the explicit purpose. Just as a digital circuit is doing information processing even if the explicit function is to display the time. Furthermore, we draw the boundaries between devices deliberately in such a way that they are composable via a common signal carrier. For example, "catalysis events per unit time" may or may not be capable of being a common signal carrier and so may have to live within a device.-[[User:Bcanton\|BC]]

	==Network layer model==		==Network layer model==

Reshma P. Shetty: /* Parts, devices and systems */

2005-09-27T17:41:11Z

Parts, devices and systems

←Older revision		Revision as of 17:41, 27 September 2005
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	===Composition-based definitions===		===Composition-based definitions===
		+
		+	''Just brainstorming ... edit excessively.''
		+
		+	One appealing aspect of this composition-based distinction between parts, devices and systems is that it makes it easier to think about classes of standards that might be useful. There are assembly standards which apply to parts and performance standards (for instance, definitions of high and low signal thresholds) that apply to devices. These standards facilitate interoperability of parts with other parts and devices with other devices. Systems, on the other hand, are unlikely (?) to be subject to standards. Instead, systems are designed to meet a set of specifications. For example, I want to design a system in which cells that detect a chemical X glow green. At this point the line between parts, devices and systems might be somewhat artificial but these distinctions might serve to stimulate discussion on how to systematically engineer biological systems.
		+
	====Attempt 1====		====Attempt 1====
	Obviously, the distinctions are somewhat vague. The idea that dawned on [[Reshma Shetty \| me]] during the course of the discussion with [[Jason Kelly \| Jason]] and [[User:Ilya \| Ilya]] is to use the following (slightly more crisp?) distinctions		Obviously, the distinctions are somewhat vague. The idea that dawned on [[Reshma Shetty \| me]] during the course of the discussion with [[Jason Kelly \| Jason]] and [[User:Ilya \| Ilya]] is to use the following (slightly more crisp?) distinctions
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	Note that I am not satisfied with the wording I use above. So if you have a better idea, feel free to revise. --[[User:Rshetty\|Reshma]] 11:02, 27 Sep 2005 (EDT)		Note that I am not satisfied with the wording I use above. So if you have a better idea, feel free to revise. --[[User:Rshetty\|Reshma]] 11:02, 27 Sep 2005 (EDT)
-
-	~~===Justification===~~
-	~~''Just brainstorming ... edit excessively.''~~
-
-	One appealing aspect of this composition-based distinction between parts, devices and systems is that it makes it easier to think about classes of standards that might be useful. There are assembly standards which apply to parts and performance standards (for instance, definitions of high and low signal thresholds) that apply to devices. These standards facilitate interoperability of parts with other parts and devices with other devices. Systems, on the other hand, are unlikely (?) to be subject to standards. Instead, systems are designed to meet a set of specifications. For example, I want to design a system in which cells that detect a chemical X glow green. At this point the line between parts, devices and systems might be somewhat artificial but might help stimulate discussion on how to systematically engineer biological systems.

	====Attempt 4====		====Attempt 4====
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	We should discuss this idea of specific function further at the device and system level. Is a non-functioning device a device? Probably. Is a system that doesn't do anything a system? Maybe. Again, I feel that a well-formed device/system (i.e one that conforms to the composition standard) can't not have a function and hence we don't necessarily need the specific function clause at these levels either.		We should discuss this idea of specific function further at the device and system level. Is a non-functioning device a device? Probably. Is a system that doesn't do anything a system? Maybe. Again, I feel that a well-formed device/system (i.e one that conforms to the composition standard) can't not have a function and hence we don't necessarily need the specific function clause at these levels either.
		+
		+	:The reason why I am inclined to include the clause that a part must have a specific function is that thus far we've tried to draw the lines between parts at places that "made sense." We could have defined a part as half a promoter with half an RBS but delineating a part in this way seems foolish because it ignores the fact that a promoter and RBS are (somewhat) separate functional units. And since it is quite reasonable for engineers to want to combine a promoter with several different RBS's or vice versa, it makes sense to keep the promoter and RBS as separate parts. The definition of a part should reflect this philosophy of modularity that we try to keep. --[[User:Rshetty\|Reshma]]

