The discussion on the Synthetic Biology:Abstraction hierarchy brings up problems with terminology and with the abstraction model. Deriving inspiration from the Wikipedia:OSI model for computer network protocols, I propose a biological network layer model. Although we may currently use specific standard protocols such as BioBricks, PoPS, etc., we may not want to do so forever. This proposed model is general and not limited to a particular standard or implementation.
==Silicon Network Layer Model== For comparison, here's an overview of the standard network layer model:
|Layer Number||Layer Name||Example Standard||Purpose|
|Layer 7||Application||http||what does the user want to do?|
|Layer 6||Presentation||jpg||how do we encode the data?|
|Layer 5||Session||SSL||how do we manage sessions?|
|Layer 4||Transport||TCP/UDP||how do we reliably transport info?|
|Layer 3||Network||IP||how does the network transmit info?|
|Layer 2||Link||Ethernet||how do computers talk to each other?|
|Layer 1||Physical||10base-T/cat5||what is the form of the physical cabling?|
In theory, each layer should only interface with the layer above or below it. By standardizing these interfaces, different components on the networks can then work together. A layer performs its function by taking requests from the higher layer and making use of the lower layer.
The purpose of a biological network layer model is to specify abstraction boundaries, interfaces, and standards to allow engineered biological components to work seamlessly together in a biological circuit/network. This table summarizes the model:
|Layer Number||Layer Name||Example Standard||Role of User||Category|
|Layer 7||Application||chemical detector||Brainstorm need||System|
|Layer 6||Packaging||pSB plasmids||Physical handling of system||System|
|Layer 5||Environment||wavelengths of light||Provide input or observe output||System|
|Layer 4||Cell||cell-cell signaling||none||Cell|
|Layer 3||Protein||dimerization interface||none||Part|
|Layer 1||DNA||BioBricks assembly||none||Part|
|Layer 0||Chassis||nucleotides/amino acids||none||Chassis|
There can be standards at each of the abstraction layers which should be mostly independent of standards at the other layers.
We break up the layers into a couple of larger named categories for easier discussion of biological networks. We define:
A tricky term to define is a device. The term seems to be a useful one to have, yet has not been easy to define precisely. We propose defining a device orthogonally to parts and systems. Unlike the Synthetic Biology:Abstraction hierarchy/Composition model where devices are "between" parts and systems, devices are defined here in a functional manner:
The network layer model provides layers at which interface standards are defined. However, real biological components can often work between layers, so devices can work between layers. Just as the notion of a biological device is an abstract one, the requirement for a device to have inputs and outputs is arbitrarily/abstractly defined, but they must be defined for a device to exist. Furthermore, all defined inputs and outputs must be in terms of standards existing within some layer.
We use the shorthand Lx/Ly device (e.g. L3/L5 device) to represent a device that has inputs conforming to Layer x standards and outputs conforming to Layer y standards. We can also generalize this: if a device has inputs or outputs conforming to multiple layers, then we can use Lx1 Lx2 / Ly1 Ly2. If all inputs and outputs are at the same layer (all x=y) and conform to the same standard, then we just refer to something a Lx device (e.g. L2 device). For devices that have either no defined input or output, we use layer 0 (L0), as all biological components will have some impact on and from the chassis components.
For example, an inverter that takes PoPS input and output is a L2 device or, more specifically, a L2-inverter (even more specifically, a L2(PoPS)-inverter). We can also, for example, imagine L5-inverters.
Some other examples:
We see that in the definition of the device given here, almost anything can be considered a device as long as it is characterized according to a standard with well-defined inputs and outputs. The same component, uncharacterized, is not a device, as it is does not provide a useful device abstraction layer.
This is an attempt to reconcile the Synthetic Biology:Abstraction hierarchy/Composition model, which is the way that we think about building up to useful systems, and the network layer model proposed above. The network layer model offers a good framework to extend the abstraction hierarchy but defines devices somewhat differently. I'm not sure that the network layer model below is entirely consistent with the theory of the OSI network model but it may provide some substrate for thought.--BC 13:57, 27 Sep 2005 (EDT)
|Layer Number||Layer Name||Example Standard||Role of User|
|6||User||Detector of Chemical X|
|5||Environment||Batch/continuous, Temp., Media||Provide input or observe output|
|4||Population||cell-cell signaling||Design interactions between different cells|
|3||System||Signaling molecules, fluorescence||Design system to process external inputs into detectable outputs|
|2||Device||PoPS, RiPS||Use parts to design device with particular transfer curve|
|1||Part||BioBricks assembly||Plan and assemble|
|0||Materials||nucleotides/amino acids||Choose the materials|
Thoughts or comments? Contact: Austin Che