[BBF Standards] Questions about functional composition, functional definition, data exchange

[Raik Gruenberg]

Ralph, thanks for the comment -- you are right, the discussion became a bit 
unfocused.

 > Come to think of it, the whole matter of data exchange sort of begs the
 > question of who is exchanging data and what those people are attempting
 > to accomplish. Beyond the definition of a biobrick, could the BBF data
 > exchange standards articulate the tasks and scenarios it is trying to
 > cover with its data exchange standards and how it's trying to realize
 > them?

Indeed. The mission needs to be stated. Please have a look at:
http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical
where Mac and I tried to start structuring the discussion a bit. We start out 
with something like a one-sentence goal:

This working group aims to define standards for the description of biobricks and 
formats / technologies for the exchange (or networking) of biobrick-related data.

I've now added a dedicated section "Aim / Application scenarios for this 
standard" because that single sentence was clearly not enough (or may be 
disagreed upon).

Please, everyone interested, go and hit the Edit button!

/Raik

Ralph Santos wrote:
> I have several questions about an earlier discussion thread, and I 
> suppose it centers around this definition from Raik Gruenberg's email of 
> 4 February ["Biobrick data exchange format"]. He writes:
> 
> ------- 8< -- cut here -- 8< --------
> 
> For data exchange purposes 
> we adopt the following draft:
> 
> * BioBrick™ are standard DNA parts that encode basic biological function.
> * A BioBrick has a unique DNA sequence.
> * Basic parts are defined by this DNA sequence.
> * Composite parts are defined as "sequence" of Basic BioBricks, along with 
> intervening "scar" sequences.
> 
> 
> ------- 8< -- cut here -- 8< --------
> 
> the discussion about data exchange that has followed since (at least as 
> far as I have followed it from digests and archives) seems heavily 
> focused on describing the specifics of biobricks and paying less 
> attention to providing a workable abstraction of biobricks. To 
> illustrate what I mean, consider the difference between two part 
> descriptions: JC Anderson's library of tuned promoters (BBa_J23100) 
> versus the signaling part Drew Endy cited earlier today in a discussion 
> of input/output (BBa_F2620).
> 
> Notice how BBa_J23100 describes (elegantly, if I might add) the 
> relationships among the parts in the family, there is little explicit 
> mention of its behavior which is separable from the actual composition 
> of the parts beyond the mention that the part is a promoter in the part 
> title. On the other hand, BBa_F2620's part description is mostly about 
> its external behavior. F2620's page lays out a simple abstraction on 
> several levels quite elegantly using the set of figures at the top: on 
> the left a simple citation of input and output, at center a black box 
> graphical representation relating input and output leaving the part 
> itself completely abstract, and at right a graphical overview of the 
> part's internal composition.
> 
> While it is critical to effectively describe the internal composition of 
> parts, it seems equally critical to provide an abstraction allowing 
> users to completely abstract a part away and focus on its behavior in 
> terms of some external job to be done. Both have their place in an 
> engineering community. By way of analogy, consider the two attached 
> diagrams both describing NAND gates taken from the ON Semiconductor TTL 
> data book (shamelessly acquired from the following URL):
> 
> http://ece-www.colorado.edu/~mcclurel/ON_Semiconductor_LSTTL_Data_DL121-D.pdf
> 
> "74LS00_circuitdiagram.png" is a perfectly reasonable description of a 
> NAND gate describing its behavior in terms of discrete components, for 
> those who need to pay careful attention to the analog behavior of a 
> circuit using one of these gates. On the other hand, 
> "74LS00_chipdiagram.png" is a completely abstract description where the 
> "NAND" gate symbol (familiar to those who have studied digital design) 
> would be more of use to an engineer actually trying to use one of these 
> chips (or, more generally, any digital designer trying to put together a 
> system needing some combinatorial logic). The "NAND" symbol says nothing 
> about the internals but is in fact intimately related to the other 
> diagram, at least for those components built by ON semiconductor.
> 
> Anyhow, back to the questions. It seems that to address the data 
> exchange issue one must not only be able to describe parts in a 
> machine-processable fashion, but one must also be able to describe the 
> parts one has in a way more similar to BBa_F2620, and furthermore do it 
> in a way that is machine-processable so that users could mechanistically 
> query for parts functionally compatible to a part of interest or for 
> particular dynamic behaviors. I don't wish to detract from current 
> efforts, but I just wanted to make sure this matter stayed in the 
> discussion.
> 
> Come to think of it, the whole matter of data exchange sort of begs the 
> question of who is exchanging data and what those people are attempting 
> to accomplish. Beyond the definition of a biobrick, could the BBF data 
> exchange standards articulate the tasks and scenarios it is trying to 
> cover with its data exchange standards and how it's trying to realize 
> them? It would be useful not only to define what the standards want to 
> accomplish, but help people understand not only the thinking that goes 
> into the standard but help describe a line of attack for how the 
> standard may be put together and help focus thinking on the matter and 
> allow others to pitch in. That way as the scenarios become clarified it 
> becomes clearer what the requirements are to get the job done and as the 
> standard evolves it can be easier to check the standard against those 
> requirements and see how things are developing.
> 
> ---ralf
> 
> 
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> 
> 

-- 
________________________________

Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________