	One hair-splitting problem I see with the definitions we are using here is that they imply that a system (and a device) must be a part. This might not need to be true even though the current assembly standard forces any combination of parts to also be a part. We might need to replace part or composite part with just "sequence of DNA" in the device and system definition. Or we can just make a more limited definition of these that does require them to also be parts as defined here. Furthermore, systems don't need to be on the one sequence of DNA. We could say that a system must be a collection of devices.		One hair-splitting problem I see with the definitions we are using here is that they imply that a system (and a device) must be a part. This might not need to be true even though the current assembly standard forces any combination of parts to also be a part. We might need to replace part or composite part with just "sequence of DNA" in the device and system definition. Or we can just make a more limited definition of these that does require them to also be parts as defined here. Furthermore, systems don't need to be on the one sequence of DNA. We could say that a system must be a collection of devices.
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	These definitions are starting to emphasize the fact that the idea of a part is solely related to physically joining biological components (the part may or not be able to do anything by itself) whereas the idea of a device is concerned with design of function and signal processing. -[[User:Bcanton\|BC]]		These definitions are starting to emphasize the fact that the idea of a part is solely related to physically joining biological components (the part may or not be able to do anything by itself) whereas the idea of a device is concerned with design of function and signal processing. -[[User:Bcanton\|BC]]
		+
		+	I agree. Devices and systems should not need to reside on a single piece of DNA. Oftentimes they can't ... for instance, a two input NAND gate. Another thing that we may want to take into account in phrasing these definitions is that not all devices will be used in information processing. In some cases, a device might consist of an enzyme that catalyzes a metabolic reaction. So the signal is perhaps catalysis events per unit time? Do we want our definitions to be sufficiently generalizable to apply to these other branches of devices? Quite possibly yes. --[[User:Rshetty\|Reshma]]

	==Network layer model==		==Network layer model==

Barry Canton: /* Network layer model */

2005-09-27T17:30:24Z

Network layer model

←Older revision		Revision as of 17:30, 27 September 2005
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	I propose a more general/different model based on the OSI network model:		I propose a more general/different model based on the OSI network model:
	[[Network Layer Model]] --[[User:Austin\|Austin]] 16:40, 21 Sep 2005 (EDT)		[[Network Layer Model]] --[[User:Austin\|Austin]] 16:40, 21 Sep 2005 (EDT)
		+
		+	I like Austin's idea so I think it would be worth trying to amalgamate the two approaches. The drawback of the current definitions of parts, devices, and systems is that they are limited, they ignore the functional aspect of the different concepts. For example, a system is defined in a very negative way, i.e a system is anything that is not a device. We are all clear though that a system should have some higher level function and probably as Austin suggests should have inputs and outputs that a user can interact with via addition of inducer or fluorescent measurements for example. So I think adding some of the extra layers proposed by Austin would be useful.
		+	-[[User:Bcanton\|BC]]

Barry Canton: /* Attempt 4 */

2005-09-27T17:29:21Z

Attempt 4

←Older revision		Revision as of 17:29, 27 September 2005
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	One hair-splitting problem I see with the definitions we are using here is that they imply that a system (and a device) must be a part. This might not need to be true even though the current assembly standard forces any combination of parts to also be a part. We might need to replace part or composite part with just "sequence of DNA" in the device and system definition. Or we can just make a more limited definition of these that does require them to also be parts as defined here. Furthermore, systems don't need to be on the one sequence of DNA. We could say that a system must be a collection of devices.		One hair-splitting problem I see with the definitions we are using here is that they imply that a system (and a device) must be a part. This might not need to be true even though the current assembly standard forces any combination of parts to also be a part. We might need to replace part or composite part with just "sequence of DNA" in the device and system definition. Or we can just make a more limited definition of these that does require them to also be parts as defined here. Furthermore, systems don't need to be on the one sequence of DNA. We could say that a system must be a collection of devices.
-
-	Finally, I like Austin's idea below so I think it would be worth trying to amalgamate the two at some point. The drawback of the current definitions of parts, devices, and systems is that they are limited, they ignore the functional aspect of the different concepts. For example, a system is defined in a very negative way, i.e a system is anything that is not a device. We are all clear though that a system should have some higher level function and probably as Austin suggests should have inputs and outputs that a user can interact with via addition of inducer or fluorescent measurements for example. So I think adding some of the extra layers proposed by Austin would be useful.
-	~~-[[User:Bcanton\|BC]]~~

	====Attempt 5====		====Attempt 5====

Barry Canton: /* Attempt 4 */

2005-09-27T17:28:35Z

Attempt 4

←Older revision		Revision as of 17:28, 27 September 2005
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	One hair-splitting problem I see with the definitions we are using here is that they imply that a system (and a device) must be a part. This might not need to be true even though the current assembly standard forces any combination of parts to also be a part. We might need to replace part or composite part with just "sequence of DNA" in the device and system definition. Or we can just make a more limited definition of these that does require them to also be parts as defined here. Furthermore, systems don't need to be on the one sequence of DNA. We could say that a system must be a collection of devices.		One hair-splitting problem I see with the definitions we are using here is that they imply that a system (and a device) must be a part. This might not need to be true even though the current assembly standard forces any combination of parts to also be a part. We might need to replace part or composite part with just "sequence of DNA" in the device and system definition. Or we can just make a more limited definition of these that does require them to also be parts as defined here. Furthermore, systems don't need to be on the one sequence of DNA. We could say that a system must be a collection of devices.

