[BBF Standards] data exchange issue 1: Abstraction

[Raik Gruenberg]

Hi all,

your 1st of March meeting is approaching and I would like to focus the 
discussion back to more mundane data exchange problems -- let's try to have some 
draft ready which is covering:

(1) Aim / Application scenarios for this standard
(2) What is a Biobrick?
(3) Datamodel 1 -- minimal Biobrick information

This should be doable in the remaining time (just think: "yes we can!" :-)

Let's start with (2). The current state of debate is as always here:
http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Exchange#What_is_a_Biobrick.3F

We have two (related) unresolved questions in this section:

(A) If a Biobrick is defined by its unique sequence, already a minor variation 
(e.g. silent mutation) of this sequence creates an entirely new biobrick. We may 
want to create the concept of Biobrick-families on top of the Biobrick or one 
could introduce a 'biobrick implementation' layer underneath.

(B) Even worse, what happens if I put the exactly same sequence into a different 
format? Is that a new Biobrick? -- Only then can we include a "Format" record in 
the minimal data model. For the experimentalist this information is essential.

Moreover, I think we need a second definition of "Device" (built from 
biobricks). Some of the discussions we had here may overlook that a single 
Biobrick will often *not* encapsulate a self-standing function but will often 
depend on additional biobricks that are not fused to it on the DNA level and may 
even be distributed over different cells (e.g. the quorum sensing device). I 
think we should treat this with a separate "Device" concept. Some Biobricks may 
turn out to be self-sufficient devices, most others not. Some functional 
characterizations (Pops-in/out) only make sense for full devices, but not for 
every single Biobrick.

Comments?
Greetings,
Raik

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