Synthetic Biology:Abstraction hierarchy

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After lab meeting, a few of us were having a discussion on what the schema for the Registry should look like. (Some notes from that discussion are posted here). During the discussion, we started talking about the abstraction hierarchy that is on the Registry page and originally from one of Drew's slides.


Current definitions of abstraction layers

The question that arose is, what is the distinction between a device and system? Generally, to date we haven't had a crisp distinction between parts, devices and systems. The working definitions to date are something like

  • DNA = low level DNA sequence ... a string of A,T,G,C's
  • Part = RBS, CDS, promoter, terminator; a piece of DNA in BioBricks format that has a specific function.
  • Device = inverter; something else with a higher level function; composed of multiple parts
  • System = ring oscillator; composed of many devices

Proposed definitions of abstraction layers

Obviously, the distinctions are somewhat vague. The idea that dawned on me during the course of the discussion with Jason and Ilya is to use the following (slightly more crisp?) distinctions

  • DNA = low level DNA sequence ... a string of A,T,G,C's
  • Part = a piece of DNA in BioBricks format which usually has a specific function.
    • a terminator stop transcription
    • a promoter initiates transcription
  • Device = a basic or composite part whose input OR output has units of PoPS (or whatever units the general information signal in the devices have).
    Another way of thinking of this definition is that a device is any part for which a transfer curve can be drawn in which one of the axes is in PoPS.
    The key thing to note in this description is that certain BioBricks in the database might be considered a part in one context and a device in another context.

I think this definition could be rephrased to say - A device is any basic or composite part that can be combined with at least one other device using the PoPS framework. I think this might make the reason for defining a device as you have done more clear (at least to me). --BC 09:30, 15 Sep 2005 (EDT)
Jason has been using an operational distinction between devices and systems saying that a device is something whose behavior you can screen for whereas a system's behavior cannot be screened. Thus, what is a system today might be a device tomorrow if a clever screen is devised. We should think about whether that definition is more useful than this one or if the two could be merged.

    • an inverter is a device. Its input and output are PoPS
    • an RBS.GFP.Term is a device. Its input is PoPS and its output is fluorescence.
    • a constitutive promoter is a device. It has no input and its output is PoPS. (Note: a promoter is a part in other contexts).
    • UT-Austin's photons to PoPS converter is a device.
  • System = Any device which has neither an input nor an output in PoPS.
    Some systems can easily be transformed to devices.
    • a promoter.GFP.Term is a system. It has no input and its output is fluorescence.
    • The UT-Austin's project is a system. Its input is photons and its output is blue/white color.
    • the repressilator is a system. It has no input (or its input could be IPTG/aTc) and its output is fluorescence. The repressilator could easily become a device however. If a duplicate copy of one of the promoters is present. Then that promoter has an output of PoPS which could be hooked up to some device. Thus in this case, the repressilator becomes a device.

When you add the promoter, I think the repressilator is still a system but it is part of a device. I'm not sure you can add another promoter and still say that it is the repressilator since you have added a new output. You cant connect I7101 or the repressilator to another device via the PoPS framework hence they are exlusively systems.--BC 09:30, 15 Sep 2005 (EDT)

Following on from what I wrote above - A system is a collection of parts that does not have a PoPS input or output to allow composition with other parts or devices via the PoPS framework. So a device has at least one input or output that can be connected to other devices and so can form part of a larger system whereas a system is a complete and "closed" collection of parts. I don't think I'm changing the definitions too much, just wording them in a way that makes more sense to me. Worded this way I think they emphasize the composability property of the element which seems like the most clear, since interpreting the function of the elements is subjective as we all agree.--BC 09:30, 15 Sep 2005 (EDT)

Thus, the exact classification of a particular BioBrick is not fixed. In some situations, you might think of promoter as a part because you are referring to a promoter than can be regulated by a certain repressor. In another situation, you think of a promoter as a device because you need a constant PoPS source in your device/system. In other words, parts, devices and systems are not disjoint.

So if I get this right, everything that is on the one piece of DNA is always a part. However, I think that systems and devices are disjoint sets. The caveat being that you can easily convert one to the other by adding or removing a PoPS i/o. --BC 09:30, 15 Sep 2005 (EDT)

Actually this might mean -

  • Part - a piece of DNA that can be combined with other parts via BioBricks standard assembly.
  • Device - a part or composite part that can be combined with other parts via PoPS-based composition.
  • System - a part or composite part that cannot be combined with other parts via PoPS-based composition.

I propose a more general/different model based on the OSI network model: Network Layer Model --Austin 16:40, 21 Sep 2005 (EDT)