-	Finally, I like Austin's idea below ~~but believe that the above definitions are also of practical benefit~~ so I think it would be worth trying to amalgamate the two at some point.	+	Finally, I like Austin's idea below so I think it would be worth trying to amalgamate the two at some point. The drawback of the current definitions of parts, devices, and systems is that they are limited, they ignore the functional aspect of the different concepts. For example, a system is defined in a very negative way, i.e a system is anything that is not a device. We are all clear though that a system should have some higher level function and probably as Austin suggests should have inputs and outputs that a user can interact with via addition of inducer or fluorescent measurements for example. So I think adding some of the extra layers proposed by Austin would be useful.
	-[[User:Bcanton\|BC]]		-[[User:Bcanton\|BC]]

Barry Canton: /* Attempt 4 */

2005-09-27T17:19:44Z

Attempt 4

←Older revision		Revision as of 17:19, 27 September 2005
Line 74:		Line 74:
	We should discuss this idea of specific function further at the device and system level. Is a non-functioning device a device? Probably. Is a system that doesn't do anything a system? Maybe. Again, I feel that a well-formed device/system (i.e one that conforms to the composition standard) can't not have a function and hence we don't necessarily need the specific function clause at these levels either.		We should discuss this idea of specific function further at the device and system level. Is a non-functioning device a device? Probably. Is a system that doesn't do anything a system? Maybe. Again, I feel that a well-formed device/system (i.e one that conforms to the composition standard) can't not have a function and hence we don't necessarily need the specific function clause at these levels either.

-	One hair-splitting problem I see with the definitions we are using here is that they imply that a system (and a device) must be a part. This might not need to be true even though the current assembly standard forces any combination of parts to also be a part. We might need to replace part or composite part with just sequence of DNA in the device and system definition. Or we can just make a more limited definition of these that does require them to also be parts as defined here.	+	One hair-splitting problem I see with the definitions we are using here is that they imply that a system (and a device) must be a part. This might not need to be true even though the current assembly standard forces any combination of parts to also be a part. We might need to replace part or composite part with just "sequence of DNA" in the device and system definition. Or we can just make a more limited definition of these that does require them to also be parts as defined here. Furthermore, systems don't need to be on the one sequence of DNA. We could say that a system must be a collection of devices.

	Finally, I like Austin's idea below but believe that the above definitions are also of practical benefit so I think it would be worth trying to amalgamate the two at some point.		Finally, I like Austin's idea below but believe that the above definitions are also of practical benefit so I think it would be worth trying to amalgamate the two at some point.
	-[[User:Bcanton\|BC]]		-[[User:Bcanton\|BC]]

		+	====Attempt 5====
		+	*'''Part''' = a sequence of DNA that can be physically combined with other parts via an assembly standard.
		+	*'''Device''' = a set of parts that can be functionally combined with other devices via a common, standard signal(i.e. PoPS, RiPS, PhPS).
		+	*'''System''' = a set of devices that cannot be functionally combined with other devices via a common, standard signal.
		+	Changes:
		+	#Devices and systems need not be one linear sequence of DNA and so should be defined in terms of their functional components rather than the physical components.
		+	#For brevity, a set of parts/devices may contain one or more parts/devices.

		+	These definitions are starting to emphasize the fact that the idea of a part is solely related to physically joining biological components (the part may or not be able to do anything by itself) whereas the idea of a device is concerned with design of function and signal processing. -[[User:Bcanton\|BC]]

	==Network layer model==		==Network layer model==

Barry Canton: /* Attempt 3 */

2005-09-27T16:30:29Z

Attempt 3

←Older revision		Revision as of 16:30, 27 September 2005
Line 56:		Line 56:

	Note that I am not satisfied with the wording I use above. So if you have a better idea, feel free to revise. --[[User:Rshetty\|Reshma]] 11:02, 27 Sep 2005 (EDT)		Note that I am not satisfied with the wording I use above. So if you have a better idea, feel free to revise. --[[User:Rshetty\|Reshma]] 11:02, 27 Sep 2005 (EDT)
		+
		+	===Justification===
		+	''Just brainstorming ... edit excessively.''
		+
		+	One appealing aspect of this composition-based distinction between parts, devices and systems is that it makes it easier to think about classes of standards that might be useful. There are assembly standards which apply to parts and performance standards (for instance, definitions of high and low signal thresholds) that apply to devices. These standards facilitate interoperability of parts with other parts and devices with other devices. Systems, on the other hand, are unlikely (?) to be subject to standards. Instead, systems are designed to meet a set of specifications. For example, I want to design a system in which cells that detect a chemical X glow green. At this point the line between parts, devices and systems might be somewhat artificial but might help stimulate discussion on how to systematically engineer biological systems.

	====Attempt 4====		====Attempt 4====