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Motivation

Abstraction hierarchies are a human invention designed to assist people in engineering very complex systems by ignoring unnecessary details. If the process to design a biological system was to write down the string of nucleotides, it would immediately become untenable even for experts to design anything but very simple systems. Most people just aren't capable of processing that kind of detail all at once. If instead, an abstraction hierarchy is specified, it allows the designer of a biological system to ignore some of the implementation details and focus only on the high-level design issues.

Engineers in all disciplines take advantage of abstraction hierarchies to design and build complicated systems. For instance, software engineers write in high level programming languages like C++ or Java which are designed to be easy for humans to read and write. These programs are then translated into lower level sets of instructions that are more easily translatable to bit strings that are machine interpretable and implementable. Thus, the people who write C++ programs do not need to know how to translate their programs to machine code and the people who work on instruction sets do not need to envision all possible programs that the software engineer might write.

To enable the engineering of very complex biological systems, it will be necessary to develop abstraction hierarchies for biological engineering. At this point, it is not necessarily clear which hierarchies are most useful and in fact it may be slightly premature to try and develop them. Nevertheless, thinking about what an abstraction hierarchy in synthetic biology should look like might help us think about the "right" way to engineer biological systems and to design biological parts.

Below several abstraction hierachies are listed that might be appropriate for biological engineering. Anyone should feel free to revise them, add new candidate hierarchies or add comments as this is very much a work in progress. An attempt has been made to give credit to the originators of each of the candidate abstraction hierarchies; however, this should in no way be a deterrent to those interested in offering revisions. The abstraction hierarchies have been listed in chronological order of inception.

Candidate abstraction hierarchies

DNA, parts, devices and systems model

Image:AbstractionHierarchy.jpg


Layer name Definition Example
DNA sequence of nucleotides ATGGATCATGATG
Part a finite sequence of nucleotides with a specific function RBS, CDS, promoter, terminator
Device multiple parts with a higher level function inverter
System multiple devices hooked together ring oscillator

The original abstraction hierarchy is posted on the Registry page and is originally from one of Drew's slides.

by Drew Endy.


Screenability model

Layer name Definition Example
DNA sequence of nucleotides ATGGATCATGATG
Part a finite sequence of nucleotides with a specific function RBS, CDS, promoter, terminator
Device one or more parts which can be screened for functionality promoter, terminator, inverter
System multiple devices which cannot be screened for functionality ring oscillator

by Jason Kelly.


Composition model

Layer name Definition Example
DNA sequence of nucleotides ATGGATCATGATG
Part a sequence of DNA with a specific function that can be physically combined with other parts via an assembly standard RBS, CDS, promoter, terminator
Device a set of parts that can be functionally combined with other devices via a common, standard signal carrier (i.e. PoPS, RiPS, PhPS) inverter
System a set of devices that cannot be functionally combined with other devices via a common, standard signal ring oscillator

See Synthetic Biology:Abstraction hierarchy/Composition model for notes on the abstraction hierarchy developed based on composability.

by Reshma Shetty and Barry Canton.


Network layer model

This model derives inspiration from the Wikipedia:OSI model for computer network protocols.

Version 1

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 2 RNA PoPS none Part
Layer 1 DNA BioBricks assembly none Part
Layer 0 Chassis nucleotides/amino acids none Chassis

by Austin Che.

Version 2

This version attempts to reconcile the network layer model with the composition model.

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

by Barry Canton.

See Synthetic Biology:Abstraction hierarchy/Network layer model for more detailed and extensive notes on the network layer model.

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