[BBF Standards] Two separate standards

[Drew Endy]

Parts are parts.  I'd use the language basic parts if you need a  
modifier.

Devices are composite parts.  But, not all combinations of parts are  
devices.  Devices are limited by the requirements bounding device  
specification.  For example, polymerase per second (PoPS) serves to  
define a common signal carrier for inputs and outputs when dealing  
with gene expression devices.

Note that there is no absolute physical definition of a part.  You can  
keep drilling down into particles and sub-atomics.  So, I believe that  
the standards should be linked to the human-invented abstraction  
hierarchy (i.e., parts, devices, systems), which was invented for  
practical reasons (i.e., it is good for something).  Support for  
reliable physical and functional composition is definitely one of the  
first and best goods that we can have.

For the small amount of protein engineering work going on.  Docking  
and phosphorylation motifs are typically though of as parts.  For the  
small amount of RNA engineering work going on, aptamers and ribozyme  
active sites are also thought of as parts.



On Mar 14, 2008, at 12:14 PM, Deepak Chandran wrote:

> Hello standards group,
>
> From all the standards discussion, I think that there are two separate
> standards for parts. If this is the case, then it should be made  
> explicit.
>
> The first type of standard is for atomic parts (better word needed?)
> such as promoters, rbs, etc. (that cannot be broken down further). The
> "standards" for these parts is simply a list of characteristics. For
> example, a promoter would have its sequence and Jason-units as its
> characteristic feature. RBS would have sequence and some other units.
> The list of characteristic features are probably best if developed by
> experimentalists -- the question to ask is: what is it that makes this
> promoter unique?
> Sequence information is definitely needed for atomic parts.
>
> The second type of standard is for composite parts (better word?) such
> as iGEM projects. I do not think that the sequence for composite parts
> is needed -- if we know the atomic parts that make up this composite
> part, then we can easily determine the sequence. What is needed is the
> order in which the atomic parts are arranged on the plasmid and the
> circuit-diagram that explains the mechanism of the part. Someone  
> should
> be able to take a composite parts and replace some of the atomic parts
> just like upgrading a computer by replacing the RAM.
>
> One can wonder whether things like protein domains or fusion proteins
> are atomic or composites. I think the question is whether the part is
> modular (i.e. whether it can be taken apart and reconstructed using
> slightly different components).
>
> In summary:
> A language is needed for composite parts.  (sequence not needed)
> A list of characteristics is needed for atomic parts. (sequence  
> needed)
>
> If there is disagreement on this, please let me know why, so that I  
> can
> eliminate my confusion. If there is agreement, then perhaps we should
> make this fact explicit and categorize our proposals to one of the  
> two.
> We can make more directed progress that way.
>
> By the way, this categorization is not meant to disturb the
> part/device/system hierarchy.
>
> Ralf, I think that you language makes more sense if it is for  
> composite
> parts, because you would need more descriptions for an atomic part. I
> will comment on that later.
>
> --Deepak
>
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